diff --git a/_sources/intro.md b/_sources/intro.md
index 18e3092..ecdc192 100644
--- a/_sources/intro.md
+++ b/_sources/intro.md
@@ -58,6 +58,8 @@ Available notebooks:
   (Kimberly Siletti)**
 
 ## Release Notes
+* **[abc_atlas_access (v0.1.0)]**
+  * Fixed issue with loading 10X mouse data with the `get_gene_data` function.
 * **[Spring 2024 Public Beta (version 20240330)]**
   * Added Whole Human Brain transcriptomic, taxonomy and clustering datasets
     from Siletti et al. 2023 to the ABC Atlas.
diff --git a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
index c7a38c0..d4df1d5 100644
--- a/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
+++ b/_sources/notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb
@@ -983,7 +983,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/_sources/notebooks/getting_started.ipynb b/_sources/notebooks/getting_started.ipynb
index df30b21..efb2930 100644
--- a/_sources/notebooks/getting_started.ipynb
+++ b/_sources/notebooks/getting_started.ipynb
@@ -121,7 +121,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# get_ipython().kernel.do_shutdown()"
+    "get_ipython().kernel.do_shutdown(restart=True)"
    ]
   },
   {
@@ -1321,7 +1321,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
diff --git a/intro.html b/intro.html
index 49e3f5b..b9325a6 100644
--- a/intro.html
+++ b/intro.html
@@ -508,6 +508,11 @@ <h1>Allen Brain Cell Atlas - Data Access<a class="headerlink" href="#allen-brain
 <section id="release-notes">
 <h2>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this heading">#</a></h2>
 <ul class="simple">
+<li><p><strong>[abc_atlas_access (v0.1.0)]</strong></p>
+<ul>
+<li><p>Fixed issue with loading 10X mouse data with the <code class="docutils literal notranslate"><span class="pre">get_gene_data</span></code> function.</p></li>
+</ul>
+</li>
 <li><p><strong>[Spring 2024 Public Beta (version 20240330)]</strong></p>
 <ul>
 <li><p>Added Whole Human Brain transcriptomic, taxonomy and clustering datasets
diff --git a/notebooks/getting_started.html b/notebooks/getting_started.html
index 1ed191f..5827040 100644
--- a/notebooks/getting_started.html
+++ b/notebooks/getting_started.html
@@ -556,7 +556,7 @@ <h1>Getting started<a class="headerlink" href="#getting-started" title="Permalin
 <p>After installing these new packages we need to restart the python kernel in this notebook. This can either be done by selecting <code class="docutils literal notranslate"><span class="pre">Restart</span> <span class="pre">Kernel...</span></code> under the <code class="docutils literal notranslate"><span class="pre">Kernel</span></code> drop down menu above or uncommenting and running the cell below.</p>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># get_ipython().kernel.do_shutdown()</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_ipython</span><span class="p">()</span><span class="o">.</span><span class="n">kernel</span><span class="o">.</span><span class="n">do_shutdown</span><span class="p">(</span><span class="n">restart</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>
diff --git a/searchindex.js b/searchindex.js
index edae1c8..8529fbf 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["descriptions/Allen-CCF-2020", "descriptions/MERFISH-C57BL6J-638850", "descriptions/MERFISH-C57BL6J-638850-CCF", "descriptions/WHB-10X-clustering", "descriptions/WHB-10Xv3", "descriptions/WHB-taxonomy", "descriptions/WHB_dataset", "descriptions/WHB_notebooks", "descriptions/WMB-10X", "descriptions/WMB-10XMulti", "descriptions/WMB-10Xv2", "descriptions/WMB-10Xv3", "descriptions/WMB-neighborhoods", "descriptions/WMB-taxonomy", "descriptions/WMB_dataset", "descriptions/Zhuang-ABCA-1", "descriptions/Zhuang-ABCA-2", "descriptions/Zhuang-ABCA-3", "descriptions/Zhuang-ABCA-4", "descriptions/Zhuang_dataset", "descriptions/notebook_subtitle1", "descriptions/notebook_subtitle2", "descriptions/notebook_subtitle3", "descriptions/notebook_subtitle4", "docs/README", "docs/cluster_annotations/README", "docs/gene_lists/README", "docs/parcellation_annotations/README", "intro", "notebooks/10x_snRNASeq_tutorial_part_1", "notebooks/10x_snRNASeq_tutorial_part_2a", "notebooks/10x_snRNASeq_tutorial_part_2b", "notebooks/WHB-10x_snRNASeq_tutorial_part_1", "notebooks/WHB-10x_snRNASeq_tutorial_part_2", "notebooks/WHB_cluster_annotation_tutorial", "notebooks/ccf_and_parcellation_annotation_tutorial", "notebooks/cluster_annotation_tutorial", "notebooks/cluster_groups_and_embeddings_tutorial", "notebooks/cluster_neighborhood_gallery", "notebooks/general_accessing_10x_snRNASeq_tutorial", "notebooks/getting_started", "notebooks/merfish_ccf_registration_tutorial", "notebooks/merfish_tutorial_part_1", "notebooks/merfish_tutorial_part_2a", "notebooks/merfish_tutorial_part_2b", "notebooks/zhuang_merfish_tutorial"], "filenames": ["descriptions/Allen-CCF-2020.md", "descriptions/MERFISH-C57BL6J-638850.md", "descriptions/MERFISH-C57BL6J-638850-CCF.md", "descriptions/WHB-10X-clustering.md", "descriptions/WHB-10Xv3.md", "descriptions/WHB-taxonomy.md", "descriptions/WHB_dataset.md", "descriptions/WHB_notebooks.md", "descriptions/WMB-10X.md", "descriptions/WMB-10XMulti.md", "descriptions/WMB-10Xv2.md", "descriptions/WMB-10Xv3.md", "descriptions/WMB-neighborhoods.md", "descriptions/WMB-taxonomy.md", "descriptions/WMB_dataset.md", "descriptions/Zhuang-ABCA-1.md", "descriptions/Zhuang-ABCA-2.md", "descriptions/Zhuang-ABCA-3.md", "descriptions/Zhuang-ABCA-4.md", "descriptions/Zhuang_dataset.md", "descriptions/notebook_subtitle1.md", "descriptions/notebook_subtitle2.md", "descriptions/notebook_subtitle3.md", "descriptions/notebook_subtitle4.md", "docs/README.md", "docs/cluster_annotations/README.md", "docs/gene_lists/README.md", "docs/parcellation_annotations/README.md", "intro.md", "notebooks/10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2a.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2b.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb", "notebooks/WHB_cluster_annotation_tutorial.ipynb", "notebooks/ccf_and_parcellation_annotation_tutorial.ipynb", "notebooks/cluster_annotation_tutorial.ipynb", "notebooks/cluster_groups_and_embeddings_tutorial.ipynb", "notebooks/cluster_neighborhood_gallery.ipynb", "notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb", "notebooks/getting_started.ipynb", "notebooks/merfish_ccf_registration_tutorial.ipynb", "notebooks/merfish_tutorial_part_1.ipynb", "notebooks/merfish_tutorial_part_2a.ipynb", "notebooks/merfish_tutorial_part_2b.ipynb", "notebooks/zhuang_merfish_tutorial.ipynb"], "titles": ["Allen Mouse Common Coordinate Framework (2020 version)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain", "MERFISH CCF mapped coordinates", "Clustering analysis of whole human brain 10X single nucleus transcriptomes", "Human brain 10Xv3 single nucleus transcriptomes", "Human brain taxonomy of cell types", "Human whole-brain transcriptomic cell type atlas (Kimberly Siletti)", "Whole Human Brain 10x scRNA-seq gene expression data", "Clustering analysis of whole adult mouse brain 10X single cell transcriptomes", "Whole mouse brain 10XMulti single cell transcriptomes", "Whole mouse brain 10Xv2 single cell transcriptomes", "Whole mouse brain 10Xv3 single cell transcriptomes", "Cluster groups and neighborhood specific UMAP embeddings", "Whole adult mouse brain taxonomy of cell types", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-1)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-2)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-3)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-4)", "A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "10x scRNA-seq gene expression data", "MERFISH whole brain spatial transcriptomics", "A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)", "Resource Pages", "Cluster annotations", "Gene lists", "Parcellation annotations", "Allen Brain Cell Atlas - Data Access", "10x RNA-seq gene expression data (part 1)", "10x RNA-seq gene expression data (part 2a)", "10x RNA-seq gene expression data (part 2b)", "Whole Human Brain (WHB) 10x RNA-seq gene expression data (part 1)", "Whole Human Brain 10x RNA-seq gene expression data (part 2)", "Whole Human Brain 10x RNA-seq clustering analysis and annotation", "Allen Mouse Common Coordinate Framework (2020 version)", "10x RNA-seq clustering analysis and annotation (CCN20230722)", "Cluster neighborhoods and embeddings", "Cell type neighborhood gallery", "Accessing 10x RNA-seq gene expression data", "Getting started", "MERFISH CCF mapped coordinates", "MERFISH whole brain spatial transcriptomics (part 1)", "MERFISH whole brain spatial transcriptomics (part 2a)", "MERFISH whole brain spatial transcriptomics (part 2b)", "MERFISH whole mouse brain spatial transcriptomics (Xiaowei Zhuang)"], "terms": {"brain": [0, 2, 12, 21, 29, 30, 35, 38, 39, 40, 41], "ccfv3": [0, 2, 14, 19, 20, 35, 41, 45], "wang": [0, 35], "et": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 45], "al": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 32, 33, 34, 35, 37, 38, 39, 41, 45], "3d": [0, 2, 15, 16, 17, 18, 35, 41, 45], "refer": [0, 15, 16, 17, 18, 29, 34, 41, 45], "space": [0, 2, 15, 16, 17, 18, 35, 41, 42, 45], "an": [0, 2, 14, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "averag": [0, 29, 31, 33, 35, 36, 41, 42, 44], "10um": [0, 35], "voxel": [0, 41], "resolut": [0, 1, 8, 9, 10, 11, 13, 35, 36, 41], "creat": [0, 2, 8, 12, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "from": [0, 2, 3, 4, 5, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45], "serial": [0, 35], "two": [0, 4, 5, 17, 29, 30, 33, 35, 39, 40, 42, 43, 45], "photon": [0, 35], "tomographi": [0, 35], "imag": [0, 2, 15, 16, 17, 18, 31, 35, 41, 42, 45], "1": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 19, 21, 22, 26, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45], "675": [0, 35], "young": [0, 35], "adult": [0, 3, 4, 5, 6, 9, 10, 11, 14, 35, 42], "c57bl6": [0, 35], "j": [0, 35], "mice": [0, 29, 31, 35, 42, 44], "us": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 31, 32, 38, 39, 41, 43, 44], "multimod": [0, 35], "data": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 22, 38, 43, 44], "entir": [0, 13, 29, 35, 36, 42], "parcel": [0, 2, 20, 24, 40], "directli": [0, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "label": [0, 15, 16, 17, 18, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45], "everi": [0, 35], "structur": [0, 3, 4, 5, 7, 12, 33, 37, 41, 45], "span": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 30, 35, 43, 45], "43": [0, 35, 37, 38], "isocort": [0, 35], "area": [0, 29, 32, 35, 37], "layer": [0, 14, 34, 35], "314": [0, 35], "subcort": [0, 29, 31, 35, 42, 44], "grai": [0, 35], "matter": [0, 35], "81": [0, 1, 35], "fiber": [0, 35, 41], "tract": [0, 35, 41], "8": [0, 14, 15, 17, 19, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "ventricular": [0, 35], "The": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "add": [0, 28, 34, 35, 36, 40], "new": [0, 28, 35, 37, 40], "annot": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 24, 29, 32, 33, 37, 40, 41, 42], "ammon": [0, 14, 35], "s": [0, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "horn": [0, 14, 35], "ca": [0, 35], "main": [0, 14, 31, 32, 35, 40, 42, 44], "olfactori": [0, 14, 31, 35, 37, 42, 44], "bulb": [0, 35, 37], "mob": [0, 31, 35, 42, 44], "minor": [0, 35], "modif": [0, 35], "surround": [0, 35], "For": [0, 12, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "purpos": [0, 28, 29, 32, 34, 35, 36, 41], "abc": [0, 15, 16, 17, 18, 19, 28, 35, 39, 45], "atla": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 31, 32, 34, 35, 36, 39, 40, 42, 44, 45], "visual": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 29, 31, 32, 33, 38, 42, 44, 45], "analysi": [0, 1, 2, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 20, 29, 31, 35, 37, 39, 41, 42, 44], "we": [0, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "have": [0, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "also": [0, 13, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "simplifi": [0, 2, 14, 20], "5": [0, 2, 13, 14, 16, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "level": [0, 2, 6, 13, 14, 20, 29, 30, 31, 32, 42, 44, 45], "anatom": [0, 2, 13, 14, 20, 28, 29, 31, 32, 33, 36, 38, 42, 44, 45], "hierarchi": [0, 2, 14, 20, 34, 36], "associ": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 42, 43, 45], "metadata": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 43, 44], "host": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "aw": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40, 45], "s3": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "bucket": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40, 45], "public": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "dataset": [0, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 36, 37, 39, 40, 43, 44, 45], "compon": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 37], "current": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 40], "size": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 35, 36, 39, 40, 41], "volum": [0, 2, 35, 41], "cell": [0, 1, 2, 3, 4, 7, 12, 15, 16, 17, 18, 21, 30, 31, 35, 37, 39, 40, 43, 44], "image_volum": [0, 2, 40], "ccf": [0, 13, 14, 15, 16, 17, 18, 20, 27, 35, 36, 40], "20230630": [0, 2, 10, 11, 29, 40], "379": 0, "mb": [0, 2, 3, 5, 29, 30, 35, 36, 37, 40, 41], "18": [0, 15, 29, 31, 33, 36, 37, 38, 39, 42], "being": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 35, 36, 40], "share": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 36, 45], "under": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 40], "institut": [0, 15, 16, 17, 18, 28, 45], "term": [0, 24, 29, 32, 42, 45], "notebook": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "learn": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 33], "about": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 33, 35, 36], "through": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 32, 34, 35, 36, 41, 42], "some": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 29, 31, 33, 34, 35, 37, 42], "exampl": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 31, 32, 39, 40, 41, 43, 44], "case": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 32, 41], "A": [1, 2, 6, 13, 14, 28, 30, 34, 35, 36, 41, 42, 45], "4": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "0": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "million": [1, 3, 4, 5, 6, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 29, 30, 33, 34, 36, 45], "500": [1, 13, 14, 26, 36, 42], "gene": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 28, 34, 36, 40, 43], "panel": [1, 13, 14, 15, 16, 17, 18, 19, 36], "map": [1, 14, 15, 16, 17, 18, 19, 20, 37, 38, 42, 45], "whole": [1, 2, 4, 5, 12, 15, 16, 17, 18, 21, 28, 30, 38, 39], "taxonomi": [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 25, 28, 29, 32, 33, 40, 42, 45], "It": [1, 9, 10, 11, 29, 34, 35, 36, 42, 45], "wa": [1, 2, 9, 10, 11, 29, 31, 33, 36, 37, 40, 41, 42, 44], "creation": [1, 9, 10, 11], "high": [1, 8, 9, 10, 11, 13, 31, 36, 44], "type": [1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 28, 29, 31, 32, 33, 34, 36, 37, 39, 40, 41, 42, 44, 45], "describ": [1, 8, 9, 10, 11, 29, 40], "yao": [1, 2, 8, 9, 10, 11, 12, 37, 38, 41], "express": [1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 28, 34, 36, 40, 43], "matric": [1, 4, 9, 10, 11, 15, 16, 17, 18, 28, 33, 42, 43], "version": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 34, 36, 40, 42], "allen": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 29, 31, 36, 40, 41, 42, 44, 45], "expression_matric": [1, 4, 9, 10, 11, 15, 16, 17, 18, 29, 30, 40, 42, 43], "c57bl6j": [1, 2, 12, 13, 14, 26, 37, 38, 40, 41, 42, 43, 44], "638850": [1, 2, 12, 13, 14, 26, 37, 38, 40, 41, 42, 43, 44], "20230830": [1, 9, 15, 16, 17, 18, 30, 40, 42, 43], "14": [1, 29, 32, 33, 40, 45], "2": [1, 2, 3, 4, 5, 7, 8, 11, 14, 15, 17, 19, 30, 32, 34, 35, 36, 37, 38, 39, 40, 41, 45], "gb": [1, 2, 4, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 39, 40], "20231215": [1, 2, 8, 12, 13, 15, 16, 17, 18, 29, 40], "cc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 31, 32, 33, 37, 38, 41, 42, 45], "BY": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18], "nc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13], "licens": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18], "relat": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 29, 33, 36, 39, 40, 42], "resourc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13], "cluster": [1, 2, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 17, 18, 20, 24, 28, 29, 31, 32, 33, 35, 38, 40, 41, 42, 44], "wmb": [1, 2, 8, 9, 10, 11, 12, 13, 14, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 42, 45], "10x": [1, 2, 4, 5, 6, 9, 10, 11, 12, 13, 14, 20, 26, 28, 37, 38, 40, 42], "get": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 31, 33, 34, 35, 36, 37, 41, 42, 44], "start": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 31, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45], "how": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "abcprojectcach": [1, 2, 8, 12, 13, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "facilit": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28], "download": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "usag": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 36, 40], "scrna": [1, 2, 4, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 36, 45], "seq": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 45], "part": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22, 35, 37, 40, 41, 45], "section": [1, 2, 12, 13, 15, 16, 17, 18, 19, 22, 29, 30, 33, 35, 37, 40, 42, 43, 44, 45], "2a": [1, 2, 8, 9, 10, 11, 12, 13, 21, 22, 31, 37, 44], "access": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 21, 22, 29, 30, 33, 34, 35, 36, 42], "prepar": [1, 2, 12, 13, 22, 30, 40, 43], "2b": [1, 2, 8, 9, 10, 11, 12, 13, 21, 22, 30, 43], "explor": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44], "analys": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22], "set": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 20, 21, 22, 29, 31, 32, 37, 38, 39, 40, 41, 42, 44, 45], "interest": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22, 29, 31, 32, 33, 44], "each": [2, 12, 13, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "regist": [2, 13, 15, 16, 17, 18, 36, 45], "combin": [2, 8, 13, 14, 28, 29, 32, 33, 36, 42, 43], "global": [2, 41], "wise": [2, 41], "midlin": [2, 15, 16, 41, 42, 45], "manual": [2, 15, 16, 17, 41, 45], "determin": [2, 15, 16, 34, 36, 40, 41], "rotat": [2, 15, 16, 17, 18, 41, 42, 45], "upright": [2, 41, 42, 45], "center": [2, 15, 16, 17, 18, 34, 36, 41, 45], "middl": [2, 41, 42, 45], "thi": [2, 4, 8, 9, 10, 11, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "rectifi": [2, 41], "were": [2, 15, 16, 17, 18, 29, 31, 33, 37, 39, 40, 41, 42, 44, 45], "stack": [2, 34, 36, 41], "sequenti": [2, 41, 42], "order": [2, 29, 31, 32, 33, 34, 35, 36, 41], "initi": 2, "configur": [2, 41], "registr": [2, 15, 16, 17, 18, 41], "affin": [2, 41], "12": [2, 17, 29, 33, 39, 40, 41, 45], "dof": [2, 41], "perform": [2, 15, 16, 17, 18, 41, 45], "align": [2, 15, 16, 17, 18, 29, 41, 45], "deform": [2, 41], "its": [2, 28, 35], "resampl": 2, "target": [2, 41, 42], "step": [2, 8, 15, 16, 17, 18, 37, 41, 45], "preserv": [2, 41], "concaten": [2, 29, 32, 41], "appropri": [2, 41], "invers": [2, 41], "allow": [2, 40, 41, 44], "point": [2, 15, 16, 17, 18, 41, 42, 45], "between": [2, 12, 13, 14, 31, 33, 34, 35, 36, 37, 40, 41, 42], "origin": [2, 28, 31, 35, 40, 41, 44], "see": [2, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "further": [2, 12, 15, 16, 17, 18, 29, 31, 32, 37, 39, 41, 45], "detail": [2, 3, 4, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "115": 2, "01": [2, 13, 18, 29, 30, 36, 37, 38, 40, 42, 44, 45], "mous": [2, 12, 28, 29, 31, 34, 37, 38, 39, 42, 44], "spatial": [2, 8, 9, 10, 11, 12, 13, 14, 20, 28, 31, 36, 37, 38, 41], "transcriptom": [2, 5, 12, 13, 19, 23, 28, 34, 36], "2020": [2, 14, 15, 16, 17, 18, 27, 40, 41, 45], "singl": [2, 5, 6, 12, 13, 14, 22, 32, 34, 35, 36, 41, 42, 44], "over": [3, 4, 5, 6, 29, 31, 39, 40, 42, 44, 45], "3": [3, 4, 5, 6, 11, 12, 14, 15, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "result": [3, 8, 15, 16, 17, 18, 30, 31, 34, 35, 36, 37, 39, 42, 43, 44, 45], "461": [3, 5, 32, 34], "3313": [3, 5, 32, 34], "subclust": [3, 5, 32, 33, 36], "link": [3, 29, 40], "below": [3, 29, 32, 33, 34, 39, 40], "contain": [3, 5, 13, 33, 34, 36, 40], "all": [3, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45], "geen": 3, "whb": [3, 4, 5, 6, 25, 26, 33, 34, 36, 39, 40], "full": [3, 4, 32, 34, 39, 40], "can": [3, 4, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "found": [3, 4, 29, 30, 33, 34, 39, 40], "siletti": [3, 4, 5, 28, 32, 33, 34, 39], "2023": [3, 4, 5, 15, 16, 17, 18, 28, 32, 33, 34, 35, 39, 45], "10xv3": [3, 5, 6, 8, 12, 14, 29, 30, 32, 33, 39, 40], "20240330": [3, 4, 5, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "862": 3, "manifest": [3, 4, 5, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "json": [3, 4, 5, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "file": [3, 4, 5, 15, 16, 17, 18, 28, 29, 30, 32, 33, 35, 39, 41, 42, 43, 45], "snrna": [3, 5], "load": [3, 4, 5, 28, 29, 30, 32, 33, 40, 42], "individu": [3, 4, 5, 28, 42, 45], "understand": [3, 4, 5, 7, 28], "basic": [3, 4, 5, 7, 35], "region": [3, 4, 5, 7, 12, 13, 14, 29, 31, 32, 33, 34, 35, 36, 37, 42, 44], "umap": [3, 4, 5, 7, 14, 20, 31, 33, 37, 38], "consist": [4, 5, 9, 10, 11, 29, 34, 35, 36, 39, 42, 45], "nuclei": [4, 5, 31, 32, 33, 34, 37, 39, 44], "extract": [4, 39], "three": [4, 5, 6, 15, 18, 29, 34, 36, 41], "approxim": [4, 29, 32, 37], "neuron": [4, 5, 12, 14, 29, 31, 32, 33, 34, 37, 38, 39, 42, 44], "one": [4, 5, 8, 16, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 42, 43, 45], "non": [4, 5, 32, 33, 34, 37, 38, 39], "100": [4, 5, 29, 30, 31, 32, 33, 34, 36, 37, 39, 40, 41, 42, 44, 45], "locat": [4, 5, 13, 32, 33, 34, 36, 40, 44], "across": [4, 5, 13, 28, 29, 31, 33, 34, 36, 39, 40, 41, 44], "forebrain": [4, 5, 32, 34, 35], "midbrain": [4, 5, 31, 32, 34, 35, 37, 38, 39], "hindbrain": [4, 5, 34, 37, 38], "ar": [4, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "70": 4, "present": [5, 31, 32, 33, 39], "here": [5, 28, 32, 34, 35, 39, 40], "collect": [5, 40, 45], "apprixm": 5, "integr": [5, 13, 15, 16, 17, 18, 28, 34, 35, 36, 45], "31": [5, 9, 11, 32, 34, 39, 40, 41, 42, 44, 45], "superclust": [5, 32, 33, 36], "6": [5, 15, 17, 19, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 45], "nucleu": [5, 31, 35, 44], "chemistri": [6, 9, 10, 11, 14, 29], "whb_cluster_annotation_tutori": 7, "ipynb": [7, 20, 21, 22, 23, 28, 30, 32, 33], "10x_snrnaseq_tutorial_part_1": [7, 21], "10x_snrnaseq_tutorial_part_2": 7, "10xv2": [8, 12, 14, 29, 30, 40], "5196": [8, 36], "toward": 8, "39": 8, "10xmulti": [8, 14, 29, 30, 40], "thalamu": [8, 9, 10, 11, 12, 13, 21, 30, 31, 32, 37, 38, 42], "iter": [8, 9, 10, 11, 12, 13, 21], "packag": [8, 9, 10, 11, 12, 13, 21, 28, 29, 30, 31, 32, 39, 40, 42, 45], "1687": [9, 14, 29, 30], "multiom": [9, 14], "176": [9, 11, 35], "abcprojecctcach": 9, "7": [10, 14, 15, 29, 35, 37, 39, 40, 41, 42, 45], "104": [10, 40], "05": 10, "abcporjectcach": [10, 11], "To": [12, 28, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 45], "investig": [12, 37], "divers": [12, 34, 37], "within": [12, 14, 29, 32, 34, 35, 36, 37, 41], "major": [12, 34, 36, 37, 41], "concept": [12, 37], "them": [12, 28, 29, 32, 37, 38, 39, 42, 44], "thei": [12, 33, 37, 40, 42], "gener": [12, 33, 34, 37, 40, 42, 45], "re": [12, 28, 29, 31, 32, 33, 35, 37, 41, 42, 44, 45], "reveal": [12, 13, 31, 36, 37, 44], "fine": [12, 13, 14, 36, 37], "grain": [12, 14, 37], "relationship": [12, 31, 33, 34, 35, 36, 37], "00": [12, 29, 30, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "merfish": [12, 13, 14, 20, 23, 26, 36, 37, 38, 40], "galleri": [12, 20], "sever": [13, 29, 36, 40], "rna": [13, 42], "sequenc": [13, 29, 33, 34, 36], "total": [13, 30, 36, 39, 40], "pass": [13, 15, 16, 17, 18, 19, 36, 40, 45], "rigor": [13, 36], "qualiti": [13, 15, 16, 17, 18, 36, 45], "control": [13, 15, 16, 17, 18, 36, 45], "qc": [13, 36], "criteria": [13, 36], "322": [13, 36, 40], "organ": [13, 28, 29, 32, 35, 36, 42], "hierarch": [13, 34, 36], "manner": [13, 36], "nest": [13, 36], "group": [13, 20, 28, 29, 31, 32, 33, 34, 35, 36, 38, 40, 42, 44], "34": [13, 29, 32, 34, 36, 40, 42], "class": [13, 28, 29, 31, 37, 41, 42, 44, 45], "338": [13, 29, 36, 42], "subclass": [13, 15, 16, 17, 18, 29, 31, 36, 37, 41, 42, 44, 45], "201": [13, 36], "supertyp": [13, 29, 36, 41, 42, 45], "wide": [13, 36], "co": [13, 36], "pattern": [13, 29, 31, 32, 36, 44], "ha": [13, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "been": [13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "comprehens": [13, 36], "segment": [13, 15, 16, 17, 18, 36, 42, 45], "probe": [13, 36, 42], "common": [13, 36, 45], "coordin": [13, 14, 15, 16, 17, 18, 20, 29, 32, 36, 37, 38, 42, 45], "framework": [13, 36, 41, 45], "v3": [13, 36, 41], "onli": [13, 29, 31, 32, 34, 35, 36, 37, 39, 42, 44], "provid": [13, 28, 29, 30, 32, 34, 35, 36, 39, 41, 42, 45], "accur": [13, 36], "distinct": [13, 31, 33, 34, 36, 44], "gradient": [13, 34, 36], "degre": [13, 36], "correspond": [13, 29, 32, 34, 36, 41, 42, 45], "ident": [13, 29, 31, 32, 36, 42, 44, 45], "specif": [13, 20, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44], "well": [13, 31, 36, 37, 44], "uniqu": [13, 29, 32, 34, 35, 36, 37, 41, 42, 45], "featur": [13, 36, 37, 38, 44], "differ": [13, 28, 32, 33, 36, 40], "tabl": [13, 29, 31, 32, 33, 34, 35, 36, 39, 41, 42, 44, 45], "along": [13, 15, 16, 17, 18, 36, 45], "inform": [13, 32, 34, 35, 36, 37, 41], "membership": [13, 32, 33], "neurotransmitt": [13, 30, 32, 33, 37, 38, 41, 43, 45], "marker": [13, 29, 31, 32, 33, 36, 37, 38, 41, 42, 44, 45], "transcript": [13, 29, 36, 39, 42], "factor": [13, 29, 32, 36, 42], "neuropeptid": [13, 29, 31, 36, 42, 44], "other": [13, 15, 16, 29, 30, 32, 33, 34, 36, 39, 42, 45], "four": [14, 15, 16, 17, 18, 36, 44, 45], "9": [14, 16, 19, 29, 31, 33, 34, 36, 39, 40, 41, 42, 44, 45], "definit": [14, 34, 36], "neighborhood": [14, 20, 40], "embed": [14, 20, 38], "updat": [14, 28, 40], "addit": [14, 33, 37, 39, 40], "blub": [14, 31, 42, 44], "147": [15, 19, 41, 45], "coron": [15, 16, 19, 35, 42, 43, 45], "1122": [15, 16, 17, 18, 19, 26, 45], "150": 15, "anim": [15, 16, 17, 18, 45], "obtain": [15, 16, 17, 18, 34, 35, 36, 42, 45], "includ": [15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "classifi": [15, 16, 17, 18, 45], "appli": [15, 16, 17, 18, 34, 38, 41, 45], "seri": [15, 16, 17, 18, 29, 34, 36, 42, 45], "filter": [15, 16, 17, 18, 29, 31, 35, 36, 37, 38, 40, 41, 44, 45], "select": [15, 16, 17, 18, 28, 32, 37, 39, 40, 42, 45], "subset": [15, 16, 17, 18, 29, 30, 39, 45], "first": [15, 16, 17, 29, 30, 32, 33, 34, 35, 36, 37, 41, 42, 45], "remov": [15, 16, 17, 18, 45], "fractur": [15, 16, 17, 45], "tissu": [15, 16, 17, 18, 45], "slice": [15, 16, 17, 18, 34, 35, 36, 39, 45], "remain": [15, 16, 17, 18, 36, 41, 45], "after": [15, 16, 17, 18, 40, 45], "Then": [15, 16, 17, 45], "defin": [15, 16, 17, 18, 28, 29, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "substanti": [15, 16, 17, 18, 45], "hemispher": [15, 16, 45], "which": [15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "anterior": [15, 16, 35, 41, 42, 45], "posterior": [15, 16, 17, 18, 35, 41, 42, 45], "end": [15, 16, 40], "cannot": [15, 16, 17, 40, 45], "orient": [15, 16, 17, 35, 45], "x": [15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "y": [15, 16, 17, 18, 29, 31, 32, 33, 35, 37, 38, 39, 40, 41, 42, 44, 45], "experiment": [15, 16, 17, 18, 45], "measur": [15, 16, 17, 18, 42, 45], "z": [15, 16, 17, 18, 35, 41, 42, 45], "estim": [15, 16, 17, 18, 45], "posit": [15, 16, 17, 18, 29, 34, 36, 42, 45], "axi": [15, 16, 17, 18, 29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "base": [15, 16, 17, 18, 29, 31, 34, 36, 39, 42, 44, 45], "either": [15, 16, 17, 33, 39, 40, 41, 42, 44, 45], "dure": [15, 16, 17, 18, 29, 31, 42, 44, 45], "zero": [15, 16, 34, 35, 36, 45], "when": [15, 16, 33, 36, 39, 40, 45], "becom": [15, 16, 40, 45], "neg": [15, 16, 45], "therefor": 15, "multipl": [15, 28, 32, 39, 40, 41], "valu": [15, 29, 31, 33, 34, 35, 36, 37, 41, 42, 44, 45], "matrix": [15, 16, 17, 18, 28, 29, 33, 37, 39, 40], "classif": [15, 16, 17, 18, 19, 29, 32, 34, 36, 42, 45], "transfer": [15, 16, 17, 18, 28, 29, 30, 45], "confid": [15, 16, 17, 18, 19, 45], "score": [15, 16, 17, 18, 19, 42, 45], "calcul": [15, 16, 17, 18, 45], "scrnaseq": [15, 16, 17, 18, 45], "threshold": [15, 16, 17, 18, 19, 45], "These": [15, 16, 17, 18, 33, 36, 39, 45], "displai": [15, 16, 17, 18, 19, 29, 45], "awb": [15, 16, 17, 18, 45], "zhang": [15, 16, 17, 18, 45], "more": [15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "09": [15, 30, 41], "33": [15, 29, 38, 45], "21": [15, 29, 30, 39, 40, 41], "66": [16, 19, 40, 45], "67": [16, 32, 36, 38], "13": [16, 29, 32, 33, 37, 39, 40, 41, 42, 45], "30": [16, 29, 31, 32, 33, 38, 39, 40, 42, 44, 45], "57": [16, 32], "08": [16, 18, 33, 38, 41, 45], "23": [17, 19, 29, 30, 37, 39, 40, 41, 42, 45], "sagitt": [17, 18, 19, 45], "25": [17, 29, 33, 40, 41, 42, 45], "edg": [17, 18, 45], "later": [17, 18, 29, 31, 33, 35, 37, 42, 44, 45], "medial": [17, 18, 29, 31, 37, 42, 44], "69": [17, 35, 44], "75": [17, 40], "22": [18, 19, 29, 39, 40, 41, 45], "19": [18, 29, 32, 37, 39, 40, 44, 45], "16": [18, 19, 29, 31, 35, 36, 38, 39, 40, 42, 44], "abca": [19, 26, 40, 45], "cluster_annotation_tutori": 20, "cluster_groups_and_embeddings_tutori": 20, "cluster_neighborhood_galleri": 20, "ccf_and_parcellation_annotation_tutori": 20, "merfish_ccf_registration_tutori": 20, "10x_snrnaseq_tutorial_part_2a": 21, "10x_snrnaseq_tutorial_part_2b": 21, "merfish_tutorial_part_1": 22, "merfish_tutorial_part_2a": 22, "merfish_tutorial_part_2b": 22, "zhuang_merfish_tutori": 23, "list": [24, 29, 32, 33, 34, 36, 38, 39, 40, 42, 44], "ccn20230504": 25, "ccn20230722": 25, "32285": [26, 29, 40], "59357": [26, 33, 39], "zhuang": [26, 28, 40], "aim": 28, "empow": 28, "research": [28, 35], "worldwid": 28, "analyz": [28, 35], "simultan": 28, "As": [28, 30, 31, 36, 43, 44], "collabor": 28, "continu": [28, 30, 31, 43, 44], "modal": 28, "speci": 28, "insight": 28, "groundbreak": 28, "platform": [28, 29, 42], "keep": [28, 40, 41], "grow": 28, "open": [28, 29, 30, 33, 35, 39, 42, 45], "up": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "endless": 28, "possibl": 28, "discoveri": [28, 42], "breakthrough": 28, "neurosci": 28, "With": [28, 31, 44], "everywher": 28, "gain": 28, "complex": [28, 32], "work": 28, "advanc": 28, "our": [28, 31, 33, 39, 44], "amaz": 28, "wai": [28, 33, 34, 35, 36, 40], "never": 28, "thought": 28, "primari": [28, 29, 32, 35], "method": [28, 29, 32, 39, 40, 42], "interact": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "ani": [28, 40, 42], "question": 28, "issu": [28, 39], "best": [28, 29, 42, 45], "direct": [28, 35, 41], "commnitui": 28, "forum": 28, "repositori": 28, "intend": 28, "user": [28, 29, 30, 31, 33, 37, 40, 42, 43], "who": 28, "wish": 28, "process": [28, 29, 32, 39, 40, 41], "local": [28, 31, 40, 44], "amazon": [28, 40], "web": [28, 40], "servic": [28, 40], "arn": [28, 40], "No": [28, 40], "account": [28, 40, 42], "login": [28, 40], "requir": [28, 29, 39, 40, 42], "repo": [28, 40], "overview": [28, 41], "avail": [28, 29, 33, 34, 35, 36, 39, 40, 41, 42, 45], "spring": 28, "2024": [28, 40], "beta": 28, "hongkui": 28, "zeng": 28, "molecularli": 28, "resolv": [28, 40, 45], "xiaowei": 28, "human": [28, 29, 35, 36, 37, 39, 40], "kimberli": 28, "lightweight": 28, "python": [28, 40], "object": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "handl": [28, 29, 39], "manag": 28, "store": [28, 29, 30, 32, 35, 36, 37, 39, 40, 42, 45], "anndata": [28, 29, 30, 31, 32, 33, 39, 40, 42, 43, 44, 45], "h5ad": [28, 29, 30, 33, 39, 40, 42, 43, 45], "format": [28, 29, 30, 33, 35, 37, 39, 40, 42, 45], "need": [28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44], "system": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "make": [28, 29, 30, 42], "effici": [28, 29, 30], "subdivid": [28, 29], "smaller": [28, 29, 30, 42, 45], "code": [28, 29, 30, 39, 40, 42, 44, 45], "getting_start": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "matrici": [28, 30, 32, 33, 40], "ad": [28, 29, 30, 40, 41, 42], "hash": 28, "check": 28, "cach": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "jupyt": 28, "book": 28, "webpag": 28, "24": [29, 30, 32, 33, 35, 40, 41], "where": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "broad": [29, 34, 36], "dissect": [29, 31, 32, 33, 44], "you": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "connect": [29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45], "internet": [29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44], "run": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44], "via": [29, 31, 33, 34, 35, 36, 41, 42, 44], "import": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "os": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "panda": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "pd": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "pathlib": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "path": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "numpi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "np": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "time": [29, 30, 31, 32, 33, 37, 38, 39, 42, 43, 44, 45], "matplotlib": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "pyplot": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "plt": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "abc_atlas_access": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_atlas_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_project_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "track": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "serv": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "requst": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "disk": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "datafram": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "instal": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "alreadi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "chang": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "download_bas": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "variabl": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "your": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_download_root": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "from_s3_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "current_manifest": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "releas": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "latest_manifest_fil": 29, "essenti": [29, 32, 42, 45], "row": [29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "repres": [29, 32, 34, 35, 36, 37, 41, 42, 45], "index": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45], "barcod": [29, 32, 42], "name": [29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 44, 45], "sampl": [29, 32], "In": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45], "context": [29, 32, 33, 34, 35, 36, 38, 42, 44, 45], "port": [29, 32], "chromium": [29, 32], "note": [29, 30, 32, 33, 34, 36, 39, 40, 41, 42, 45], "same": [29, 32, 33, 34, 35, 36, 37, 39, 41, 42, 44, 45], "reus": [29, 32, 36, 37], "databas": [29, 32, 34, 35, 36, 37], "librari": [29, 32, 35, 40], "donor": [29, 32, 33, 42, 45], "genotyp": [29, 42, 45], "sex": [29, 32, 42, 45], "acronym": [29, 31, 35], "coars": [29, 32, 36], "divis": [29, 32, 35, 41, 42, 45], "matrix_prefix": [29, 32, 45], "identifi": [29, 32, 35, 42, 45], "alia": [29, 32, 34, 36, 42, 45], "member": [29, 32, 35, 36, 37, 40, 42], "figur": [29, 32, 38], "manuscript": [29, 32], "tutori": [29, 31, 32, 33, 36, 37, 38, 40, 41, 42, 45], "list_metadata_fil": [29, 32, 33, 34, 40], "cell_metadata": [29, 30, 32, 33, 39, 40, 42, 43, 45], "cell_metadata_with_cluster_annot": [29, 31, 37, 40, 41, 42, 44, 45], "example_genes_all_cells_express": [29, 31, 32, 33, 37, 39, 40, 44], "region_of_interest_metadata": [29, 31, 40], "cluster_annotation_term": [29, 32, 34, 36, 40], "cluster_annotation_term_set": [29, 32, 33, 34, 36, 40], "cluster_annotation_term_with_count": [29, 36, 40], "cluster_to_cluster_annotation_membership": [29, 32, 33, 34, 36, 40], "cluster_to_cluster_annotation_membership_color": [29, 36, 40, 42, 45], "cluster_to_cluster_annotation_membership_pivot": [29, 36, 40, 42, 45], "get_directory_metadata": [29, 40], "posixpath": [29, 40], "chri": [29, 30, 31, 40, 42, 43], "morrison": [29, 30, 31, 40, 42, 43], "src": [29, 30, 31, 39, 40, 42, 43], "csv": [29, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "view": [29, 31, 37, 40], "list_data_fil": [29, 30, 35, 40, 41, 42, 45], "cb": [29, 30, 37, 39, 41], "log2": [29, 30, 39, 40, 42, 43, 45], "raw": [29, 30, 39, 40, 42, 45], "ctxsp": [29, 30, 40], "hpf": [29, 30, 40, 41], "hy": [29, 30, 35, 37, 40, 41], "isocortex": [29, 30, 31, 35, 37, 40, 41, 42, 44], "my": [29, 30, 36, 41, 45], "olf": [29, 30, 40, 41], "p": [29, 30, 35, 41, 42], "pal": [29, 30], "str": [29, 30, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45], "th": [29, 30, 34, 36, 37, 40, 41], "repeat": [29, 30, 32, 41, 43], "throughout": [29, 32, 40], "get_metadata_datafram": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "directori": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "file_nam": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "dtype": [29, 31, 32, 33, 35, 37, 38, 41, 42, 43, 44, 45], "cell_label": [29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45], "set_index": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "inplac": [29, 30, 31, 32, 33, 35, 37, 38, 41, 42, 43, 44, 45], "true": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45], "print": [29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 45], "number": [29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 45], "len": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45], "head": [29, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "858m": 29, "7mmb": [29, 39, 41, 45], "4042976": [29, 37, 38], "cell_barcod": [29, 32, 33, 39], "barcoded_cell_sample_label": [29, 32, 33, 39], "library_label": [29, 30, 32, 33, 39], "feature_matrix_label": [29, 30, 32, 33, 39, 41, 42, 45], "entiti": [29, 32, 33, 36, 39], "brain_section_label": [29, 32, 33, 37, 38, 39, 41, 42, 44, 45], "library_method": [29, 32, 33, 39], "region_of_interest_acronym": [29, 31], "donor_label": [29, 32, 33, 39, 41, 42, 45], "donor_genotyp": [29, 41, 42, 45], "donor_sex": [29, 32, 33, 39, 41, 42, 45], "dataset_label": [29, 30, 32, 33, 39], "cluster_alia": [29, 32, 33, 34, 36, 37, 39, 41, 42, 45], "gcgagaagttaagggc": 29, "410_b05": 29, "l8tx_201030_01_c12": 29, "nan": [29, 35, 40, 41], "rhp": 29, "snap25": 29, "ires2": 29, "cre": 29, "ai14": 29, "550850": 29, "rcl": 29, "tdt": 29, "wt": [29, 41, 42, 45], "f": [29, 32, 35, 40, 45], "146826": 29, "086639": 29, "aatggctcagctcctt": 29, "411_b06": 29, "l8tx_201029_01_e10": 29, "550851": 29, "138481": 29, "022000": 29, "aacacacgttgcttga": 29, "472557": 29, "992709": 29, "cacagatagaggcgga": 29, "410_a05": 29, "l8tx_201029_01_a10": 29, "379622": 29, "043442": 29, "aaagtgaagcatttcg": 29, "909480": 29, "601536": 29, "panada": 29, "groupbi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "function": [29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "mani": [29, 32, 33, 39, 42], "item": [29, 32, 42], "field": [29, 32, 42], "out": [29, 32, 34, 35, 36, 37, 39, 41, 42, 44], "small": [29, 31, 32, 40, 42, 44, 45], "def": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "print_column_info": [29, 32, 42], "df": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44], "c": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "column": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "count": [29, 30, 32, 35, 39, 41, 42, 45], "d": [29, 32, 42, 45], "2375490": 29, "819": 29, "10xrseq_mult": 29, "29": [29, 31, 39, 40, 41, 42, 45], "aca": 29, "ai": 29, "aud": 29, "tea": 29, "peri": [29, 45], "ect": 29, "ent": 29, "hip": 29, "lsx": 29, "mo": 29, "frp": [29, 35], "mop": 29, "pl": 29, "ila": 29, "orb": 29, "rsp": 29, "ss": 29, "gu": 29, "visc": 29, "ssp": [29, 35, 41], "strd": 29, "strv": 29, "vi": 29, "ptlp": 29, "sami": 29, "345": 29, "gad2": 29, "ir": 29, "slc32a1": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "m": [29, 32, 33, 35, 36, 39, 41, 42], "3992539": 29, "3992791": 29, "5322": [29, 36, 37, 38, 45], "1699939": 29, "2341350": 29, "bring": [29, 42], "pivot": [29, 32, 34, 35, 36, 41, 42, 45], "cluster_detail": [29, 32, 33, 42, 45], "keep_default_na": [29, 34, 36, 42, 45], "fals": [29, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "glut": [29, 31, 36, 37, 40, 41, 42, 44, 45], "IT": [29, 36, 41, 42, 45], "018": [29, 36, 42, 45], "l2": [29, 36, 41, 42, 45], "ppp": [29, 36, 42, 45], "apr": [29, 36, 42, 45], "0082": [29, 36, 42, 45], "glut_3": [29, 36, 42, 45], "0326": [29, 36, 42, 45], "0327": [29, 36, 42, 45], "0081": [29, 36, 42, 45], "glut_2": [29, 36, 42, 45], "0322": [29, 36, 42, 45], "0323": [29, 36, 42, 45], "0325": [29, 36, 42, 45], "cluster_color": [29, 32, 33, 34, 36, 41, 42, 45], "neurotransmitter_color": [29, 31, 32, 33, 34, 36, 37, 41, 42, 44, 45], "class_color": [29, 36, 37, 41, 42, 44, 45], "subclass_color": [29, 31, 36, 37, 38, 41, 42, 44, 45], "supertype_color": [29, 36, 41, 42, 45], "2b93df": [29, 32, 36, 41, 42, 45], "fa0087": [29, 36, 42, 45], "0f6632": [29, 36, 42, 45], "266dff": [29, 36, 42, 45], "64661f": [29, 36, 42, 45], "cca73d": [29, 36, 42, 45], "002bcc": [29, 36, 42, 45], "99000d": [29, 36, 42, 45], "5c8899": [29, 36, 42, 45], "473d66": [29, 36, 42, 45], "roi": [29, 31, 32, 33], "renam": [29, 32, 33, 41, 45], "region_of_interest_ord": 29, "color_hex_triplet": [29, 32, 33, 34, 35, 36], "region_of_interest_color": [29, 32, 33], "40k": 29, "1kmb": 29, "somatomotor": 29, "frontal": [29, 35], "pole": [29, 35], "3dcc7c": 29, "motor": 29, "179968": 29, "somatosensori": [29, 35], "gustatori": 29, "viscer": 29, "2e8599": 29, "5ccccc": 29, "auditori": [29, 32], "455a99": 29, "cell_extend": [29, 32, 33, 42, 45], "join": [29, 31, 32, 33, 34, 35, 36, 37, 39, 41, 42, 44, 45], "15": [29, 31, 34, 36, 39, 40, 41, 44, 45], "ccb05c": 29, "27": [29, 31, 33, 36, 37, 38, 40, 41, 42, 45], "10": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "chol": [29, 32, 42], "dopa": [29, 36, 37, 42], "gaba": [29, 31, 32, 34, 36, 37, 42, 44, 45], "glyc": [29, 36, 42, 45], "hist": [29, 42], "nora": [29, 42], "sero": [29, 37, 42], "1201": [29, 36, 42], "03edff": [29, 42], "0a9964": [29, 36, 42], "533691": [29, 42], "666666": [29, 32, 34, 36, 41, 42, 45], "73e785": [29, 42], "820e57": [29, 36, 42, 45], "ff3358": [29, 32, 36, 42, 45], "fcf04b": [29, 36, 42], "ff7621": [29, 32, 42], "5298": [29, 45], "11": [29, 31, 32, 37, 38, 39, 40, 41, 42, 44, 45], "17": [29, 39, 40, 45], "20": [29, 32, 34, 37, 38, 39, 40, 44], "26": [29, 38, 40, 41, 42], "28": [29, 45], "0059cc": 29, "00990a": 29, "00ffcf": 29, "26aeff": 29, "300099": 29, "341fcc": 29, "34cc1f": 29, "4d58ff": 29, "6f9945": 29, "84ff4d": 29, "8ccc00": 29, "992e6a": 29, "994817": 29, "99922e": 29, "9f3dcc": 29, "b973ff": 29, "cc0026": 29, "cc5cb0": 29, "e4ff26": 29, "ff00ef": 29, "ff2678": 29, "ff7373": 29, "ff8f00": 29, "abov": [29, 30, 36, 37, 40, 41, 42, 44, 45], "written": 29, "howev": [29, 33, 39, 40], "copi": [29, 30, 37, 38, 43], "uniform": [29, 32, 37], "manifold": [29, 32, 37], "project": [29, 32, 34, 37], "dimens": [29, 32, 35], "reduct": [29, 32], "techniqu": [29, 32], "larg": [29, 30, 32, 39], "helper": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "plot": [29, 31, 32, 33, 34, 36, 37, 38, 41, 42, 44, 45], "color": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "eas": [29, 32], "demostr": [29, 32], "do": [29, 32, 36], "simpl": [29, 31, 32, 34, 36, 39], "subsampl": [29, 31, 32, 37], "reduc": [29, 32, 39], "plot_umap": [29, 31, 32, 33, 37, 38], "xx": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "yy": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "none": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "val": [29, 31, 32, 33, 37, 38, 41, 42, 45], "fig_width": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "fig_height": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "cmap": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "fig": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "ax": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "subplot": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "set_size_inch": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "scatter": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "elif": [29, 31, 32, 33, 37, 38, 40, 41, 42, 45], "equal": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "set_xlim": [29, 31, 33, 37, 38, 41, 42, 44, 45], "set_ylim": [29, 31, 33, 37, 38, 41, 42, 44, 45], "set_xtick": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "set_ytick": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "return": [29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "cell_subsampl": 29, "loc": [29, 30, 31, 34, 35, 36, 37, 38, 44], "404298": 29, "set_titl": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "Of": [29, 32], "neuortransmitt": [29, 32, 41, 42], "illumina": 29, "novaseq6000": 29, "read": [29, 31, 33, 37, 38, 39, 42, 44, 45], "mm10": 29, "gencod": 29, "vm23": 29, "ensembl": [29, 42, 45], "98": 29, "genom": 29, "cellrang": 29, "pipelin": [29, 35], "default": [29, 39, 42], "paramet": [29, 33, 39], "id": [29, 42, 45], "practic": [29, 42, 45], "interchang": [29, 42, 45], "symbol": [29, 30, 42, 43, 45], "1173": 29, "comment": [29, 39, 40], "gene_identifi": [29, 30, 33, 39, 40, 42, 43, 45], "gene_symbol": [29, 30, 33, 39, 40, 42, 43, 45], "mapped_ncbi_identifi": [29, 40, 42, 45], "ensmusg00000051951": [29, 40], "xkr4": [29, 40], "kx": [29, 40], "blood": [29, 40], "ncbigen": [29, 40, 42, 45], "497097": [29, 40], "ensmusg00000089699": [29, 40], "gm1992": [29, 40], "predict": [29, 40], "1992": [29, 40], "ensmusg00000102331": [29, 40], "gm19938": [29, 40], "19938": [29, 40], "ensmusg00000102343": [29, 40], "gm37381": [29, 40], "37381": [29, 40], "ensmusg00000025900": [29, 40], "rp1": [29, 40], "retin": [29, 40], "pigmentosa": [29, 40], "19888": [29, 40], "pred": [29, 30, 31, 34, 36, 37, 38, 41, 42, 43, 44, 45], "ensmusg00000118272": 29, "arhgef4": 29, "rho": [29, 45], "guanin": 29, "nucleotid": 29, "exchang": 29, "gef": 29, "ensmusg00000117809": 29, "asdurf": 29, "asnsd1": 29, "upstream": 29, "frame": [29, 33, 39, 42, 45], "110599589": 29, "ensmusg00000047383": 29, "ac169382": 29, "novel": [29, 39], "ensmusg00000097001": 29, "1700054k02rik": 29, "riken": 29, "cdna": 29, "1700054k02": 29, "ensmusg00000116048": 29, "sept2": 29, "septin": 29, "ensmusg00000091585": 29, "ac140365": 29, "prame": [29, 40], "famili": [29, 31, 40, 42, 44, 45], "like": [29, 33, 39, 40, 42], "ensmusg00000095523": [29, 40], "ac124606": [29, 40], "100038995": [29, 40], "ensmusg00000095475": [29, 40], "ac133095": [29, 40], "uncharacter": [29, 40], "loc545763": [29, 40], "545763": [29, 40], "ensmusg00000094855": [29, 40], "loc620639": [29, 40], "620639": [29, 40], "ensmusg00000095019": [29, 40], "ac234645": [29, 40], "divid": [29, 30, 33, 34, 36], "annadata": [29, 30, 33, 39], "minim": [29, 30, 33, 39, 42, 45], "next": [29, 30, 31, 36, 37, 40, 41, 42, 44, 45], "rich": [29, 30, 42, 45], "discuss": [29, 30, 42, 45], "log": [29, 30, 34, 36, 42, 45], "normal": [29, 30, 39, 40, 42, 45], "directoi": 29, "get_data_path": [29, 30, 35, 40, 41, 42, 43, 45], "04g": 29, "02": 29, "1mmb": [29, 40, 45], "read_h5ad": [29, 30, 42, 43, 45], "back": [29, 30, 42, 43, 45], "r": [29, 30, 42, 43, 45], "lazi": [29, 42], "By": [29, 42], "memori": [29, 39, 42], "adata": [29, 42, 43, 45], "n_ob": [29, 42], "n_var": [29, 42], "131212": 29, "ob": [29, 42, 44], "anatomical_division_label": [29, 32, 33, 39], "var": [29, 30, 34, 36, 40, 42, 43], "un": [29, 42], "parent": [29, 34, 36], "parent_lay": 29, "parent_row": 29, "observ": [29, 31, 42, 44], "caggtgcaggctagca": 29, "040_c01": 29, "tgcgcaggttgcgcac": 29, "045_c01": 29, "cgatgtatcttgccgt": 29, "042_b01": 29, "gactaacgtcctcttg": 29, "040_b01": 29, "gatcgtacaactgcta": 29, "easili": 29, "extend": [29, 32, 37, 38], "cell_filt": [29, 30], "130555": [29, 30], "look": [29, 30, 31, 33, 42, 43, 44], "nine": [29, 30, 42, 45], "second": [29, 30, 35, 36, 42, 43], "support": [29, 30, 35, 37, 42, 45], "submatrix": [29, 30, 42, 45], "oper": [29, 30, 36, 42, 45], "take": [29, 30, 33, 34, 36, 39, 42, 43, 45], "around": [29, 30, 36, 39, 42, 45], "ntgene": [29, 30, 31, 42, 43, 44], "slc17a7": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "slc17a6": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "slc17a8": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a5": [29, 30, 31, 37, 42, 43, 44, 45], "slc18a3": [29, 30, 31, 37, 43], "slc6a3": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a4": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a2": [29, 30, 31, 37, 43], "exgen": [29, 30, 31, 42, 43, 44], "gname": [29, 30, 31, 33, 37, 42, 43, 44, 45], "gene_filt": [29, 30, 42, 43, 45], "ensmusg00000037771": [29, 30, 42, 43, 45], "ensmusg00000070570": [29, 30, 42, 43, 45], "ensmusg00000039728": [29, 30, 42, 43, 45], "ensmusg00000030500": [29, 30, 42, 43, 45], "ensmusg00000055368": [29, 30], "ensmusg00000019935": [29, 30, 42, 43, 45], "ensmusg00000025400": [29, 30, 42, 43], "ensmusg00000020838": [29, 30, 42, 43, 45], "ensmusg00000021609": [29, 30, 42, 43, 45], "ensmusg00000100241": [29, 30], "process_tim": [29, 30, 42, 43, 45], "asubset": [29, 42], "to_memori": [29, 42], "taken": [29, 30, 39, 42, 43, 45], "630955": 29, "create_expression_datafram": [29, 42], "input": [29, 34, 36, 40, 42], "aggregate_by_metadata": [29, 31, 33, 42, 44], "comput": [29, 31, 33, 40, 41, 42, 44], "given": [29, 31, 33, 34, 36, 40, 42, 44], "categori": [29, 35, 42], "gf": [29, 42], "gdata": [29, 30, 42, 43, 45], "to_df": [29, 30, 42, 43, 45], "sort": [29, 31, 33, 42, 44], "mean": [29, 31, 33, 42, 44], "sort_valu": [29, 31, 32, 33, 34, 35, 36, 38, 41, 42, 44], "ascend": [29, 31, 33, 35, 38, 41, 42, 44], "assign": [29, 31, 34, 36, 42, 44, 45], "compris": [29, 31, 42, 44], "solut": [29, 31, 42, 44, 45], "carrier": [29, 31, 42, 44, 45], "heatmap": [29, 31, 33], "plot_heatmap": [29, 31, 33, 42, 44], "cm": [29, 31, 33, 35, 37, 41, 42, 44, 45], "magma_r": [29, 31, 33, 37, 42, 44, 45], "vmax": [29, 31, 33, 42, 44], "arr": [29, 31, 33, 42, 44], "to_numpi": [29, 31, 33, 42, 44], "imshow": [29, 31, 33, 35, 41, 42, 44], "aspect": [29, 31, 33, 42, 44], "auto": [29, 31, 33, 42, 44], "xlab": [29, 31, 33, 42, 44], "ylab": [29, 31, 33, 42, 44], "rang": [29, 31, 33, 42, 44], "set_xticklabel": [29, 31, 33, 42, 44], "set_yticklabel": [29, 31, 33, 34, 36, 42, 44], "most": [29, 31, 34, 35, 36, 40, 44], "enrich": [29, 31, 37, 42, 44], "cholinerg": [29, 31, 42, 44], "glutamaterg": [29, 31, 33, 34, 36, 37, 38, 42, 44], "gabaerg": [29, 31, 33, 34, 36, 37, 38, 44], "glycinerg": [29, 31, 34, 36, 44], "dopaminerg": [29, 31, 37, 38, 44], "match": [29, 41], "expect": [29, 34, 35, 36, 40], "ntexp": [29, 42], "agg": [29, 31, 33, 42, 44], "encod": [29, 31, 42, 44], "call": [29, 31, 40, 42, 44], "neurokinin": [29, 31, 42, 44], "b": [29, 31, 34, 36, 40, 42, 44], "nkb": [29, 31, 42, 44], "produc": [29, 31, 38, 42, 44], "know": [29, 31, 40, 42, 44], "invovl": [29, 31, 42, 44], "emot": [29, 31, 42, 44], "social": [29, 31, 42, 44], "behavior": [29, 31, 34, 36, 42, 44], "ish": [29, 31, 42, 44], "tac": [29, 31, 42, 44], "spars": [29, 31, 42, 44], "dens": [29, 31, 42, 44], "habenula": [29, 31, 37, 42, 44], "mh": [29, 31, 41, 42, 44], "amygdala": [29, 31, 32, 37, 42, 44], "hypothalamu": [29, 31, 32, 35, 37, 42, 44], "those": [29, 33, 39, 40, 42, 44], "identit": [29, 42], "highli": [29, 31, 34, 42, 44], "folder": [29, 34, 36, 40, 42], "kc": [29, 34, 36, 40, 42], "7glrmt5n67x16yj_tg86t49c0000gp": [29, 34, 36, 40, 42], "t": [29, 33, 34, 36, 40, 42], "ipykernel_15441": 29, "199257058": 29, "py": [29, 31, 34, 36, 39, 40, 42], "futurewarn": [29, 34, 36, 42], "__getitem__": [29, 34, 36, 42], "treat": [29, 34, 36, 42], "kei": [29, 34, 36, 40, 42], "deprec": [29, 34, 36, 42], "futur": [29, 34, 36, 42], "integ": [29, 34, 36, 42], "alwai": [29, 34, 36, 42], "ser": [29, 32, 34, 36, 42], "iloc": [29, 34, 36, 41, 42], "po": [29, 34, 36, 41, 42], "show": [29, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44], "lh": [29, 31, 41, 42, 44], "restrict": [29, 31, 37, 42, 44], "mixtur": [29, 31, 42, 44], "At": [29, 31, 36, 42, 44], "sublcass": [29, 42], "145": [29, 35, 41, 44], "itself": 29, "down": [29, 39, 40], "children": 29, "close": [29, 30, 42, 43, 45], "clean": [29, 42, 43], "del": [29, 30, 33, 42, 43, 45], "canon": [30, 43, 45], "transport": [30, 34, 36, 43, 45], "tac2": [30, 37, 41, 43], "so": [30, 34, 36, 42, 43, 44, 45], "minut": [30, 39, 45], "save": [30, 43], "skip": [30, 33, 42, 43], "cleaner": 30, "general_accessing_10x_snrnaseq_tutori": 30, "both": [30, 33, 36, 40], "cell_count": [30, 41], "43985": 30, "207281": 30, "99879": 30, "248776": 30, "249360": 30, "249356": 30, "248784": 30, "29781": 30, "192182": 30, "181723": 30, "78223": 30, "181055": 30, "162296": 30, "227670": 30, "227537": 30, "337101": 30, "191746": 30, "88560": 30, "143157": 30, "108046": 30, "283782": 30, "130454": 30, "write": [30, 40], "resu": 30, "empti": 30, "total_start": 30, "matindex": 30, "ds": 30, "mp": 30, "exp": [30, 31, 36, 37, 44], "break": 30, "1000140000000016": 30, "74g": 30, "9mmb": [30, 33, 41, 42, 45], "0210620000000006": 30, "10g": 30, "04": [30, 38, 39, 41, 42, 45], "48": [30, 40, 42], "2mmb": [30, 31, 40, 45], "7627419999999745": 30, "140": [30, 34, 35], "118578": 30, "notna": [30, 37, 39, 43], "deep": [30, 34, 43], "252953": 30, "expand": [31, 33, 41, 44], "39g": 31, "47": 31, "miniconda3": [31, 39, 40], "env": [31, 39, 40], "lib": [31, 39, 40], "python3": [31, 39, 40], "site": [31, 39, 40], "398": 31, "dtypewarn": 31, "mix": [31, 36], "specifi": [31, 33, 37, 39, 40, 44], "option": [31, 41], "low_memori": 31, "read_csv": [31, 40], "kwarg": 31, "318m": 31, "5mmb": [31, 44], "catergori": [31, 33, 35, 44], "im": [31, 33, 42], "vmin": [31, 33, 42, 44], "similar": [31, 33, 34, 36, 38, 42, 44], "now": [31, 32, 33, 44], "noradrenerg": [31, 44], "serotonerg": [31, 37, 38, 44], "respect": [31, 35, 36, 39, 44, 45], "cortex": [31, 32, 35, 37, 38, 39, 42], "striatum": [31, 42], "medulla": [31, 35], "rest": [31, 44], "axesimag": 31, "0x11bfd4990": 31, "06": [31, 35, 44, 45], "ctx": [31, 35, 36, 41, 44, 45], "cge": [31, 44, 45], "caudal": [31, 32, 44], "ganglion": [31, 44], "emin": [31, 44], "0x11ccfced0": 31, "bed": [31, 42, 44], "stria": [31, 42, 44], "terminali": [31, 42, 44], "bst": [31, 42, 44], "spinal": [31, 32, 35, 44], "trigemin": [31, 35, 44], "spvc": [31, 44], "central": [31, 35, 44], "amygdalar": [31, 44], "cea": [31, 44], "arcuat": [31, 44], "hypothalam": [31, 37, 44], "arh": [31, 44], "subclass_list": [31, 44], "0x29808f7d0": 31, "enabl": [31, 41, 42, 45], "compar": [31, 33, 41, 42], "profil": [31, 45], "top": [31, 34, 36, 37, 41, 44], "quick": 32, "precomput": [32, 33], "acces": 32, "general_acessing_10x_snrnaseq_tutori": [32, 33], "region_of_interest_label": [32, 33, 39], "1b": 32, "overlap": 32, "should": [32, 33, 39, 40], "seper": [32, 33], "anatomical_division_structure_map": [32, 33], "region_of_interest_structure_map": [32, 33], "3369219": [32, 33, 39], "2205155": 32, "606": 32, "nonneuron": [32, 33, 39], "h18": [32, 39], "001": [32, 33, 39], "002": [32, 33, 39, 45], "h19": [32, 33, 39], "109": [32, 41], "amygdaloid": 32, "basal": [32, 39], "cerebellum": [32, 37, 39], "cerebr": [32, 35, 37, 38, 39], "claustrum": 32, "hippocampu": [32, 42], "myelencephalon": [32, 33, 39], "pon": [32, 33, 35, 39], "cord": [32, 35], "membership_groupbi": 32, "cluster_annotation_term_set_nam": [32, 33, 34, 36], "02m": 32, "20mmb": 32, "cluster_annotation_term_label": [32, 34, 36], "cluster_annotation_term_set_label": [32, 34, 36], "cluster_annotation_term_nam": [32, 33, 34, 36], "number_of_cel": [32, 34, 36, 37, 38, 41], "cs202210140_494": [32, 34], "ccn202210140_subc": [32, 34], "url_297_0": [32, 34], "7e807a": [32, 34], "cs202210140_495": [32, 34], "url_308_1": [32, 34], "220": [32, 34], "c54945": [32, 34], "cs202210140_496": [32, 34], "url_308_2": [32, 34], "187": [32, 34], "5232b7": [32, 34], "cs202210140_497": [32, 34], "url_308_3": [32, 34], "246": [32, 34, 40], "31beba": [32, 34], "cs202210140_498": [32, 34], "url_308_4": [32, 34], "188": [32, 34], "c8a9bc": [32, 34], "term_set": [32, 33, 34, 35, 36], "unstack": [32, 33, 34, 35, 36, 37], "fillna": [32, 33, 34, 36], "33k": 32, "7kmb": [32, 40], "2461": 32, "amex_153_2461": 32, "amex_153": 32, "excitatori": 32, "vglut1": [32, 33, 34], "vglut2": 32, "2462": 32, "amex_153_2462": 32, "2463": 32, "amex_153_2463": 32, "2464": 32, "amex_153_2464": 32, "2465": 32, "amex_153_2465": 32, "2218": 32, "374b8a": 32, "062463": 32, "003380": 32, "2bdfd1": [32, 33, 34], "2216": 32, "4bcbc6": 32, "2217": 32, "83c943": 32, "2219": 32, "bc4440": 32, "2220": 32, "cb7aba": 32, "82k": 32, "125kmb": 32, "structure_identifi": 32, "structure_symbol": 32, "structure_nam": 32, "a13": 32, "dhba": 32, "10202": 32, "ofci": 32, "cab781": 32, "a14": 32, "10196": 32, "a14r": 32, "rostral": 32, "subdivis": 32, "b8a26d": 32, "10197": 32, "a14c": 32, "a19": 32, "10272": 32, "psc": 32, "peristri": 32, "d14d46": 32, "a1c": 32, "10236": 32, "core": [32, 40], "d670a0": 32, "rsuffix": [32, 33, 37], "_color": [32, 33], "subcluster_color": [32, 33, 34], "supercluster_color": [32, 33, 34], "10x386_2": [32, 33, 39], "catggattctcgacgg": [32, 33, 39], "lktx_210825_01_b01": [32, 33, 39], "cx": [32, 33, 39], "51": [32, 33, 39, 44], "url_312_20": [32, 33], "url_312": [32, 33], "upper": [32, 33, 34], "rhombic": [32, 33, 34], "lip": [32, 33, 34], "4cb941": [32, 33], "97b8c8": [32, 33], "80ba": [32, 33, 34], "5d6cb2": [32, 33], "10x383_5": [32, 33, 39], "tcttgcggtgaattga": [32, 33, 39], "lktx_210818_02_e01": [32, 33, 39], "bs": [32, 33, 39], "94": [32, 33, 39], "ctcatcggtcgagcaa": [32, 33, 39], "url_312_17": [32, 33], "c85e40": [32, 33], "10x378_8": [32, 33, 39], "ttggatgagacaagcc": [32, 33, 39], "lktx_210809_01_h01": [32, 33, 39], "93": [32, 33, 34, 39], "url_312_18": [32, 33], "61c1c2": [32, 33], "517dbe": [32, 33], "10x387_7": [32, 33, 39], "tgaacgtagtattccg": [32, 33, 39], "lktx_210825_02_g01": [32, 33, 39], "url_312_16": [32, 33], "45328f": [32, 33], "vglut3": 32, "da": 32, "hdc": 32, "gly": [32, 36, 45], "196aa5": 32, "2252c2": 32, "22a5bb": 32, "2b39df": 32, "3f38b8": 32, "423b77": 32, "4f90b2": 32, "4fe3ab": 32, "6b0c48": 32, "8bad78": 32, "8c4f7f": 32, "8c7063": 32, "95369c": 32, "c6525e": 32, "ff553d": 32, "ve": 32, "merg": 32, "neurons_subsampl": [32, 33], "non_neurons_subsampl": [32, 33], "n": [32, 34, 36, 37, 38, 39, 40], "303681": 32, "107871": 32, "ll": [32, 33, 39, 40], "focu": 32, "done": [33, 40], "previous": [33, 37], "memembership": 33, "deeper": 33, "dive": 33, "again": 33, "hold": 33, "biotyp": [33, 39], "ensg00000000003": [33, 39], "tspan6": [33, 39], "protein_cod": [33, 39], "tetraspanin": [33, 39], "ensg00000000005": [33, 39], "tnmd": [33, 39], "tenomodulin": [33, 39], "ensg00000000419": [33, 39], "dpm1": [33, 39], "dolichyl": [33, 39], "phosphat": [33, 39], "mannosyltransferas": [33, 39], "subunit": [33, 39], "ensg00000000457": [33, 39], "scyl3": [33, 39], "scy1": [33, 39], "pseudokinas": [33, 39], "ensg00000000460": [33, 39], "c1orf112": [33, 39], "chromosom": [33, 39], "112": [33, 35, 39], "ptprc": [33, 39], "plp1": [33, 39], "aqp4": [33, 39], "ttr": [33, 39], "example_cells_with_gen": 33, "233m": 33, "000000": [33, 35, 41], "652457": 33, "484976": 33, "006844": 33, "348821": 33, "046448": 33, "cell_extended_with_gen": 33, "becaus": 33, "immun": 33, "oligodendrocyt": [33, 34], "astrocyt": 33, "choroid": 33, "plexu": 33, "much": [33, 40], "higher": 33, "relev": 33, "what": [33, 40], "variou": 33, "seven": 33, "vs": 33, "idend": 33, "And": 33, "final": [33, 34, 36, 41], "could": [33, 39], "aren": 33, "shown": [33, 40], "than": [34, 40], "almost": 34, "overload": 34, "while": [34, 36, 40], "string": [34, 35, 36, 37, 39, 40], "84": [34, 41, 45], "8k": [34, 40], "433kmb": 34, "3308": 34, "cs202210140_3802": 34, "3309": 34, "138": 34, "cs202210140_3803": 34, "3310": 34, "85": 34, "cs202210140_3804": 34, "3311": 34, "cs202210140_3805": 34, "3312": 34, "74": 34, "cs202210140_3806": 34, "readabl": [34, 35, 36, 37], "descript": [34, 35, 36, 37, 38], "among": [34, 35, 36], "finest": [34, 36], "ccn202210140_clu": 34, "intermedi": [34, 35], "ccn202210140_supc": 34, "h": 34, "ccn202210140_neur": 34, "iterrow": [34, 36, 37], "tsindex": [34, 36, 37], "tsrow": [34, 36, 37], "louvain": 34, "independ": 34, "characterist": [34, 36], "belong": [34, 36], "state": 34, "togeth": [34, 36, 37, 41], "anoth": 34, "cytograph": 34, "broader": [34, 36], "character": 34, "lack": 34, "enzym": [34, 36], "superclass": [34, 36], "form": [34, 36], "547k": 34, "87mmb": 34, "parent_term_label": [34, 35, 36], "parent_term_set_label": [34, 35, 36], "term_set_ord": [34, 35, 36], "term_ord": [34, 35, 36], "cs202210140_476": 34, "intratelencephal": 34, "fea7ba": 34, "455006": 34, "cs202210140_477": 34, "426600": 34, "228467": 34, "cs202210140_473": 34, "ee1010": 34, "18856": 34, "cs202210140_474": 34, "corticothalam": 34, "6b": [34, 35], "5ef0f1": 34, "78396": 34, "cs202210140_484": 34, "mge": 34, "interneuron": 34, "dffe66": 34, "222434": 34, "talli": [34, 36], "unlik": 34, "term_cluster_count": [34, 36], "number_of_clust": [34, 36, 37], "cs202210140_1": 34, "cs202210140_10": 34, "cs202210140_100": 34, "cs202210140_1000": 34, "cs202210140_1001": 34, "term_by_label": [34, 36], "term_with_count": [34, 35, 36], "139": 34, "72": 34, "116": 34, "211": 34, "let": [34, 36, 42], "bar": [34, 36], "bar_plot_by_level_and_typ": [34, 36], "idx": [34, 36, 37, 38, 44], "ctype": [34, 36], "enumer": [34, 35, 36, 37, 38, 44, 45], "number_of_": [34, 36], "barh": [34, 36], "set_xscal": [34, 36], "splatter": 34, "largest": [34, 36], "1k": 34, "fuunction": [34, 35, 36, 37], "url_297": 34, "url_308": 34, "nkcell_2_3308": 34, "nkcell_2": 34, "miscellan": 34, "nkcell_2_3309": 34, "nkcell_2_3310": 34, "nkcell_2_3311": 34, "nkcell_2_3312": 34, "f9f9f9": [34, 36], "s_color": [34, 35, 36], "909ff6": 34, "a5b0d9": 34, "3d84ba": 34, "e2ee30": 34, "fefe00": 34, "c25347": 34, "b9bfb4": 34, "6cc93d": 34, "423149": 34, "pair": [34, 36], "axb": [34, 36], "b_name": [34, 36], "term_by_nam": [34, 36], "b_color": [34, 36], "stacked_bar_distribut": [34, 36], "bottom": [34, 36], "i": [34, 35, 36, 37, 45], "col": [34, 36], "left": [34, 35, 36, 37], "arrai": [34, 35, 36, 40], "legend": [34, 36], "bbox_to_anchor": [34, 36], "ipykernel_15202": 34, "1772253940": [34, 36], "sunburst": [34, 36], "diagram": [34, 36], "inherit": [34, 36], "ring": [34, 36], "outer": [34, 36], "angl": [34, 36, 41], "proport": [34, 36], "lvl": [34, 36], "pie": [34, 36], "rotatelabel": [34, 36], "labeldist": [34, 36], "025": [34, 36], "radiu": [34, 36], "wedgeprop": [34, 36], "dict": [34, 36, 40], "width": [34, 36], "edgecolor": [34, 36], "startangl": [34, 36], "els": [34, 35, 36, 40, 44], "informat": 35, "onlin": 35, "applic": 35, "multiscal": 35, "openli": 35, "asset": 35, "request": [35, 39, 40], "simpleitk": [35, 40, 41], "sitk": [35, 41], "There": [35, 40, 42, 45], "volumetr": 35, "allenccfv3": 35, "average_template_10": [35, 40], "construct": 35, "shape": 35, "intens": 35, "1675": 35, "specim": 35, "annotation_10": [35, 40], "heirach": 35, "partonomi": 35, "annotation_boundary_10": [35, 40], "mask": 35, "boundari": 35, "compress": 35, "nifti": 35, "nii": [35, 40, 41], "gz": [35, 40, 41], "average_template_imag": [35, 41], "readimag": [35, 41], "average_template_arrai": [35, 41], "getarrayviewfromimag": [35, 41], "annotation_imag": [35, 41], "annotation_arrai": [35, 41], "annotation_boundary_imag": [35, 41], "annotation_boundary_arrai": [35, 41], "image_info": [35, 41], "img": [35, 41], "getsiz": [35, 41], "getspac": [35, 41], "mm": [35, 41], "getdirect": [35, 41], "getorigin": [35, 41], "1320": 35, "800": 35, "1140": 35, "micromet": 35, "asl": 35, "superior": 35, "inferior": 35, "dorsal": 35, "ventral": 35, "third": 35, "right": 35, "009999999776482582": [35, 41], "695000171661377": 35, "349999904632568": 35, "21999979019165": 35, "voxel_volum": 35, "2e": 35, "00e": 35, "sanm": 35, "plot_sect": [35, 37, 38, 41, 42, 44, 45], "greys_r": [35, 41], "off": 35, "zindex": [35, 41], "720": 35, "zslice": 35, "transpos": 35, "average_templ": 35, "grei": [35, 41], "tile": 35, "parcellation_index": [35, 41, 45], "688": 35, "voxel_count": 35, "volume_mm3": 35, "987": 35, "allenccf": 35, "997": 35, "3564320": 35, "564320": 35, "63": 35, "68": 35, "256520": 35, "657": 35, "667": 35, "232608": 35, "1288": 35, "526157192": 35, "371584": 35, "1289": 35, "526157196": 35, "112222": 35, "135": 35, "405256": 35, "499566": 35, "148": [35, 37], "153": 35, "461680": 35, "159": 35, "164": 35, "432": 35, "000432": 35, "697783214": 35, "697": 35, "783214": 35, "simplif": 35, "heirarchi": [35, 36], "parcellation_term_set": [35, 40], "parcellation_terminology_label": 35, "ontolog": 35, "2017": [35, 40], "orga": 35, "cate": 35, "divi": 35, "stru": 35, "sub": [35, 39], "substructur": [35, 41, 45], "hex": 35, "triplet": 35, "rgb": 35, "parcellation_term": [35, 40], "1631": 35, "graph_ord": 35, "red": 35, "green": 35, "blue": 35, "parent_identifi": 35, "ffffff": [35, 41], "mba": 35, "255": 35, "bfdae3": [35, 41], "191": 35, "218": 35, "227": [35, 40], "567": [35, 40], "ch": 35, "cerebrum": 35, "b0f0ff": 35, "240": [35, 40], "b0ffb8": 35, "184": 35, "695": 35, "ctxpl": 35, "cortic": [35, 37, 42], "plate": [35, 42], "70ff70": 35, "memership": 35, "parcellation_term_set_membership": [35, 40], "1293": 35, "parcellation_term_label": 35, "parcellation_term_set_label": 35, "1009": 35, "73": [35, 41], "315": 35, "parcellation_annot": [35, 41, 45], "parcellation_to_parcellation_term_membership": [35, 40], "3440": 35, "parcellation_label": 35, "parcellation_term_nam": 35, "parcellation_term_acronym": 35, "parcellation_term_set_nam": 35, "70ff71": [35, 41], "113": 35, "268f45": 35, "38": [35, 37, 38, 40, 42, 44], "143": [35, 36], "3435": 35, "v4": 35, "aaaaaa": 35, "170": 35, "fourth": 35, "ventricl": 35, "unassign": [35, 41], "367": [35, 40], "3436": 35, "885": 35, "3437": 35, "v4r": 35, "recess": 35, "886": 35, "3438": 35, "canal": 35, "369": [35, 40], "3439": 35, "887": 35, "term_parcellation_count": 35, "number_of_parcel": 35, "687": 35, "597": 35, "241": [35, 40], "313": 35, "59": [35, 36, 41, 42], "10703": 35, "10704": 35, "1072": 35, "1074": 35, "998": 35, "term_voxel_count": 35, "sum": [35, 36], "ca1": [35, 41], "000006": 35, "1051": [35, 37], "000004": 35, "ca3": 35, "000002": 35, "545": 35, "inner": [35, 41, 45], "506056786": 35, "506": 35, "056786": 35, "449681182": 35, "449": 35, "681182": 35, "123282624": 35, "123": 35, "282624": 35, "973876": 35, "frp1": 35, "valid": [35, 40], "alist": 35, "aa": 35, "vlist": 35, "parcellation_term_with_count": [35, 40], "distribut": 35, "tmv": [35, 41], "m6b": [35, 41], "lfb": [35, 41], "cst": [35, 41], "int": [35, 39, 41], "psv": [35, 41], "1323": 35, "ipn": 35, "ipi": 35, "1324": 35, "ipdm": 35, "1325": 35, "ipdl": 35, "1326": 35, "iprl": 35, "1327": 35, "pag": [35, 39, 41], "su3": 35, "tuberomammillari": 35, "mouth": 35, "bundl": 35, "corticospin": 35, "intern": 35, "capsul": 35, "princip": [35, 37], "sensori": 35, "interpeduncular": 35, "dorsomedi": 35, "dorsolater": 35, "rostrolater": 35, "periaqueduct": 35, "supraoculomotor": 35, "organ_color": 35, "category_color": 35, "division_color": 35, "structure_color": 35, "substructure_color": 35, "e64438": [35, 41], "ff4c3e": [35, 41], "188064": [35, 41], "cccccc": [35, 41], "ff9b88": [35, 41], "ffae6f": [35, 41], "ff64ff": 35, "ffa6ff": 35, "ff90ff": 35, "channel": 35, "230": 35, "204": 35, "parcellation_to_parcellation_term_membership_acronym": [35, 40, 41, 45], "parcellation_to_parcellation_term_membership_nam": [35, 40], "parcellation_to_parcellation_term_membership_color": [35, 40, 41, 45], "parcellation_to_parcellation_term_membership_": 35, "sshape": 35, "uint8": 35, "temp": 35, "flat": [35, 45], "represnt": [36, 37], "727": 36, "cs20230722_0001": 36, "740": 36, "cs20230722_0010": 36, "1053": 36, "cs20230722_0100": 36, "1000": [36, 42], "cs20230722_1000": 36, "1001": 36, "96": [36, 40], "cs20230722_1001": 36, "ccn20230722_neur": 36, "ccn20230722_cla": 36, "ccn20230722_subc": 36, "ccn20230722_supt": 36, "definitio": 36, "ccn20230722_clu": 36, "synthes": 36, "primarili": 36, "categor": 36, "cs20230722_neur_glut": 36, "cs20230722_neur_na": 36, "na": 36, "cs20230722_neur_gaba": 36, "cs20230722_neur_dopa": 36, "particular": 36, "0001": 36, "cla": 36, "epd": 36, "car3": 36, "glut_1": [36, 41, 42], "instead": 36, "cs20230722_supt_0001": 36, "cs20230722_clus_000": 36, "find": [36, 39, 44], "term_name_count": 36, "usage_count": 36, "name_clash_term": 36, "382": 36, "1583": 36, "cs20230722_clus_0001": 36, "00664e": 36, "1584": 36, "cs20230722_clus_0002": 36, "0002": 36, "5c79cc": 36, "1585": 36, "cs20230722_clus_0003": 36, "0003": 36, "86ff4d": 36, "1586": 36, "cs20230722_clus_0004": 36, "0004": 36, "cc563d": 36, "128": [36, 37], "4262": 36, "129": [36, 37], "3222": 36, "130": [36, 37], "12216": 36, "9334": 36, "cs20230722_clus_0005": 36, "131": 36, "0005": 36, "1056": 36, "e7ff26": 36, "cs20230722_clas_01": 36, "402": 36, "cs20230722_clas_02": 36, "83": 36, "cs20230722_clas_03": 36, "cs20230722_clas_04": 36, "cs20230722_clas_05": 36, "105": 36, "term_cell_count": 36, "1095484": 36, "310198": 36, "4767": 36, "84352": 36, "107502": 36, "2561": 36, "2054137": 36, "127": 36, "1089152": 36, "1991": 36, "834601": 36, "9396": 36, "62": [36, 39], "8989": 36, "datafarm": 36, "600": 36, "34368": [36, 37, 45], "288": [36, 45], "mdrn": [36, 45], "hoxb5": [36, 45], "ebf2": [36, 45], "1102": [36, 45], "gaba_1": [36, 45], "4955": [36, 45], "34372": [36, 37, 45], "285": [36, 45], "lhx1": [36, 45], "1091": [36, 45], "gaba_3": [36, 45], "4901": [36, 45], "34374": [36, 37, 45], "4902": [36, 45], "34376": [36, 37, 45], "4903": [36, 45], "34380": [36, 37, 45], "1095": [36, 45], "gaba_7": [36, 45], "4924": [36, 45], "0096c7": [36, 45], "660038": [36, 45], "5ccca4": [36, 45], "500099": [36, 45], "f20985": [36, 45], "976df9": [36, 45], "0f6627": [36, 45], "2e4799": [36, 45], "15ff00": [36, 45], "ff2b26": [36, 45], "459988": [36, 45], "50": [36, 38, 39, 42], "ipykernel_77026": 36, "cluster_group": 37, "62k": 37, "0kmb": 37, "group_typ": 37, "ccn20230722_hy": [37, 38], "ea": 37, "hypotha": [37, 38], "1404": 37, "ccn20230722_mb": [37, 38], "hb": 37, "1040": 37, "1431": 37, "ccn20230722_nn": [37, 38], "imn": [37, 41, 42], "gc": 37, "nn": [37, 45], "immatur": [37, 38], "granul": [37, 38], "248": 37, "ccn20230722_pallium": [37, 38], "pallium": 37, "de": [37, 38], "517": 37, "ccn20230722_subpallium": [37, 38], "subpallium": 37, "telencephal": [37, 38], "ccn20230722_th": [37, 38], "epi": [37, 40], "epitha": [37, 38], "ccn20230722_wholebrain": [37, 38], "wholebrain": [37, 38], "clust": [37, 38], "dentat": 37, "gyru": 37, "pineal": 37, "gland": 37, "deriv": 37, "development": 37, "hippocamp": 37, "subplat": 37, "preoptic": 37, "epithalamu": 37, "e": [37, 40], "group_membership": 37, "cluster_group_membership": 37, "674k": 37, "78mmb": 37, "cluster_label": 37, "cluster_group_label": [37, 38], "cluster_group_nam": 37, "cs20230722_0128": 37, "cs20230722_0129": 37, "cs20230722_0130": 37, "pca": 37, "preform": 37, "pc": 37, "2d": [37, 41], "dimension_reduct": [37, 38], "68k": 37, "6kmb": 37, "umap20230830": [37, 38, 40], "295448": [37, 38], "186775": [37, 38], "180669": [37, 38], "1418529": [37, 38], "1494801": [37, 38], "611423": [37, 38], "126171": [37, 38, 40], "boolean": 37, "cluster_group_membership_pivot": 37, "conveni": 37, "joined_10x": 37, "glabel": 37, "f5f5f5": [37, 38], "maps_by_group": 37, "mlabel": [37, 38], "coord": [37, 38], "7m": 37, "31mmb": 37, "neighborhoo": 37, "orig": 37, "resus": 37, "neighborhood_exp": 37, "slc17ab": 37, "glutamerg": 37, "begin": 37, "02g": 37, "49": [37, 39, 40], "6mmb": [37, 41, 45], "joined_merfish": 37, "properti": 37, "blist": [37, 38, 44], "bsl": [37, 38, 44], "vv": [37, 38, 44], "subplots_adjust": [37, 38, 44], "wspace": [37, 38, 44], "hspace": [37, 38, 44], "subgroup": 37, "46": [37, 38, 41, 44], "40": [37, 38, 41, 42, 45], "36": [37, 38, 40, 41, 45], "32": [37, 39, 45], "cell_10x": 38, "10x_cell_metadata_with_group_membership": 38, "cell_merfish": 38, "merfish_cell_metadata_with_group_membership": 38, "3938808": [38, 42, 43], "fetch_coord": 38, "52": 38, "44": 38, "60": 38, "amount": 39, "analy": 39, "care": 39, "simplili": 39, "paral": 39, "scale": [39, 41], "leav": 39, "still": 39, "attempt": [39, 40], "too": 39, "anndata_util": 39, "get_gene_data": 39, "similarli": 39, "piec": 39, "instanti": [39, 40], "705m": 39, "533584": 39, "230048": 39, "moan": 39, "307856": 39, "542040": 39, "mosr": 39, "740066": 39, "186017": 39, "926133": 39, "015151": 39, "pnan": 39, "622083": 39, "561958": 39, "10x194_8": 39, "gaaatgagttcggctg": 39, "lktx_190529_02_h01": 39, "154318": 39, "585480": 39, "3264": 39, "sn": 39, "10x350_4": 39, "tttaccatcgcacgac": 39, "lktx_210421_03_d01": 39, "906175": 39, "914979": 39, "3265": 39, "cbdn": 39, "10x225_1": 39, "agaagcgtccatatgg": 39, "lktx_190913_02_a01": 39, "091915": 39, "212210": 39, "10x221_5": 39, "ttgaacgcagccttct": 39, "lktx_190830_01_e01": 39, "665837": 39, "993120": 39, "stg": 39, "10x385_3": 39, "ctacccagtggcgctt": 39, "lktx_210818_04_c01": 39, "579284": 39, "853419": 39, "gpi": 39, "23m": 39, "17mmb": 39, "ensg00000288638": 39, "al627443": 39, "lncrna": 39, "ensg00000288639": 39, "ac093246": 39, "protein": [39, 42, 45], "ensg00000288642": 39, "cdr1": 39, "cerebellar": 39, "degener": 39, "ensg00000288643": 39, "ac114982": 39, "ensg00000288645": 39, "ac084756": 39, "would": [39, 40], "onc": [39, 40], "uncompress": 39, "avoid": [39, 40], "chunk": 39, "recombin": 39, "output": [39, 40], "gene_nam": 39, "adjust": 39, "addition": [39, 40], "funciton": 39, "31msignatur": 39, "0m": 39, "0mget_gene_data": 39, "34m": 39, "0mabc_atlas_cach": 39, "0mabc_atlas_access": 39, "0mabc_project_cach": 39, "0mabcprojectcach": 39, "0mall_cel": 39, "0mpanda": 39, "0mcore": 39, "0mframe": 39, "0mdatafram": 39, "0mall_gen": 39, "0mselected_gen": 39, "0mlist": 39, "0mstr": 39, "0mdata_typ": 39, "0mchunk_siz": 39, "0mint": 39, "36m8192": 39, "31mdocstr": 39, "mai": [39, 40], "potenti": 39, "instanc": 39, "all_cel": 39, "all_gen": 39, "selected_gen": 39, "data_typ": 39, "kind": [39, 40], "chunk_siz": 39, "8192": 39, "io": 39, "output_gene_data": 39, "31mfile": 39, "31mtype": 39, "hour": 39, "depend": [39, 40, 45], "speed": 39, "gene_data": 39, "ngene_data": 39, "quicker": 39, "roughli": 39, "hand": [39, 42], "complet": [39, 40], "nonneuron_cel": 39, "78g": 39, "0mmb": [39, 40, 41, 45], "133": 39, "182634": 39, "219": 39, "19582499999999": 39, "10x362_3": 39, "tcagtgagtattgacc": 39, "177927": 39, "10x362_5": 39, "tccgtgtgtgaaagtt": 39, "262379": 39, "cacgggtagagcagaa": 39, "240114": 39, "gattcttgtatgtcac": 39, "314513": 39, "10x362_6": 39, "aggacttgtatccttt": 39, "736156": 39, "210833": 39, "587301": 39, "006084": 39, "567961": 39, "119619": 39, "888263": 39, "thu": 39, "recommend": 40, "enviro": 40, "pip": 40, "u": 40, "git": 40, "http": 40, "github": 40, "com": 40, "alleninstitut": 40, "morriscb": 40, "updatejupyterbook": 40, "clone": 40, "revis": 40, "privat": 40, "req": 40, "build": 40, "k_k2xa_5": 40, "command": 40, "blob": 40, "quiet": 40, "checkout": 40, "switch": 40, "branch": 40, "commit": 40, "5cbeb4e1fe7ebb6492696b6dae9a76697b8c4cd0": 40, "25ldone": 40, "25h": 40, "wheel": 40, "pyproject": 40, "toml": 40, "25hrequir": 40, "satisfi": 40, "post1": 40, "boto3": 40, "55": 40, "ghp": 40, "moto": 40, "pydant": 40, "pytest": 40, "scipi": 40, "tqdm": 40, "api": 40, "compat": 40, "h5py": 40, "natsort": 40, "dateutil": 40, "post0": 40, "pytz": 40, "tzdata": 40, "2022": 40, "botocor": 40, "35": [40, 41], "jmespath": 40, "s3transfer": 40, "contourpi": 40, "cycler": 40, "fonttool": 40, "kiwisolv": 40, "pillow": 40, "pypars": 40, "cryptographi": 40, "42": 40, "xmltodict": 40, "werkzeug": 40, "respons": 40, "jinja2": 40, "charset": 40, "idna": 40, "urllib3": 40, "certifi": 40, "extens": 40, "iniconfig": 40, "pluggi": 40, "cffi": 40, "markupsaf": 40, "six": [40, 45], "pyyaml": 40, "pycpars": 40, "filenam": 40, "py3": 40, "whl": 40, "20811": 40, "sha256": 40, "d8098f32f446e44b53e54ad633cdea61188d55b3cc708d45cb702c309ee9224c": 40, "ephem": 40, "c8464kd3": 40, "d8": 40, "c5": 40, "498927e9ff1fdc24cca5fd8a35f6daeb0d2b61623f3ee82a07": 40, "successfulli": 40, "built": 40, "uninstal": 40, "exist": 40, "restart": 40, "kernel": 40, "drop": [40, 41], "menu": 40, "uncom": 40, "get_ipython": 40, "do_shutdown": 40, "setup": 40, "usabl": 40, "just": 40, "list_manifest_file_nam": 40, "load_manifest": 40, "last": 40, "session": 40, "upon": 40, "warn": 40, "thrown": 40, "older": 40, "recent": 40, "stick": 40, "confus": 40, "old": 40, "latest": 40, "load_latest_manifest": 40, "cloud_cach": 40, "outdatedmanifestwarn": 40, "date": 40, "compare_manifest": 40, "onto": 40, "self": 40, "list_all_downloaded_manifest": 40, "If": 40, "want": 40, "msg": 40, "rais": 40, "except": 40, "g": 40, "expression_matrici": 40, "list_directori": 40, "befor": 40, "get_directory_data_s": 40, "get_directory_metadata_s": 40, "65": 40, "guid": 40, "signific": 40, "allen_ccf_list": 40, "get_directory_data": 40, "5m": 40, "8mmb": [40, 45], "4m": 40, "3mmb": [40, 45], "343m": 40, "131k": 40, "838kmb": 40, "861k": 40, "60mmb": 40, "11k": 40, "902k": 40, "30mmb": 40, "21m": 40, "239k": 40, "99mmb": 40, "531k": 40, "41mmb": 40, "without": 40, "get_metadata_path": 40, "30m": 40, "95mmb": 40, "accept": 40, "argment": 40, "32280": 40, "32281": 40, "32282": 40, "32283": 40, "32284": 40, "ensmusg00000095041": 40, "ac149090": 40, "throw": 40, "error": [40, 42, 45], "ambigu": 40, "89": [40, 45], "3m": 40, "03": [40, 42, 45], "keyerror": 40, "traceback": 40, "line": 40, "477": 40, "force_download": 40, "skip_hash_check": 40, "472": 40, "data_path": 40, "_get_local_path": 40, "473": 40, "474": 40, "475": 40, "476": 40, "download_data": 40, "478": 40, "479": 40, "480": 40, "481": 40, "482": 40, "483": 40, "822": 40, "cloudcachebas": 40, "788": 40, "789": 40, "790": 40, "793": 40, "bool": 40, "794": 40, "795": 40, "796": 40, "797": 40, "necessari": 40, "820": 40, "821": 40, "super_attribut": 40, "823": 40, "824": 40, "file_attribut": 40, "825": 40, "395": 40, "basiclocalcach": 40, "366": 40, "368": 40, "test": 40, "393": 40, "394": 40, "_get_file_path": 40, "397": 40, "321": 40, "292": 40, "293": 40, "294": 40, "295": 40, "319": [40, 45], "320": 40, "_manifest": 40, "get_file_attribut": 40, "323": 40, "324": 40, "325": 40, "_file_exist": 40, "326": 40, "local_path": 40, "238": 40, "226": 40, "_create_file_attribut": 40, "remote_path": 40, "files_data": 40, "file_typ": 40, "228": 40, "url": 40, "235": [40, 41, 42], "file_hash": 40, "noqa": 40, "e501": 40, "236": 40, "237": 40, "239": 40, "pleas": 40, "242": 40, "243": 40, "244": 40, "245": [40, 45], "247": 40, "corrupt": 40, "accidenti": 40, "delet": 40, "inividu": 40, "64mmb": 40, "07": [40, 45], "against": 40, "recommened": 40, "overhead": 40, "assum": 40, "46m": 40, "ctcacactcgtagatc": 40, "044_d01": 40, "603476": 40, "148670": 40, "ccgtactcatccaaca": 40, "036_d01": 40, "817812": 40, "366151": 40, "agcggtccatgggaac": 40, "037_a01": 40, "798783": 40, "577992": 40, "gatgaggcatgttccc": 40, "037_b01": 40, "188138": 40, "892220": 40, "tagtggtaggcgacat": 40, "715829": 40, "606307": 40, "126166": 40, "tttgttgtccgacata": 40, "290_b01": 40, "042111": 40, "349521": 40, "126167": 40, "tttgttgtcgtctacc": 40, "294_b05": 40, "630137": 40, "033476": 40, "126168": 40, "tttgttgtcgttcctg": 40, "463_a05": 40, "848272": 40, "645908": 40, "126169": 40, "tttgttgtcgttgcct": 40, "621_a02": 40, "982306": 40, "718120": 40, "126170": 40, "tttgttgtctttcgat": 40, "574_a02": 40, "292696": 40, "804039": 40, "41": 40, "2k": 40, "606kmb": 40, "177k": 40, "27mmb": 40, "628": 40, "04kmb": 40, "114k": 40, "956kmb": 40, "137k": 40, "908kmb": 40, "680k": 40, "71mmb": 40, "3k": 40, "8kmb": 40, "parcellation_to_parcellation_term_membership_blu": 40, "4k": [40, 42], "232kmb": 40, "5k": 40, "432kmb": 40, "parcellation_to_parcellation_term_membership_green": 40, "234kmb": 40, "315kmb": 40, "parcellation_to_parcellation_term_membership_r": 40, "0k": 40, "215kmb": 40, "micron": [41, 42], "plane": 41, "init": 41, "ant": 41, "establish": 41, "5d": 41, "multi": 41, "symmetr": 41, "diffeomorph": 41, "finer": 41, "x_section": 41, "y_section": 41, "z_section": 41, "average_correlation_scor": [41, 42], "1019171907102340387": [41, 42], "37": [41, 42], "1408": [41, 42], "596276": [41, 42], "226245": [41, 42], "148963": [41, 42], "dg": [41, 42], "038": [41, 42], "pir": [41, 42], "ex": [41, 42], "0141": [41, 42], "imn_2": [41, 42], "0515": [41, 42], "16f2f2": [41, 42], "3d53cc": [41, 42], "cc7a3d": [41, 42], "73ffbf": [41, 42], "1104095349101460194": [41, 42], "4218": [41, 42], "641180": [41, 42], "064889": [41, 42], "309543": [41, 42], "pg": [41, 42], "trn": [41, 42], "lrn": [41, 42], "fat2": [41, 42], "0953": [41, 42], "4199": [41, 42], "6b5ca5": [41, 42], "9b7acc": [41, 42], "990041": [41, 42], "663d63": [41, 42], "1017092617101450577": [41, 42], "763531": [41, 42], "792921": [41, 42], "189973": [41, 42], "1018093344101130233": [41, 42], "558073": [41, 42], "195950": [41, 42], "868655": [41, 42], "1019171912201610094": [41, 42], "591009": [41, 42], "635732": [41, 42], "995842": [41, 42], "reconstructed_coord": 41, "reconstructed_coordin": 41, "x_reconstruct": 41, "y_reconstruct": 41, "z_reconstruct": 41, "256m": 41, "1019171911101460569": 41, "143894": 41, "890964": 41, "945": 41, "1019171911101550321": 41, "188673": 41, "962972": 41, "1019171911100841066": 41, "859447": 41, "908534": 41, "893": 41, "1019171911101400425": 41, "952014": 41, "564086": 41, "842": 41, "1019171911101380264": 41, "803546": 41, "221688": 41, "cell_join": 41, "255606": 41, "007680": 41, "1160": 41, "036436": 41, "264429": 41, "564": 41, "784270": 41, "007646": 41, "761": 41, "161528": 41, "719814": 41, "718": 41, "618763": 41, "847877": 41, "ccf_coord": 41, "ccf_coordin": [41, 45], "x_ccf": [41, 45], "y_ccf": [41, 45], "z_ccf": [41, 45], "296m": 41, "282330": 41, "987808": 41, "385773": 41, "192214": 41, "002155": 41, "366855": 41, "500341": 41, "750392": 41, "074634": 41, "231647": 41, "544816": 41, "128568": 41, "238502": 41, "135836": 41, "948194": 41, "495417": 41, "445872": 41, "455066": 41, "227966": 41, "133693": 41, "225024": 41, "344912": 41, "989939": 41, "002664": 41, "977068": 41, "398568": 41, "305223": 41, "997138": 41, "798329": 41, "827197": 41, "pcmap": 41, "extent": [41, 42], "bcmap": 41, "alpha": [41, 42], "zorder": 41, "sinc": 41, "spread": 41, "brain_sect": 41, "104572": 41, "32598314": 41, "32656693": 41, "3266852": 41, "16574148": 41, "16579943": 41, "16598123": 41, "parcellation_": [41, 45], "parcellation_organ": 41, "parcellation_categori": 41, "parcellation_divis": 41, "parcellation_structur": 41, "parcellation_substructur": 41, "parcellation_color": [41, 45], "parcellation_organ_color": 41, "parcellation_category_color": 41, "parcellation_division_color": [41, 45], "parcellation_structure_color": [41, 45], "parcellation_substructure_color": [41, 45], "7ed04b": 41, "ffba86": 41, "cbf": 41, "arb": 41, "cell_metadata_with_parcellation_annot": 41, "parcellation_cell_count": 41, "935742": 41, "401346": 41, "383127": 41, "304642": 41, "281852": 41, "274354": 41, "147562": 41, "136569": 41, "133805": 41, "132902": 41, "bfd": 41, "8865": 41, "sss": 41, "7210": 41, "cp": 41, "4715": 41, "4491": 41, "visa": 41, "4462": 41, "3705": 41, "3119": 41, "3000": 41, "2858": 41, "rspv": 41, "2853": 41, "4696": 41, "4404": 41, "132": 41, "mfsbshy": 41, "chpl": 41, "lp": 41, "md": 41, "146": 41, "pou4f1": 41, "sox1": 41, "1067": 41, "851": 41, "pf": 41, "spa": 41, "serpinb7": 41, "1190": 41, "1036": 41, "ld": 41, "am": 41, "mfbc": 41, "007": 41, "121784": 41, "mos2": 41, "12762": 41, "mop2": 41, "10586": 41, "visp2": 41, "9250": 41, "sss2": 41, "7149": 41, "m2": 41, "5203": 41, "bfd2": 41, "5032": 41, "tea2": 41, "4396": 41, "ul2": 41, "3337": 41, "rspagl2": 41, "3142": 41, "acav2": 41, "3085": 41, "resampled_annot": 41, "resampled_annotation_boundari": 41, "resampled_average_templ": 41, "117m": 41, "12m": 41, "55m": 41, "1100": 41, "76": 41, "20000000298023224": 41, "476531505584717": 41, "600000381469727": 41, "435669422149658": 41, "template_slic": 41, "annotation_slic": 41, "boundary_slic": 41, "help": 41, "thick": 42, "cover": 42, "200": 42, "apart": 42, "male": 42, "assai": 42, "merscop": 42, "design": 42, "combinatori": 42, "robust": [42, 45], "quantit": 42, "bind": 42, "dot": 42, "cellpos": 42, "softwar": 42, "dapi": 42, "polyt": 42, "stain": 42, "pupros": 42, "approximatedli": [42, 45], "phyiscal": 42, "hierach": 42, "correl": 42, "564m": 42, "fuction": 42, "5320": 42, "3932069": 42, "5296": 42, "facili": [42, 45], "blank": 42, "codeword": 42, "codebook": 42, "rate": 42, "detect": 42, "531kmb": 42, "550": 42, "transcript_identifi": [42, 43], "ensmusg00000026778": 42, "prkcq": 42, "ensmust00000028118": 42, "kinas": 42, "theta": 42, "18761": 42, "ensmusg00000026837": 42, "col5a1": 42, "ensmust00000028280": 42, "collagen": 42, "v": 42, "12831": 42, "ensmusg00000001985": 42, "grik3": 42, "ensmust00000030676": 42, "glutam": 42, "receptor": [42, 45], "ionotrop": 42, "kainat": 42, "14807": 42, "ensmusg00000039323": 42, "igfbp2": 42, "ensmust00000047328": 42, "insulin": 42, "growth": 42, "16008": 42, "ensmusg00000048387": 42, "osr1": 42, "ensmust00000057021": 42, "odd": 42, "23967": 42, "63g": 42, "4334174": [42, 43], "accessed_on": 42, "pick": [42, 44], "120186": 42, "ensmust00000032710": [42, 43], "ensmust00000045738": [42, 43], "ensmust00000026466": [42, 43], "ensmust00000056442": [42, 43], "ensmust00000085374": [42, 43], "ensmust00000020102": [42, 43], "ensmust00000022100": [42, 43], "ensmust00000021195": [42, 43], "642314999999996": 42, "On": 42, "ipykernel_17089": 42, "2280752953": 42, "muclei": 42, "amydala": 42, "402895000000001": 43, "inlin": 44, "360m": 44, "revers": 44, "aggreg": 44, "class_list": 44, "abl": 44, "recapitul": 44, "088": 44, "083": 44, "rai14": 44, "pdyn": 44, "crh": 44, "258": 44, "nmu": 44, "043": 44, "mi": 44, "frmd7": 44, "047": 44, "sncg": 44, "082": 44, "ebf1": 44, "046": 44, "vip": 44, "103": 44, "pvhd": 44, "dmh": 44, "lhx6": 44, "126": 44, "pvp": 44, "tbx3": 44, "situ": 45, "multiplex": 45, "fluoresc": 45, "hybrid": 45, "specimen": 45, "example_sect": 45, "079": 45, "037": 45, "010": 45, "sdf": 45, "556m": 45, "2846908": 45, "240m": 45, "1227408": 45, "310m": 45, "1585843": 45, "9m": 45, "162578": 45, "subclass_confidence_scor": 45, "cluster_confidence_scor": 45, "high_quality_transf": 45, "182941331246012878296807398333956011710": 45, "089": 45, "704": 45, "682522": 45, "366483": 45, "829530": 45, "969933": 45, "718088": 45, "221260934538535633595532020856387724686": 45, "5243": 45, "667690": 45, "442241": 45, "850554": 45, "22228792606814781533240955623030943708": 45, "14939": 45, "638731": 45, "474328": 45, "888285": 45, "649581": 45, "272043042552227961220474294517855477150": 45, "653425": 45, "433218": 45, "900000": 45, "607080": 45, "110116287883089187971185374239350249328": 45, "5254": 45, "623896": 45, "513574": 45, "999978": 45, "689511": 45, "94310525370042131911495836073267655162": 45, "110": 45, "5255": 45, "997247": 45, "823236": 45, "717769": 45, "971385": 45, "943456": 45, "298798481479578578007190103666214714353": 45, "043871": 45, "706231": 45, "956377": 45, "905493": 45, "330756942354980576352210203729462562749": 45, "5261": 45, "037680": 45, "759890": 45, "811520": 45, "788901": 45, "47305871059582831548494138048361484565": 45, "5252": 45, "044169": 45, "758463": 45, "991924": 45, "634152": 45, "64578198410898899234789748167671783948": 45, "5263": 45, "042301": 45, "589421": 45, "889413": 45, "645770": 45, "049": 45, "lamp5": 45, "0199": 45, "0709": 45, "ccff33": 45, "ff764d": 45, "dc00ff": 45, "998900": 45, "vascular": 45, "331": 45, "1191": 45, "nn_1": 45, "5304": 45, "858881": 45, "82992e": 45, "2f00cc": 45, "bb1fcc": 45, "astro": 45, "epen": 45, "te": 45, "1163": 45, "nn_3": 45, "5225": 45, "594a26": 45, "3dccb1": 45, "a8afa5": 45, "551799": 45, "333": 45, "endo": 45, "1193": 45, "5310": 45, "994567": 45, "00992a": 45, "ffb473": 45, "5311": 45, "cc3d76": 45, "330": 45, "vlmc": 45, "1188": 45, "nn_2": 45, "5301": 45, "653d66": 45, "4d5cff": 45, "79cc5c": 45, "5309": 45, "5c9994": 45, "1187": 45, "66391f": 45, "3b9900": 45, "7k": 45, "632kmb": 45, "ensmusg00000024798": 45, "htr7": 45, "hydroxytryptamin": 45, "serotonin": 45, "15566": 45, "ensmusg00000042385": 45, "gzmk": 45, "granzym": 45, "k": 45, "14945": 45, "ensmusg00000036198": 45, "arhgap36": 45, "gtpase": 45, "activ": 45, "75404": 45, "ensmusg00000028780": 45, "sema3c": 45, "sema": 45, "domain": 45, "immunoglobulin": 45, "ig": 45, "short": 45, "20348": 45, "ensmusg00000015843": 45, "rxrg": 45, "retinoid": 45, "gamma": 45, "20183": 45, "per": 45, "subplot_sect": 45, "suptitl": 45, "fontsiz": 45, "sodium": 45, "ino": 45, "216227": 45, "tran": 45, "13162": 45, "vesicular": 45, "22348": 45, "104245": 45, "72961": 45, "15567": 45, "140919": 45, "cell_express": 45, "13g": 45, "182652000000004": 45, "871m": 45, "726561000000004": 45, "16g": 45, "556720999999996": 45, "107m": 45, "8736040000000003": 45, "221m": 45, "1m": 45, "132m": 45, "8m": 45, "902190": 45, "048426": 45, "582962": 45, "906513": 45, "145200": 45, "577602": 45, "906110": 45, "182761": 45, "553731": 45, "904627": 45, "131808": 45, "563525": 45, "907236": 45, "230647": 45, "543048": 45, "681244": 45, "453979": 45, "852027": 45, "676999": 45, "291647": 45, "899531": 45, "1109": 45, "678760": 45, "363282": 45, "894082": 45, "678641": 45, "360346": 45, "901195": 45, "673530": 45, "138034": 45, "897311": 45, "2616328": 45}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"allen": [0, 28, 35], "mous": [0, 1, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 23, 35, 36, 45], "common": [0, 35], "coordin": [0, 2, 35, 41], "framework": [0, 35], "2020": [0, 35], "version": [0, 35], "merfish": [1, 2, 15, 16, 17, 18, 22, 41, 42, 43, 44, 45], "spatial": [1, 15, 16, 17, 18, 19, 22, 23, 29, 32, 42, 43, 44, 45], "transcriptom": [1, 3, 4, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 20, 22, 29, 33, 42, 43, 44, 45], "dataset": [1, 15, 16, 17, 18], "singl": [1, 3, 4, 8, 9, 10, 11, 15, 16, 17, 18, 29, 33], "adult": [1, 8, 13, 15, 16, 17, 18], "brain": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 28, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45], "ccf": [2, 41, 45], "map": [2, 41], "cluster": [3, 8, 12, 25, 34, 36, 37, 45], "analysi": [3, 8, 34, 36], "whole": [3, 6, 7, 8, 9, 10, 11, 13, 14, 19, 20, 22, 23, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45], "human": [3, 4, 5, 6, 7, 32, 33, 34], "10x": [3, 7, 8, 21, 29, 30, 31, 32, 33, 34, 36, 39], "nucleu": [3, 4], "10xv3": [4, 11], "taxonomi": [5, 13, 34, 36], "cell": [5, 6, 8, 9, 10, 11, 13, 14, 19, 20, 23, 28, 29, 32, 33, 34, 36, 38, 41, 42, 45], "type": [5, 6, 13, 14, 20, 38], "atla": [6, 14, 19, 20, 23, 28], "kimberli": 6, "siletti": 6, "scrna": [7, 21], "seq": [7, 21, 29, 30, 31, 32, 33, 34, 36, 39], "gene": [7, 21, 26, 29, 30, 31, 32, 33, 37, 39, 42, 44, 45], "express": [7, 21, 29, 30, 31, 32, 33, 37, 39, 42, 44, 45], "data": [7, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "10xmulti": 9, "10xv2": 10, "group": [12, 37], "neighborhood": [12, 37, 38], "specif": [12, 39], "umap": [12, 29, 32], "embed": [12, 29, 32, 37], "hongkui": [14, 20], "zeng": [14, 20], "zhuang": [15, 16, 17, 18, 19, 23, 45], "abca": [15, 16, 17, 18], "1": [15, 29, 32, 42], "2": [16, 29, 31, 33, 42, 44], "3": 17, "4": 18, "A": [19, 23], "molecularli": [19, 23], "defin": [19, 23], "resolv": [19, 23], "xiaowei": [19, 23, 45], "resourc": 24, "page": 24, "annot": [25, 27, 34, 35, 36, 45], "list": 26, "parcel": [27, 35, 41, 45], "access": [28, 39], "releas": 28, "note": 28, "rna": [29, 30, 31, 32, 33, 34, 36, 39], "part": [29, 30, 31, 32, 33, 42, 43, 44], "overview": [29, 32, 34, 35, 36, 37, 42, 45], "metadata": [29, 32, 40, 42, 45], "matric": [29, 30, 39], "exampl": [29, 30, 33, 34, 35, 36, 37, 42, 45], "us": [29, 30, 33, 34, 35, 36, 37, 40, 42, 45], "case": [29, 30, 33, 34, 35, 36, 37, 42, 45], "canon": [29, 31, 42, 44], "neurotransmitt": [29, 31, 34, 36, 42, 44], "transport": [29, 31, 42, 44], "thalamu": 29, "tachykinin": [29, 31, 42, 44], "tac2": [29, 31, 42, 44], "2a": [30, 43], "2b": [31, 44], "whb": 32, "select": 33, "subclust": 34, "term": [34, 35, 36, 41], "set": [34, 35, 36], "membership": [34, 35, 36, 37], "aggreg": [34, 35, 36, 41], "count": [34, 36], "per": [34, 35, 36], "superclust": 34, "level": [34, 35, 36, 41], "visual": [34, 35, 36, 37, 41], "distribut": [34, 36], "refer": 35, "templat": [35, 41], "anatom": [35, 37, 41], "structur": 35, "voxel": 35, "each": [35, 36], "hierachi": 35, "ccn20230722": 36, "class": 36, "dimens": 37, "reduct": 37, "pivot": 37, "tabl": 37, "context": 37, "galleri": 38, "pallium": 38, "glut": 38, "subpallium": 38, "gaba": 38, "hy": 38, "ea": 38, "th": 38, "epi": 38, "mb": 38, "hb": 38, "cb": 38, "sero": 38, "dopa": 38, "nn": 38, "imn": 38, "gc": 38, "load": 39, "from": 39, "get": 40, "start": 40, "cach": 40, "download": 40, "file": 40, "all": [40, 41], "directori": 40, "individu": 40, "advanc": 40, "option": 40, "forc": 40, "redownload": 40, "skip": 40, "hash": 40, "check": 40, "read": 41, "section": 41, "reconstruct": 41, "reconstruc": 41, "associ": 41, "assign": 41, "differ": 41, "resampl": 41, "boundari": 41, "overlai": 41, "panel": [42, 45], "matrix": [42, 45], "registr": 45}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9, "sphinx": 56}})
\ No newline at end of file
+Search.setIndex({"docnames": ["descriptions/Allen-CCF-2020", "descriptions/MERFISH-C57BL6J-638850", "descriptions/MERFISH-C57BL6J-638850-CCF", "descriptions/WHB-10X-clustering", "descriptions/WHB-10Xv3", "descriptions/WHB-taxonomy", "descriptions/WHB_dataset", "descriptions/WHB_notebooks", "descriptions/WMB-10X", "descriptions/WMB-10XMulti", "descriptions/WMB-10Xv2", "descriptions/WMB-10Xv3", "descriptions/WMB-neighborhoods", "descriptions/WMB-taxonomy", "descriptions/WMB_dataset", "descriptions/Zhuang-ABCA-1", "descriptions/Zhuang-ABCA-2", "descriptions/Zhuang-ABCA-3", "descriptions/Zhuang-ABCA-4", "descriptions/Zhuang_dataset", "descriptions/notebook_subtitle1", "descriptions/notebook_subtitle2", "descriptions/notebook_subtitle3", "descriptions/notebook_subtitle4", "docs/README", "docs/cluster_annotations/README", "docs/gene_lists/README", "docs/parcellation_annotations/README", "intro", "notebooks/10x_snRNASeq_tutorial_part_1", "notebooks/10x_snRNASeq_tutorial_part_2a", "notebooks/10x_snRNASeq_tutorial_part_2b", "notebooks/WHB-10x_snRNASeq_tutorial_part_1", "notebooks/WHB-10x_snRNASeq_tutorial_part_2", "notebooks/WHB_cluster_annotation_tutorial", "notebooks/ccf_and_parcellation_annotation_tutorial", "notebooks/cluster_annotation_tutorial", "notebooks/cluster_groups_and_embeddings_tutorial", "notebooks/cluster_neighborhood_gallery", "notebooks/general_accessing_10x_snRNASeq_tutorial", "notebooks/getting_started", "notebooks/merfish_ccf_registration_tutorial", "notebooks/merfish_tutorial_part_1", "notebooks/merfish_tutorial_part_2a", "notebooks/merfish_tutorial_part_2b", "notebooks/zhuang_merfish_tutorial"], "filenames": ["descriptions/Allen-CCF-2020.md", "descriptions/MERFISH-C57BL6J-638850.md", "descriptions/MERFISH-C57BL6J-638850-CCF.md", "descriptions/WHB-10X-clustering.md", "descriptions/WHB-10Xv3.md", "descriptions/WHB-taxonomy.md", "descriptions/WHB_dataset.md", "descriptions/WHB_notebooks.md", "descriptions/WMB-10X.md", "descriptions/WMB-10XMulti.md", "descriptions/WMB-10Xv2.md", "descriptions/WMB-10Xv3.md", "descriptions/WMB-neighborhoods.md", "descriptions/WMB-taxonomy.md", "descriptions/WMB_dataset.md", "descriptions/Zhuang-ABCA-1.md", "descriptions/Zhuang-ABCA-2.md", "descriptions/Zhuang-ABCA-3.md", "descriptions/Zhuang-ABCA-4.md", "descriptions/Zhuang_dataset.md", "descriptions/notebook_subtitle1.md", "descriptions/notebook_subtitle2.md", "descriptions/notebook_subtitle3.md", "descriptions/notebook_subtitle4.md", "docs/README.md", "docs/cluster_annotations/README.md", "docs/gene_lists/README.md", "docs/parcellation_annotations/README.md", "intro.md", "notebooks/10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2a.ipynb", "notebooks/10x_snRNASeq_tutorial_part_2b.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb", "notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb", "notebooks/WHB_cluster_annotation_tutorial.ipynb", "notebooks/ccf_and_parcellation_annotation_tutorial.ipynb", "notebooks/cluster_annotation_tutorial.ipynb", "notebooks/cluster_groups_and_embeddings_tutorial.ipynb", "notebooks/cluster_neighborhood_gallery.ipynb", "notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb", "notebooks/getting_started.ipynb", "notebooks/merfish_ccf_registration_tutorial.ipynb", "notebooks/merfish_tutorial_part_1.ipynb", "notebooks/merfish_tutorial_part_2a.ipynb", "notebooks/merfish_tutorial_part_2b.ipynb", "notebooks/zhuang_merfish_tutorial.ipynb"], "titles": ["Allen Mouse Common Coordinate Framework (2020 version)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain", "MERFISH CCF mapped coordinates", "Clustering analysis of whole human brain 10X single nucleus transcriptomes", "Human brain 10Xv3 single nucleus transcriptomes", "Human brain taxonomy of cell types", "Human whole-brain transcriptomic cell type atlas (Kimberly Siletti)", "Whole Human Brain 10x scRNA-seq gene expression data", "Clustering analysis of whole adult mouse brain 10X single cell transcriptomes", "Whole mouse brain 10XMulti single cell transcriptomes", "Whole mouse brain 10Xv2 single cell transcriptomes", "Whole mouse brain 10Xv3 single cell transcriptomes", "Cluster groups and neighborhood specific UMAP embeddings", "Whole adult mouse brain taxonomy of cell types", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-1)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-2)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-3)", "MERFISH spatial transcriptomics dataset of a single adult mouse brain (Zhuang-ABCA-4)", "A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)", "Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)", "10x scRNA-seq gene expression data", "MERFISH whole brain spatial transcriptomics", "A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)", "Resource Pages", "Cluster annotations", "Gene lists", "Parcellation annotations", "Allen Brain Cell Atlas - Data Access", "10x RNA-seq gene expression data (part 1)", "10x RNA-seq gene expression data (part 2a)", "10x RNA-seq gene expression data (part 2b)", "Whole Human Brain (WHB) 10x RNA-seq gene expression data (part 1)", "Whole Human Brain 10x RNA-seq gene expression data (part 2)", "Whole Human Brain 10x RNA-seq clustering analysis and annotation", "Allen Mouse Common Coordinate Framework (2020 version)", "10x RNA-seq clustering analysis and annotation (CCN20230722)", "Cluster neighborhoods and embeddings", "Cell type neighborhood gallery", "Accessing 10x RNA-seq gene expression data", "Getting started", "MERFISH CCF mapped coordinates", "MERFISH whole brain spatial transcriptomics (part 1)", "MERFISH whole brain spatial transcriptomics (part 2a)", "MERFISH whole brain spatial transcriptomics (part 2b)", "MERFISH whole mouse brain spatial transcriptomics (Xiaowei Zhuang)"], "terms": {"brain": [0, 2, 12, 21, 29, 30, 35, 38, 39, 40, 41], "ccfv3": [0, 2, 14, 19, 20, 35, 41, 45], "wang": [0, 35], "et": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 45], "al": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 32, 33, 34, 35, 37, 38, 39, 41, 45], "3d": [0, 2, 15, 16, 17, 18, 35, 41, 45], "refer": [0, 15, 16, 17, 18, 29, 34, 41, 45], "space": [0, 2, 15, 16, 17, 18, 35, 41, 42, 45], "an": [0, 2, 14, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "averag": [0, 29, 31, 33, 35, 36, 41, 42, 44], "10um": [0, 35], "voxel": [0, 41], "resolut": [0, 1, 8, 9, 10, 11, 13, 35, 36, 41], "creat": [0, 2, 8, 12, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "from": [0, 2, 3, 4, 5, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45], "serial": [0, 35], "two": [0, 4, 5, 17, 29, 30, 33, 35, 39, 40, 42, 43, 45], "photon": [0, 35], "tomographi": [0, 35], "imag": [0, 2, 15, 16, 17, 18, 31, 35, 41, 42, 45], "1": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 19, 21, 22, 26, 28, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45], "675": [0, 35], "young": [0, 35], "adult": [0, 3, 4, 5, 6, 9, 10, 11, 14, 35, 42], "c57bl6": [0, 35], "j": [0, 35], "mice": [0, 29, 31, 35, 42, 44], "us": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 31, 32, 38, 39, 41, 43, 44], "multimod": [0, 35], "data": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 22, 38, 43, 44], "entir": [0, 13, 29, 35, 36, 42], "parcel": [0, 2, 20, 24, 40], "directli": [0, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "label": [0, 15, 16, 17, 18, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45], "everi": [0, 35], "structur": [0, 3, 4, 5, 7, 12, 33, 37, 41, 45], "span": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 30, 35, 43, 45], "43": [0, 35, 37, 38], "isocort": [0, 35], "area": [0, 29, 32, 35, 37], "layer": [0, 14, 34, 35], "314": [0, 35], "subcort": [0, 29, 31, 35, 42, 44], "grai": [0, 35], "matter": [0, 35], "81": [0, 1, 35], "fiber": [0, 35, 41], "tract": [0, 35, 41], "8": [0, 14, 15, 17, 19, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "ventricular": [0, 35], "The": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "add": [0, 28, 34, 35, 36, 40], "new": [0, 28, 35, 37, 40], "annot": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 24, 29, 32, 33, 37, 40, 41, 42], "ammon": [0, 14, 35], "s": [0, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "horn": [0, 14, 35], "ca": [0, 35], "main": [0, 14, 31, 32, 35, 40, 42, 44], "olfactori": [0, 14, 31, 35, 37, 42, 44], "bulb": [0, 35, 37], "mob": [0, 31, 35, 42, 44], "minor": [0, 35], "modif": [0, 35], "surround": [0, 35], "For": [0, 12, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "purpos": [0, 28, 29, 32, 34, 35, 36, 41], "abc": [0, 15, 16, 17, 18, 19, 28, 35, 39, 45], "atla": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 31, 32, 34, 35, 36, 39, 40, 42, 44, 45], "visual": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 29, 31, 32, 33, 38, 42, 44, 45], "analysi": [0, 1, 2, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 20, 29, 31, 35, 37, 39, 41, 42, 44], "we": [0, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "have": [0, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "also": [0, 13, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "simplifi": [0, 2, 14, 20], "5": [0, 2, 13, 14, 16, 20, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "level": [0, 2, 6, 13, 14, 20, 29, 30, 31, 32, 42, 44, 45], "anatom": [0, 2, 13, 14, 20, 28, 29, 31, 32, 33, 36, 38, 42, 44, 45], "hierarchi": [0, 2, 14, 20, 34, 36], "associ": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 42, 43, 45], "metadata": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 43, 44], "host": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "aw": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40, 45], "s3": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "bucket": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40, 45], "public": [0, 1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 40], "dataset": [0, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 36, 37, 39, 40, 43, 44, 45], "compon": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 37], "current": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 40], "size": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 35, 36, 39, 40, 41], "volum": [0, 2, 35, 41], "cell": [0, 1, 2, 3, 4, 7, 12, 15, 16, 17, 18, 21, 30, 31, 35, 37, 39, 40, 43, 44], "image_volum": [0, 2, 40], "ccf": [0, 13, 14, 15, 16, 17, 18, 20, 27, 35, 36, 40], "20230630": [0, 2, 10, 11, 29, 40], "379": 0, "mb": [0, 2, 3, 5, 29, 30, 35, 36, 37, 40, 41], "18": [0, 15, 29, 31, 33, 36, 37, 38, 39, 42], "being": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 35, 36, 40], "share": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 34, 36, 45], "under": [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 40], "institut": [0, 15, 16, 17, 18, 28, 45], "term": [0, 24, 29, 32, 42, 45], "notebook": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "learn": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 33], "about": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 33, 35, 36], "through": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 32, 34, 35, 36, 41, 42], "some": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 29, 31, 33, 34, 35, 37, 42], "exampl": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 31, 32, 39, 40, 41, 43, 44], "case": [0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 23, 28, 32, 41], "A": [1, 2, 6, 13, 14, 28, 30, 34, 35, 36, 41, 42, 45], "4": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "0": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "million": [1, 3, 4, 5, 6, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 29, 30, 33, 34, 36, 45], "500": [1, 13, 14, 26, 36, 42], "gene": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 28, 34, 36, 40, 43], "panel": [1, 13, 14, 15, 16, 17, 18, 19, 36], "map": [1, 14, 15, 16, 17, 18, 19, 20, 37, 38, 42, 45], "whole": [1, 2, 4, 5, 12, 15, 16, 17, 18, 21, 28, 30, 38, 39], "taxonomi": [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 25, 28, 29, 32, 33, 40, 42, 45], "It": [1, 9, 10, 11, 29, 34, 35, 36, 42, 45], "wa": [1, 2, 9, 10, 11, 29, 31, 33, 36, 37, 40, 41, 42, 44], "creation": [1, 9, 10, 11], "high": [1, 8, 9, 10, 11, 13, 31, 36, 44], "type": [1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 28, 29, 31, 32, 33, 34, 36, 37, 39, 40, 41, 42, 44, 45], "describ": [1, 8, 9, 10, 11, 29, 40], "yao": [1, 2, 8, 9, 10, 11, 12, 37, 38, 41], "express": [1, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 28, 34, 36, 40, 43], "matric": [1, 4, 9, 10, 11, 15, 16, 17, 18, 28, 33, 42, 43], "version": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 34, 36, 40, 42], "allen": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 29, 31, 36, 40, 41, 42, 44, 45], "expression_matric": [1, 4, 9, 10, 11, 15, 16, 17, 18, 29, 30, 40, 42, 43], "c57bl6j": [1, 2, 12, 13, 14, 26, 37, 38, 40, 41, 42, 43, 44], "638850": [1, 2, 12, 13, 14, 26, 37, 38, 40, 41, 42, 43, 44], "20230830": [1, 9, 15, 16, 17, 18, 30, 40, 42, 43], "14": [1, 29, 32, 33, 40, 45], "2": [1, 2, 3, 4, 5, 7, 8, 11, 14, 15, 17, 19, 30, 32, 34, 35, 36, 37, 38, 39, 40, 41, 45], "gb": [1, 2, 4, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 39, 40], "20231215": [1, 2, 8, 12, 13, 15, 16, 17, 18, 29, 40], "cc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 31, 32, 33, 37, 38, 41, 42, 45], "BY": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18], "nc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13], "licens": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18], "relat": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 29, 33, 36, 39, 40, 42], "resourc": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13], "cluster": [1, 2, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 17, 18, 20, 24, 28, 29, 31, 32, 33, 35, 38, 40, 41, 42, 44], "wmb": [1, 2, 8, 9, 10, 11, 12, 13, 14, 25, 26, 29, 30, 31, 36, 37, 38, 39, 40, 42, 45], "10x": [1, 2, 4, 5, 6, 9, 10, 11, 12, 13, 14, 20, 26, 28, 37, 38, 40, 42], "get": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 31, 33, 34, 35, 36, 37, 41, 42, 44], "start": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 29, 30, 31, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45], "how": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "abcprojectcach": [1, 2, 8, 12, 13, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "facilit": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28], "download": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "usag": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 28, 36, 40], "scrna": [1, 2, 4, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 36, 45], "seq": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 20, 45], "part": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22, 35, 37, 40, 41, 45], "section": [1, 2, 12, 13, 15, 16, 17, 18, 19, 22, 29, 30, 33, 35, 37, 40, 42, 43, 44, 45], "2a": [1, 2, 8, 9, 10, 11, 12, 13, 21, 22, 31, 37, 44], "access": [1, 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 21, 22, 29, 30, 33, 34, 35, 36, 42], "prepar": [1, 2, 12, 13, 22, 30, 40, 43], "2b": [1, 2, 8, 9, 10, 11, 12, 13, 21, 22, 30, 43], "explor": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44], "analys": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22], "set": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 15, 16, 20, 21, 22, 29, 31, 32, 37, 38, 39, 40, 41, 42, 44, 45], "interest": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 21, 22, 29, 31, 32, 33, 44], "each": [2, 12, 13, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "regist": [2, 13, 15, 16, 17, 18, 36, 45], "combin": [2, 8, 13, 14, 28, 29, 32, 33, 36, 42, 43], "global": [2, 41], "wise": [2, 41], "midlin": [2, 15, 16, 41, 42, 45], "manual": [2, 15, 16, 17, 41, 45], "determin": [2, 15, 16, 34, 36, 40, 41], "rotat": [2, 15, 16, 17, 18, 41, 42, 45], "upright": [2, 41, 42, 45], "center": [2, 15, 16, 17, 18, 34, 36, 41, 45], "middl": [2, 41, 42, 45], "thi": [2, 4, 8, 9, 10, 11, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "rectifi": [2, 41], "were": [2, 15, 16, 17, 18, 29, 31, 33, 37, 39, 40, 41, 42, 44, 45], "stack": [2, 34, 36, 41], "sequenti": [2, 41, 42], "order": [2, 29, 31, 32, 33, 34, 35, 36, 41], "initi": 2, "configur": [2, 41], "registr": [2, 15, 16, 17, 18, 41], "affin": [2, 41], "12": [2, 17, 29, 33, 39, 40, 41, 45], "dof": [2, 41], "perform": [2, 15, 16, 17, 18, 41, 45], "align": [2, 15, 16, 17, 18, 29, 41, 45], "deform": [2, 41], "its": [2, 28, 35], "resampl": 2, "target": [2, 41, 42], "step": [2, 8, 15, 16, 17, 18, 37, 41, 45], "preserv": [2, 41], "concaten": [2, 29, 32, 41], "appropri": [2, 41], "invers": [2, 41], "allow": [2, 40, 41, 44], "point": [2, 15, 16, 17, 18, 41, 42, 45], "between": [2, 12, 13, 14, 31, 33, 34, 35, 36, 37, 40, 41, 42], "origin": [2, 28, 31, 35, 40, 41, 44], "see": [2, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "further": [2, 12, 15, 16, 17, 18, 29, 31, 32, 37, 39, 41, 45], "detail": [2, 3, 4, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "115": 2, "01": [2, 13, 18, 29, 30, 36, 37, 38, 40, 42, 44, 45], "mous": [2, 12, 28, 29, 31, 34, 37, 38, 39, 42, 44], "spatial": [2, 8, 9, 10, 11, 12, 13, 14, 20, 28, 31, 36, 37, 38, 41], "transcriptom": [2, 5, 12, 13, 19, 23, 28, 34, 36], "2020": [2, 14, 15, 16, 17, 18, 27, 40, 41, 45], "singl": [2, 5, 6, 12, 13, 14, 22, 32, 34, 35, 36, 41, 42, 44], "over": [3, 4, 5, 6, 29, 31, 39, 40, 42, 44, 45], "3": [3, 4, 5, 6, 11, 12, 14, 15, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "result": [3, 8, 15, 16, 17, 18, 30, 31, 34, 35, 36, 37, 39, 42, 43, 44, 45], "461": [3, 5, 32, 34], "3313": [3, 5, 32, 34], "subclust": [3, 5, 32, 33, 36], "link": [3, 29, 40], "below": [3, 29, 32, 33, 34, 39, 40], "contain": [3, 5, 13, 33, 34, 36, 40], "all": [3, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45], "geen": 3, "whb": [3, 4, 5, 6, 25, 26, 33, 34, 36, 39, 40], "full": [3, 4, 32, 34, 39, 40], "can": [3, 4, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "found": [3, 4, 29, 30, 33, 34, 39, 40], "siletti": [3, 4, 5, 28, 32, 33, 34, 39], "2023": [3, 4, 5, 15, 16, 17, 18, 28, 32, 33, 34, 35, 39, 45], "10xv3": [3, 5, 6, 8, 12, 14, 29, 30, 32, 33, 39, 40], "20240330": [3, 4, 5, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "862": 3, "manifest": [3, 4, 5, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "json": [3, 4, 5, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "file": [3, 4, 5, 15, 16, 17, 18, 28, 29, 30, 32, 33, 35, 39, 41, 42, 43, 45], "snrna": [3, 5], "load": [3, 4, 5, 28, 29, 30, 32, 33, 40, 42], "individu": [3, 4, 5, 28, 42, 45], "understand": [3, 4, 5, 7, 28], "basic": [3, 4, 5, 7, 35], "region": [3, 4, 5, 7, 12, 13, 14, 29, 31, 32, 33, 34, 35, 36, 37, 42, 44], "umap": [3, 4, 5, 7, 14, 20, 31, 33, 37, 38], "consist": [4, 5, 9, 10, 11, 29, 34, 35, 36, 39, 42, 45], "nuclei": [4, 5, 31, 32, 33, 34, 37, 39, 44], "extract": [4, 39], "three": [4, 5, 6, 15, 18, 29, 34, 36, 41], "approxim": [4, 29, 32, 37], "neuron": [4, 5, 12, 14, 29, 31, 32, 33, 34, 37, 38, 39, 42, 44], "one": [4, 5, 8, 16, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 42, 43, 45], "non": [4, 5, 32, 33, 34, 37, 38, 39], "100": [4, 5, 29, 30, 31, 32, 33, 34, 36, 37, 39, 40, 41, 42, 44, 45], "locat": [4, 5, 13, 32, 33, 34, 36, 40, 44], "across": [4, 5, 13, 28, 29, 31, 33, 34, 36, 39, 40, 41, 44], "forebrain": [4, 5, 32, 34, 35], "midbrain": [4, 5, 31, 32, 34, 35, 37, 38, 39], "hindbrain": [4, 5, 34, 37, 38], "ar": [4, 13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 44, 45], "70": 4, "present": [5, 31, 32, 33, 39], "here": [5, 28, 32, 34, 35, 39, 40], "collect": [5, 40, 45], "apprixm": 5, "integr": [5, 13, 15, 16, 17, 18, 28, 34, 35, 36, 45], "31": [5, 9, 11, 32, 34, 39, 40, 41, 42, 44, 45], "superclust": [5, 32, 33, 36], "6": [5, 15, 17, 19, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 45], "nucleu": [5, 31, 35, 44], "chemistri": [6, 9, 10, 11, 14, 29], "whb_cluster_annotation_tutori": 7, "ipynb": [7, 20, 21, 22, 23, 28, 30, 32, 33], "10x_snrnaseq_tutorial_part_1": [7, 21], "10x_snrnaseq_tutorial_part_2": 7, "10xv2": [8, 12, 14, 29, 30, 40], "5196": [8, 36], "toward": 8, "39": 8, "10xmulti": [8, 14, 29, 30, 40], "thalamu": [8, 9, 10, 11, 12, 13, 21, 30, 31, 32, 37, 38, 42], "iter": [8, 9, 10, 11, 12, 13, 21], "packag": [8, 9, 10, 11, 12, 13, 21, 28, 29, 30, 31, 32, 39, 40, 42, 45], "1687": [9, 14, 29, 30], "multiom": [9, 14], "176": [9, 11, 35], "abcprojecctcach": 9, "7": [10, 14, 15, 29, 35, 37, 39, 40, 41, 42, 45], "104": [10, 40], "05": 10, "abcporjectcach": [10, 11], "To": [12, 28, 29, 30, 32, 34, 36, 37, 39, 40, 41, 42, 45], "investig": [12, 37], "divers": [12, 34, 37], "within": [12, 14, 29, 32, 34, 35, 36, 37, 41], "major": [12, 34, 36, 37, 41], "concept": [12, 37], "them": [12, 28, 29, 32, 37, 38, 39, 42, 44], "thei": [12, 33, 37, 40, 42], "gener": [12, 33, 34, 37, 40, 42, 45], "re": [12, 28, 29, 31, 32, 33, 35, 37, 41, 42, 44, 45], "reveal": [12, 13, 31, 36, 37, 44], "fine": [12, 13, 14, 36, 37], "grain": [12, 14, 37], "relationship": [12, 31, 33, 34, 35, 36, 37], "00": [12, 29, 30, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "merfish": [12, 13, 14, 20, 23, 26, 36, 37, 38, 40], "galleri": [12, 20], "sever": [13, 29, 36, 40], "rna": [13, 42], "sequenc": [13, 29, 33, 34, 36], "total": [13, 30, 36, 39, 40], "pass": [13, 15, 16, 17, 18, 19, 36, 40, 45], "rigor": [13, 36], "qualiti": [13, 15, 16, 17, 18, 36, 45], "control": [13, 15, 16, 17, 18, 36, 45], "qc": [13, 36], "criteria": [13, 36], "322": [13, 36, 40], "organ": [13, 28, 29, 32, 35, 36, 42], "hierarch": [13, 34, 36], "manner": [13, 36], "nest": [13, 36], "group": [13, 20, 28, 29, 31, 32, 33, 34, 35, 36, 38, 40, 42, 44], "34": [13, 29, 32, 34, 36, 40, 42], "class": [13, 28, 29, 31, 37, 41, 42, 44, 45], "338": [13, 29, 36, 42], "subclass": [13, 15, 16, 17, 18, 29, 31, 36, 37, 41, 42, 44, 45], "201": [13, 36], "supertyp": [13, 29, 36, 41, 42, 45], "wide": [13, 36], "co": [13, 36], "pattern": [13, 29, 31, 32, 36, 44], "ha": [13, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "been": [13, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "comprehens": [13, 36], "segment": [13, 15, 16, 17, 18, 36, 42, 45], "probe": [13, 36, 42], "common": [13, 36, 45], "coordin": [13, 14, 15, 16, 17, 18, 20, 29, 32, 36, 37, 38, 42, 45], "framework": [13, 36, 41, 45], "v3": [13, 36, 41], "onli": [13, 29, 31, 32, 34, 35, 36, 37, 39, 42, 44], "provid": [13, 28, 29, 30, 32, 34, 35, 36, 39, 41, 42, 45], "accur": [13, 36], "distinct": [13, 31, 33, 34, 36, 44], "gradient": [13, 34, 36], "degre": [13, 36], "correspond": [13, 29, 32, 34, 36, 41, 42, 45], "ident": [13, 29, 31, 32, 36, 42, 44, 45], "specif": [13, 20, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44], "well": [13, 31, 36, 37, 44], "uniqu": [13, 29, 32, 34, 35, 36, 37, 41, 42, 45], "featur": [13, 36, 37, 38, 44], "differ": [13, 28, 32, 33, 36, 40], "tabl": [13, 29, 31, 32, 33, 34, 35, 36, 39, 41, 42, 44, 45], "along": [13, 15, 16, 17, 18, 36, 45], "inform": [13, 32, 34, 35, 36, 37, 41], "membership": [13, 32, 33], "neurotransmitt": [13, 30, 32, 33, 37, 38, 41, 43, 45], "marker": [13, 29, 31, 32, 33, 36, 37, 38, 41, 42, 44, 45], "transcript": [13, 29, 36, 39, 42], "factor": [13, 29, 32, 36, 42], "neuropeptid": [13, 29, 31, 36, 42, 44], "other": [13, 15, 16, 29, 30, 32, 33, 34, 36, 39, 42, 45], "four": [14, 15, 16, 17, 18, 36, 44, 45], "9": [14, 16, 19, 29, 31, 33, 34, 36, 39, 40, 41, 42, 44, 45], "definit": [14, 34, 36], "neighborhood": [14, 20, 40], "embed": [14, 20, 38], "updat": [14, 28, 40], "addit": [14, 33, 37, 39, 40], "blub": [14, 31, 42, 44], "147": [15, 19, 41, 45], "coron": [15, 16, 19, 35, 42, 43, 45], "1122": [15, 16, 17, 18, 19, 26, 45], "150": 15, "anim": [15, 16, 17, 18, 45], "obtain": [15, 16, 17, 18, 34, 35, 36, 42, 45], "includ": [15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "classifi": [15, 16, 17, 18, 45], "appli": [15, 16, 17, 18, 34, 38, 41, 45], "seri": [15, 16, 17, 18, 29, 34, 36, 42, 45], "filter": [15, 16, 17, 18, 29, 31, 35, 36, 37, 38, 40, 41, 44, 45], "select": [15, 16, 17, 18, 28, 32, 37, 39, 40, 42, 45], "subset": [15, 16, 17, 18, 29, 30, 39, 45], "first": [15, 16, 17, 29, 30, 32, 33, 34, 35, 36, 37, 41, 42, 45], "remov": [15, 16, 17, 18, 45], "fractur": [15, 16, 17, 45], "tissu": [15, 16, 17, 18, 45], "slice": [15, 16, 17, 18, 34, 35, 36, 39, 45], "remain": [15, 16, 17, 18, 36, 41, 45], "after": [15, 16, 17, 18, 40, 45], "Then": [15, 16, 17, 45], "defin": [15, 16, 17, 18, 28, 29, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "substanti": [15, 16, 17, 18, 45], "hemispher": [15, 16, 45], "which": [15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "anterior": [15, 16, 35, 41, 42, 45], "posterior": [15, 16, 17, 18, 35, 41, 42, 45], "end": [15, 16, 40], "cannot": [15, 16, 17, 40, 45], "orient": [15, 16, 17, 35, 45], "x": [15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "y": [15, 16, 17, 18, 29, 31, 32, 33, 35, 37, 38, 39, 40, 41, 42, 44, 45], "experiment": [15, 16, 17, 18, 45], "measur": [15, 16, 17, 18, 42, 45], "z": [15, 16, 17, 18, 35, 41, 42, 45], "estim": [15, 16, 17, 18, 45], "posit": [15, 16, 17, 18, 29, 34, 36, 42, 45], "axi": [15, 16, 17, 18, 29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "base": [15, 16, 17, 18, 29, 31, 34, 36, 39, 42, 44, 45], "either": [15, 16, 17, 33, 39, 40, 41, 42, 44, 45], "dure": [15, 16, 17, 18, 29, 31, 42, 44, 45], "zero": [15, 16, 34, 35, 36, 45], "when": [15, 16, 33, 36, 39, 40, 45], "becom": [15, 16, 40, 45], "neg": [15, 16, 45], "therefor": 15, "multipl": [15, 28, 32, 39, 40, 41], "valu": [15, 29, 31, 33, 34, 35, 36, 37, 41, 42, 44, 45], "matrix": [15, 16, 17, 18, 28, 29, 33, 37, 39, 40], "classif": [15, 16, 17, 18, 19, 29, 32, 34, 36, 42, 45], "transfer": [15, 16, 17, 18, 28, 29, 30, 45], "confid": [15, 16, 17, 18, 19, 45], "score": [15, 16, 17, 18, 19, 42, 45], "calcul": [15, 16, 17, 18, 45], "scrnaseq": [15, 16, 17, 18, 45], "threshold": [15, 16, 17, 18, 19, 45], "These": [15, 16, 17, 18, 33, 36, 39, 45], "displai": [15, 16, 17, 18, 19, 29, 45], "awb": [15, 16, 17, 18, 45], "zhang": [15, 16, 17, 18, 45], "more": [15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "09": [15, 30, 41], "33": [15, 29, 38, 45], "21": [15, 29, 30, 39, 40, 41], "66": [16, 19, 40, 45], "67": [16, 32, 36, 38], "13": [16, 29, 32, 33, 37, 39, 40, 41, 42, 45], "30": [16, 29, 31, 32, 33, 38, 39, 40, 42, 44, 45], "57": [16, 32], "08": [16, 18, 33, 38, 41, 45], "23": [17, 19, 29, 30, 37, 39, 40, 41, 42, 45], "sagitt": [17, 18, 19, 45], "25": [17, 29, 33, 40, 41, 42, 45], "edg": [17, 18, 45], "later": [17, 18, 29, 31, 33, 35, 37, 42, 44, 45], "medial": [17, 18, 29, 31, 37, 42, 44], "69": [17, 35, 44], "75": [17, 40], "22": [18, 19, 29, 39, 40, 41, 45], "19": [18, 29, 32, 37, 39, 40, 44, 45], "16": [18, 19, 29, 31, 35, 36, 38, 39, 40, 42, 44], "abca": [19, 26, 40, 45], "cluster_annotation_tutori": 20, "cluster_groups_and_embeddings_tutori": 20, "cluster_neighborhood_galleri": 20, "ccf_and_parcellation_annotation_tutori": 20, "merfish_ccf_registration_tutori": 20, "10x_snrnaseq_tutorial_part_2a": 21, "10x_snrnaseq_tutorial_part_2b": 21, "merfish_tutorial_part_1": 22, "merfish_tutorial_part_2a": 22, "merfish_tutorial_part_2b": 22, "zhuang_merfish_tutori": 23, "list": [24, 29, 32, 33, 34, 36, 38, 39, 40, 42, 44], "ccn20230504": 25, "ccn20230722": 25, "32285": [26, 29, 40], "59357": [26, 33, 39], "zhuang": [26, 28, 40], "aim": 28, "empow": 28, "research": [28, 35], "worldwid": 28, "analyz": [28, 35], "simultan": 28, "As": [28, 30, 31, 36, 43, 44], "collabor": 28, "continu": [28, 30, 31, 43, 44], "modal": 28, "speci": 28, "insight": 28, "groundbreak": 28, "platform": [28, 29, 42], "keep": [28, 40, 41], "grow": 28, "open": [28, 29, 30, 33, 35, 39, 42, 45], "up": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "endless": 28, "possibl": 28, "discoveri": [28, 42], "breakthrough": 28, "neurosci": 28, "With": [28, 31, 44], "everywher": 28, "gain": 28, "complex": [28, 32], "work": 28, "advanc": 28, "our": [28, 31, 33, 39, 44], "amaz": 28, "wai": [28, 33, 34, 35, 36, 40], "never": 28, "thought": 28, "primari": [28, 29, 32, 35], "method": [28, 29, 32, 39, 40, 42], "interact": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "ani": [28, 40, 42], "question": 28, "issu": [28, 39], "best": [28, 29, 42, 45], "direct": [28, 35, 41], "commnitui": 28, "forum": 28, "repositori": 28, "intend": 28, "user": [28, 29, 30, 31, 33, 37, 40, 42, 43], "who": 28, "wish": 28, "process": [28, 29, 32, 39, 40, 41], "local": [28, 31, 40, 44], "amazon": [28, 40], "web": [28, 40], "servic": [28, 40], "arn": [28, 40], "No": [28, 40], "account": [28, 40, 42], "login": [28, 40], "requir": [28, 29, 39, 40, 42], "repo": [28, 40], "overview": [28, 41], "avail": [28, 29, 33, 34, 35, 36, 39, 40, 41, 42, 45], "spring": 28, "2024": [28, 40], "beta": 28, "hongkui": 28, "zeng": 28, "molecularli": 28, "resolv": [28, 40, 45], "xiaowei": 28, "human": [28, 29, 35, 36, 37, 39, 40], "kimberli": 28, "lightweight": 28, "python": [28, 40], "object": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "handl": [28, 29, 39], "manag": 28, "store": [28, 29, 30, 32, 35, 36, 37, 39, 40, 42, 45], "anndata": [28, 29, 30, 31, 32, 33, 39, 40, 42, 43, 44, 45], "h5ad": [28, 29, 30, 33, 39, 40, 42, 43, 45], "format": [28, 29, 30, 33, 35, 37, 39, 40, 42, 45], "need": [28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44], "system": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "make": [28, 29, 30, 42], "effici": [28, 29, 30], "subdivid": [28, 29], "smaller": [28, 29, 30, 42, 45], "code": [28, 29, 30, 39, 40, 42, 44, 45], "getting_start": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "matrici": [28, 30, 32, 33, 40], "abc_atlas_access": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "v0": 28, "fix": 28, "get_gene_data": [28, 39], "function": [28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "ad": [28, 29, 30, 40, 41, 42], "hash": 28, "check": 28, "cach": [28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "jupyt": 28, "book": 28, "webpag": 28, "24": [29, 30, 32, 33, 35, 40, 41], "where": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "broad": [29, 34, 36], "dissect": [29, 31, 32, 33, 44], "you": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "connect": [29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45], "internet": [29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44], "run": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44], "via": [29, 31, 33, 34, 35, 36, 41, 42, 44], "import": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "os": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "panda": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "pd": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "pathlib": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "path": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "numpi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "np": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "time": [29, 30, 31, 32, 33, 37, 38, 39, 42, 43, 44, 45], "matplotlib": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "pyplot": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "plt": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "abc_atlas_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_project_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "track": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "serv": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "requst": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "disk": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "datafram": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "instal": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "alreadi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "chang": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "download_bas": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "variabl": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "your": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_download_root": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "abc_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "from_s3_cach": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "current_manifest": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "releas": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "latest_manifest_fil": 29, "essenti": [29, 32, 42, 45], "row": [29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "repres": [29, 32, 34, 35, 36, 37, 41, 42, 45], "index": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45], "barcod": [29, 32, 42], "name": [29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 44, 45], "sampl": [29, 32], "In": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45], "context": [29, 32, 33, 34, 35, 36, 38, 42, 44, 45], "port": [29, 32], "chromium": [29, 32], "note": [29, 30, 32, 33, 34, 36, 39, 40, 41, 42, 45], "same": [29, 32, 33, 34, 35, 36, 37, 39, 41, 42, 44, 45], "reus": [29, 32, 36, 37], "databas": [29, 32, 34, 35, 36, 37], "librari": [29, 32, 35, 40], "donor": [29, 32, 33, 42, 45], "genotyp": [29, 42, 45], "sex": [29, 32, 42, 45], "acronym": [29, 31, 35], "coars": [29, 32, 36], "divis": [29, 32, 35, 41, 42, 45], "matrix_prefix": [29, 32, 45], "identifi": [29, 32, 35, 42, 45], "alia": [29, 32, 34, 36, 42, 45], "member": [29, 32, 35, 36, 37, 40, 42], "figur": [29, 32, 38], "manuscript": [29, 32], "tutori": [29, 31, 32, 33, 36, 37, 38, 40, 41, 42, 45], "list_metadata_fil": [29, 32, 33, 34, 40], "cell_metadata": [29, 30, 32, 33, 39, 40, 42, 43, 45], "cell_metadata_with_cluster_annot": [29, 31, 37, 40, 41, 42, 44, 45], "example_genes_all_cells_express": [29, 31, 32, 33, 37, 39, 40, 44], "region_of_interest_metadata": [29, 31, 40], "cluster_annotation_term": [29, 32, 34, 36, 40], "cluster_annotation_term_set": [29, 32, 33, 34, 36, 40], "cluster_annotation_term_with_count": [29, 36, 40], "cluster_to_cluster_annotation_membership": [29, 32, 33, 34, 36, 40], "cluster_to_cluster_annotation_membership_color": [29, 36, 40, 42, 45], "cluster_to_cluster_annotation_membership_pivot": [29, 36, 40, 42, 45], "get_directory_metadata": [29, 40], "posixpath": [29, 40], "chri": [29, 30, 31, 40, 42, 43], "morrison": [29, 30, 31, 40, 42, 43], "src": [29, 30, 31, 39, 40, 42, 43], "csv": [29, 31, 32, 33, 34, 37, 39, 40, 41, 42, 44, 45], "view": [29, 31, 37, 40], "list_data_fil": [29, 30, 35, 40, 41, 42, 45], "cb": [29, 30, 37, 39, 41], "log2": [29, 30, 39, 40, 42, 43, 45], "raw": [29, 30, 39, 40, 42, 45], "ctxsp": [29, 30, 40], "hpf": [29, 30, 40, 41], "hy": [29, 30, 35, 37, 40, 41], "isocortex": [29, 30, 31, 35, 37, 40, 41, 42, 44], "my": [29, 30, 36, 41, 45], "olf": [29, 30, 40, 41], "p": [29, 30, 35, 41, 42], "pal": [29, 30], "str": [29, 30, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45], "th": [29, 30, 34, 36, 37, 40, 41], "repeat": [29, 30, 32, 41, 43], "throughout": [29, 32, 40], "get_metadata_datafram": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "directori": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "file_nam": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45], "dtype": [29, 31, 32, 33, 35, 37, 38, 41, 42, 43, 44, 45], "cell_label": [29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45], "set_index": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45], "inplac": [29, 30, 31, 32, 33, 35, 37, 38, 41, 42, 43, 44, 45], "true": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45], "print": [29, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 45], "number": [29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 45], "len": [29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45], "head": [29, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "858m": 29, "7mmb": [29, 39, 41, 45], "4042976": [29, 37, 38], "cell_barcod": [29, 32, 33, 39], "barcoded_cell_sample_label": [29, 32, 33, 39], "library_label": [29, 30, 32, 33, 39], "feature_matrix_label": [29, 30, 32, 33, 39, 41, 42, 45], "entiti": [29, 32, 33, 36, 39], "brain_section_label": [29, 32, 33, 37, 38, 39, 41, 42, 44, 45], "library_method": [29, 32, 33, 39], "region_of_interest_acronym": [29, 31], "donor_label": [29, 32, 33, 39, 41, 42, 45], "donor_genotyp": [29, 41, 42, 45], "donor_sex": [29, 32, 33, 39, 41, 42, 45], "dataset_label": [29, 30, 32, 33, 39], "cluster_alia": [29, 32, 33, 34, 36, 37, 39, 41, 42, 45], "gcgagaagttaagggc": 29, "410_b05": 29, "l8tx_201030_01_c12": 29, "nan": [29, 35, 40, 41], "rhp": 29, "snap25": 29, "ires2": 29, "cre": 29, "ai14": 29, "550850": 29, "rcl": 29, "tdt": 29, "wt": [29, 41, 42, 45], "f": [29, 32, 35, 40, 45], "146826": 29, "086639": 29, "aatggctcagctcctt": 29, "411_b06": 29, "l8tx_201029_01_e10": 29, "550851": 29, "138481": 29, "022000": 29, "aacacacgttgcttga": 29, "472557": 29, "992709": 29, "cacagatagaggcgga": 29, "410_a05": 29, "l8tx_201029_01_a10": 29, "379622": 29, "043442": 29, "aaagtgaagcatttcg": 29, "909480": 29, "601536": 29, "panada": 29, "groupbi": [29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45], "mani": [29, 32, 33, 39, 42], "item": [29, 32, 42], "field": [29, 32, 42], "out": [29, 32, 34, 35, 36, 37, 39, 41, 42, 44], "small": [29, 31, 32, 40, 42, 44, 45], "def": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "print_column_info": [29, 32, 42], "df": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44], "c": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "column": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "count": [29, 30, 32, 35, 39, 41, 42, 45], "d": [29, 32, 42, 45], "2375490": 29, "819": 29, "10xrseq_mult": 29, "29": [29, 31, 39, 40, 41, 42, 45], "aca": 29, "ai": 29, "aud": 29, "tea": 29, "peri": [29, 45], "ect": 29, "ent": 29, "hip": 29, "lsx": 29, "mo": 29, "frp": [29, 35], "mop": 29, "pl": 29, "ila": 29, "orb": 29, "rsp": 29, "ss": 29, "gu": 29, "visc": 29, "ssp": [29, 35, 41], "strd": 29, "strv": 29, "vi": 29, "ptlp": 29, "sami": 29, "345": 29, "gad2": 29, "ir": 29, "slc32a1": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "m": [29, 32, 33, 35, 36, 39, 41, 42], "3992539": 29, "3992791": 29, "5322": [29, 36, 37, 38, 45], "1699939": 29, "2341350": 29, "bring": [29, 42], "pivot": [29, 32, 34, 35, 36, 41, 42, 45], "cluster_detail": [29, 32, 33, 42, 45], "keep_default_na": [29, 34, 36, 42, 45], "fals": [29, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "glut": [29, 31, 36, 37, 40, 41, 42, 44, 45], "IT": [29, 36, 41, 42, 45], "018": [29, 36, 42, 45], "l2": [29, 36, 41, 42, 45], "ppp": [29, 36, 42, 45], "apr": [29, 36, 42, 45], "0082": [29, 36, 42, 45], "glut_3": [29, 36, 42, 45], "0326": [29, 36, 42, 45], "0327": [29, 36, 42, 45], "0081": [29, 36, 42, 45], "glut_2": [29, 36, 42, 45], "0322": [29, 36, 42, 45], "0323": [29, 36, 42, 45], "0325": [29, 36, 42, 45], "cluster_color": [29, 32, 33, 34, 36, 41, 42, 45], "neurotransmitter_color": [29, 31, 32, 33, 34, 36, 37, 41, 42, 44, 45], "class_color": [29, 36, 37, 41, 42, 44, 45], "subclass_color": [29, 31, 36, 37, 38, 41, 42, 44, 45], "supertype_color": [29, 36, 41, 42, 45], "2b93df": [29, 32, 36, 41, 42, 45], "fa0087": [29, 36, 42, 45], "0f6632": [29, 36, 42, 45], "266dff": [29, 36, 42, 45], "64661f": [29, 36, 42, 45], "cca73d": [29, 36, 42, 45], "002bcc": [29, 36, 42, 45], "99000d": [29, 36, 42, 45], "5c8899": [29, 36, 42, 45], "473d66": [29, 36, 42, 45], "roi": [29, 31, 32, 33], "renam": [29, 32, 33, 41, 45], "region_of_interest_ord": 29, "color_hex_triplet": [29, 32, 33, 34, 35, 36], "region_of_interest_color": [29, 32, 33], "40k": 29, "1kmb": 29, "somatomotor": 29, "frontal": [29, 35], "pole": [29, 35], "3dcc7c": 29, "motor": 29, "179968": 29, "somatosensori": [29, 35], "gustatori": 29, "viscer": 29, "2e8599": 29, "5ccccc": 29, "auditori": [29, 32], "455a99": 29, "cell_extend": [29, 32, 33, 42, 45], "join": [29, 31, 32, 33, 34, 35, 36, 37, 39, 41, 42, 44, 45], "15": [29, 31, 34, 36, 39, 40, 41, 44, 45], "ccb05c": 29, "27": [29, 31, 33, 36, 37, 38, 40, 41, 42, 45], "10": [29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45], "chol": [29, 32, 42], "dopa": [29, 36, 37, 42], "gaba": [29, 31, 32, 34, 36, 37, 42, 44, 45], "glyc": [29, 36, 42, 45], "hist": [29, 42], "nora": [29, 42], "sero": [29, 37, 42], "1201": [29, 36, 42], "03edff": [29, 42], "0a9964": [29, 36, 42], "533691": [29, 42], "666666": [29, 32, 34, 36, 41, 42, 45], "73e785": [29, 42], "820e57": [29, 36, 42, 45], "ff3358": [29, 32, 36, 42, 45], "fcf04b": [29, 36, 42], "ff7621": [29, 32, 42], "5298": [29, 45], "11": [29, 31, 32, 37, 38, 39, 40, 41, 42, 44, 45], "17": [29, 39, 40, 45], "20": [29, 32, 34, 37, 38, 39, 40, 44], "26": [29, 38, 40, 41, 42], "28": [29, 45], "0059cc": 29, "00990a": 29, "00ffcf": 29, "26aeff": 29, "300099": 29, "341fcc": 29, "34cc1f": 29, "4d58ff": 29, "6f9945": 29, "84ff4d": 29, "8ccc00": 29, "992e6a": 29, "994817": 29, "99922e": 29, "9f3dcc": 29, "b973ff": 29, "cc0026": 29, "cc5cb0": 29, "e4ff26": 29, "ff00ef": 29, "ff2678": 29, "ff7373": 29, "ff8f00": 29, "abov": [29, 30, 36, 37, 40, 41, 42, 44, 45], "written": 29, "howev": [29, 33, 39, 40], "copi": [29, 30, 37, 38, 43], "uniform": [29, 32, 37], "manifold": [29, 32, 37], "project": [29, 32, 34, 37], "dimens": [29, 32, 35], "reduct": [29, 32], "techniqu": [29, 32], "larg": [29, 30, 32, 39], "helper": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "plot": [29, 31, 32, 33, 34, 36, 37, 38, 41, 42, 44, 45], "color": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "eas": [29, 32], "demostr": [29, 32], "do": [29, 32, 36], "simpl": [29, 31, 32, 34, 36, 39], "subsampl": [29, 31, 32, 37], "reduc": [29, 32, 39], "plot_umap": [29, 31, 32, 33, 37, 38], "xx": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "yy": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "none": [29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45], "val": [29, 31, 32, 33, 37, 38, 41, 42, 45], "fig_width": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "fig_height": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "cmap": [29, 31, 32, 33, 35, 37, 38, 41, 42, 44, 45], "fig": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "ax": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "subplot": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "set_size_inch": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "scatter": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "elif": [29, 31, 32, 33, 37, 38, 40, 41, 42, 45], "equal": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "set_xlim": [29, 31, 33, 37, 38, 41, 42, 44, 45], "set_ylim": [29, 31, 33, 37, 38, 41, 42, 44, 45], "set_xtick": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "set_ytick": [29, 31, 32, 33, 37, 38, 41, 42, 44, 45], "return": [29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45], "cell_subsampl": 29, "loc": [29, 30, 31, 34, 35, 36, 37, 38, 44], "404298": 29, "set_titl": [29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 44, 45], "Of": [29, 32], "neuortransmitt": [29, 32, 41, 42], "illumina": 29, "novaseq6000": 29, "read": [29, 31, 33, 37, 38, 39, 42, 44, 45], "mm10": 29, "gencod": 29, "vm23": 29, "ensembl": [29, 42, 45], "98": 29, "genom": 29, "cellrang": 29, "pipelin": [29, 35], "default": [29, 39, 42], "paramet": [29, 33, 39], "id": [29, 42, 45], "practic": [29, 42, 45], "interchang": [29, 42, 45], "symbol": [29, 30, 42, 43, 45], "1173": 29, "comment": [29, 39, 40], "gene_identifi": [29, 30, 33, 39, 40, 42, 43, 45], "gene_symbol": [29, 30, 33, 39, 40, 42, 43, 45], "mapped_ncbi_identifi": [29, 40, 42, 45], "ensmusg00000051951": [29, 40], "xkr4": [29, 40], "kx": [29, 40], "blood": [29, 40], "ncbigen": [29, 40, 42, 45], "497097": [29, 40], "ensmusg00000089699": [29, 40], "gm1992": [29, 40], "predict": [29, 40], "1992": [29, 40], "ensmusg00000102331": [29, 40], "gm19938": [29, 40], "19938": [29, 40], "ensmusg00000102343": [29, 40], "gm37381": [29, 40], "37381": [29, 40], "ensmusg00000025900": [29, 40], "rp1": [29, 40], "retin": [29, 40], "pigmentosa": [29, 40], "19888": [29, 40], "pred": [29, 30, 31, 34, 36, 37, 38, 41, 42, 43, 44, 45], "ensmusg00000118272": 29, "arhgef4": 29, "rho": [29, 45], "guanin": 29, "nucleotid": 29, "exchang": 29, "gef": 29, "ensmusg00000117809": 29, "asdurf": 29, "asnsd1": 29, "upstream": 29, "frame": [29, 33, 39, 42, 45], "110599589": 29, "ensmusg00000047383": 29, "ac169382": 29, "novel": [29, 39], "ensmusg00000097001": 29, "1700054k02rik": 29, "riken": 29, "cdna": 29, "1700054k02": 29, "ensmusg00000116048": 29, "sept2": 29, "septin": 29, "ensmusg00000091585": 29, "ac140365": 29, "prame": [29, 40], "famili": [29, 31, 40, 42, 44, 45], "like": [29, 33, 39, 40, 42], "ensmusg00000095523": [29, 40], "ac124606": [29, 40], "100038995": [29, 40], "ensmusg00000095475": [29, 40], "ac133095": [29, 40], "uncharacter": [29, 40], "loc545763": [29, 40], "545763": [29, 40], "ensmusg00000094855": [29, 40], "loc620639": [29, 40], "620639": [29, 40], "ensmusg00000095019": [29, 40], "ac234645": [29, 40], "divid": [29, 30, 33, 34, 36], "annadata": [29, 30, 33, 39], "minim": [29, 30, 33, 39, 42, 45], "next": [29, 30, 31, 36, 37, 40, 41, 42, 44, 45], "rich": [29, 30, 42, 45], "discuss": [29, 30, 42, 45], "log": [29, 30, 34, 36, 42, 45], "normal": [29, 30, 39, 40, 42, 45], "directoi": 29, "get_data_path": [29, 30, 35, 40, 41, 42, 43, 45], "04g": 29, "02": 29, "1mmb": [29, 40, 45], "read_h5ad": [29, 30, 42, 43, 45], "back": [29, 30, 42, 43, 45], "r": [29, 30, 42, 43, 45], "lazi": [29, 42], "By": [29, 42], "memori": [29, 39, 42], "adata": [29, 42, 43, 45], "n_ob": [29, 42], "n_var": [29, 42], "131212": 29, "ob": [29, 42, 44], "anatomical_division_label": [29, 32, 33, 39], "var": [29, 30, 34, 36, 40, 42, 43], "un": [29, 42], "parent": [29, 34, 36], "parent_lay": 29, "parent_row": 29, "observ": [29, 31, 42, 44], "caggtgcaggctagca": 29, "040_c01": 29, "tgcgcaggttgcgcac": 29, "045_c01": 29, "cgatgtatcttgccgt": 29, "042_b01": 29, "gactaacgtcctcttg": 29, "040_b01": 29, "gatcgtacaactgcta": 29, "easili": 29, "extend": [29, 32, 37, 38], "cell_filt": [29, 30], "130555": [29, 30], "look": [29, 30, 31, 33, 42, 43, 44], "nine": [29, 30, 42, 45], "second": [29, 30, 35, 36, 42, 43], "support": [29, 30, 35, 37, 42, 45], "submatrix": [29, 30, 42, 45], "oper": [29, 30, 36, 42, 45], "take": [29, 30, 33, 34, 36, 39, 42, 43, 45], "around": [29, 30, 36, 39, 42, 45], "ntgene": [29, 30, 31, 42, 43, 44], "slc17a7": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "slc17a6": [29, 30, 31, 33, 37, 39, 42, 43, 44, 45], "slc17a8": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a5": [29, 30, 31, 37, 42, 43, 44, 45], "slc18a3": [29, 30, 31, 37, 43], "slc6a3": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a4": [29, 30, 31, 37, 42, 43, 44, 45], "slc6a2": [29, 30, 31, 37, 43], "exgen": [29, 30, 31, 42, 43, 44], "gname": [29, 30, 31, 33, 37, 42, 43, 44, 45], "gene_filt": [29, 30, 42, 43, 45], "ensmusg00000037771": [29, 30, 42, 43, 45], "ensmusg00000070570": [29, 30, 42, 43, 45], "ensmusg00000039728": [29, 30, 42, 43, 45], "ensmusg00000030500": [29, 30, 42, 43, 45], "ensmusg00000055368": [29, 30], "ensmusg00000019935": [29, 30, 42, 43, 45], "ensmusg00000025400": [29, 30, 42, 43], "ensmusg00000020838": [29, 30, 42, 43, 45], "ensmusg00000021609": [29, 30, 42, 43, 45], "ensmusg00000100241": [29, 30], "process_tim": [29, 30, 42, 43, 45], "asubset": [29, 42], "to_memori": [29, 42], "taken": [29, 30, 39, 42, 43, 45], "630955": 29, "create_expression_datafram": [29, 42], "input": [29, 34, 36, 40, 42], "aggregate_by_metadata": [29, 31, 33, 42, 44], "comput": [29, 31, 33, 40, 41, 42, 44], "given": [29, 31, 33, 34, 36, 40, 42, 44], "categori": [29, 35, 42], "gf": [29, 42], "gdata": [29, 30, 42, 43, 45], "to_df": [29, 30, 42, 43, 45], "sort": [29, 31, 33, 42, 44], "mean": [29, 31, 33, 42, 44], "sort_valu": [29, 31, 32, 33, 34, 35, 36, 38, 41, 42, 44], "ascend": [29, 31, 33, 35, 38, 41, 42, 44], "assign": [29, 31, 34, 36, 42, 44, 45], "compris": [29, 31, 42, 44], "solut": [29, 31, 42, 44, 45], "carrier": [29, 31, 42, 44, 45], "heatmap": [29, 31, 33], "plot_heatmap": [29, 31, 33, 42, 44], "cm": [29, 31, 33, 35, 37, 41, 42, 44, 45], "magma_r": [29, 31, 33, 37, 42, 44, 45], "vmax": [29, 31, 33, 42, 44], "arr": [29, 31, 33, 42, 44], "to_numpi": [29, 31, 33, 42, 44], "imshow": [29, 31, 33, 35, 41, 42, 44], "aspect": [29, 31, 33, 42, 44], "auto": [29, 31, 33, 42, 44], "xlab": [29, 31, 33, 42, 44], "ylab": [29, 31, 33, 42, 44], "rang": [29, 31, 33, 42, 44], "set_xticklabel": [29, 31, 33, 42, 44], "set_yticklabel": [29, 31, 33, 34, 36, 42, 44], "most": [29, 31, 34, 35, 36, 40, 44], "enrich": [29, 31, 37, 42, 44], "cholinerg": [29, 31, 42, 44], "glutamaterg": [29, 31, 33, 34, 36, 37, 38, 42, 44], "gabaerg": [29, 31, 33, 34, 36, 37, 38, 44], "glycinerg": [29, 31, 34, 36, 44], "dopaminerg": [29, 31, 37, 38, 44], "match": [29, 41], "expect": [29, 34, 35, 36, 40], "ntexp": [29, 42], "agg": [29, 31, 33, 42, 44], "encod": [29, 31, 42, 44], "call": [29, 31, 40, 42, 44], "neurokinin": [29, 31, 42, 44], "b": [29, 31, 34, 36, 40, 42, 44], "nkb": [29, 31, 42, 44], "produc": [29, 31, 38, 42, 44], "know": [29, 31, 40, 42, 44], "invovl": [29, 31, 42, 44], "emot": [29, 31, 42, 44], "social": [29, 31, 42, 44], "behavior": [29, 31, 34, 36, 42, 44], "ish": [29, 31, 42, 44], "tac": [29, 31, 42, 44], "spars": [29, 31, 42, 44], "dens": [29, 31, 42, 44], "habenula": [29, 31, 37, 42, 44], "mh": [29, 31, 41, 42, 44], "amygdala": [29, 31, 32, 37, 42, 44], "hypothalamu": [29, 31, 32, 35, 37, 42, 44], "those": [29, 33, 39, 40, 42, 44], "identit": [29, 42], "highli": [29, 31, 34, 42, 44], "folder": [29, 34, 36, 40, 42], "kc": [29, 34, 36, 40, 42], "7glrmt5n67x16yj_tg86t49c0000gp": [29, 34, 36, 40, 42], "t": [29, 33, 34, 36, 40, 42], "ipykernel_15441": 29, "199257058": 29, "py": [29, 31, 34, 36, 39, 40, 42], "futurewarn": [29, 34, 36, 42], "__getitem__": [29, 34, 36, 42], "treat": [29, 34, 36, 42], "kei": [29, 34, 36, 40, 42], "deprec": [29, 34, 36, 42], "futur": [29, 34, 36, 42], "integ": [29, 34, 36, 42], "alwai": [29, 34, 36, 42], "ser": [29, 32, 34, 36, 42], "iloc": [29, 34, 36, 41, 42], "po": [29, 34, 36, 41, 42], "show": [29, 31, 32, 33, 34, 36, 37, 38, 40, 42, 44], "lh": [29, 31, 41, 42, 44], "restrict": [29, 31, 37, 42, 44], "mixtur": [29, 31, 42, 44], "At": [29, 31, 36, 42, 44], "sublcass": [29, 42], "145": [29, 35, 41, 44], "itself": 29, "down": [29, 39, 40], "children": 29, "close": [29, 30, 42, 43, 45], "clean": [29, 42, 43], "del": [29, 30, 33, 42, 43, 45], "canon": [30, 43, 45], "transport": [30, 34, 36, 43, 45], "tac2": [30, 37, 41, 43], "so": [30, 34, 36, 42, 43, 44, 45], "minut": [30, 39, 45], "save": [30, 43], "skip": [30, 33, 42, 43], "cleaner": 30, "general_accessing_10x_snrnaseq_tutori": 30, "both": [30, 33, 36, 40], "cell_count": [30, 41], "43985": 30, "207281": 30, "99879": 30, "248776": 30, "249360": 30, "249356": 30, "248784": 30, "29781": 30, "192182": 30, "181723": 30, "78223": 30, "181055": 30, "162296": 30, "227670": 30, "227537": 30, "337101": 30, "191746": 30, "88560": 30, "143157": 30, "108046": 30, "283782": 30, "130454": 30, "write": [30, 40], "resu": 30, "empti": 30, "total_start": 30, "matindex": 30, "ds": 30, "mp": 30, "exp": [30, 31, 36, 37, 44], "break": 30, "1000140000000016": 30, "74g": 30, "9mmb": [30, 33, 41, 42, 45], "0210620000000006": 30, "10g": 30, "04": [30, 38, 39, 41, 42, 45], "48": [30, 40, 42], "2mmb": [30, 31, 40, 45], "7627419999999745": 30, "140": [30, 34, 35], "118578": 30, "notna": [30, 37, 39, 43], "deep": [30, 34, 43], "252953": 30, "expand": [31, 33, 41, 44], "39g": 31, "47": 31, "miniconda3": [31, 39, 40], "env": [31, 39, 40], "lib": [31, 39, 40], "python3": [31, 39, 40], "site": [31, 39, 40], "398": 31, "dtypewarn": 31, "mix": [31, 36], "specifi": [31, 33, 37, 39, 40, 44], "option": [31, 41], "low_memori": 31, "read_csv": [31, 40], "kwarg": 31, "318m": 31, "5mmb": [31, 44], "catergori": [31, 33, 35, 44], "im": [31, 33, 42], "vmin": [31, 33, 42, 44], "similar": [31, 33, 34, 36, 38, 42, 44], "now": [31, 32, 33, 44], "noradrenerg": [31, 44], "serotonerg": [31, 37, 38, 44], "respect": [31, 35, 36, 39, 44, 45], "cortex": [31, 32, 35, 37, 38, 39, 42], "striatum": [31, 42], "medulla": [31, 35], "rest": [31, 44], "axesimag": 31, "0x11bfd4990": 31, "06": [31, 35, 44, 45], "ctx": [31, 35, 36, 41, 44, 45], "cge": [31, 44, 45], "caudal": [31, 32, 44], "ganglion": [31, 44], "emin": [31, 44], "0x11ccfced0": 31, "bed": [31, 42, 44], "stria": [31, 42, 44], "terminali": [31, 42, 44], "bst": [31, 42, 44], "spinal": [31, 32, 35, 44], "trigemin": [31, 35, 44], "spvc": [31, 44], "central": [31, 35, 44], "amygdalar": [31, 44], "cea": [31, 44], "arcuat": [31, 44], "hypothalam": [31, 37, 44], "arh": [31, 44], "subclass_list": [31, 44], "0x29808f7d0": 31, "enabl": [31, 41, 42, 45], "compar": [31, 33, 41, 42], "profil": [31, 45], "top": [31, 34, 36, 37, 41, 44], "quick": 32, "precomput": [32, 33], "acces": 32, "general_acessing_10x_snrnaseq_tutori": [32, 33], "region_of_interest_label": [32, 33, 39], "1b": 32, "overlap": 32, "should": [32, 33, 39, 40], "seper": [32, 33], "anatomical_division_structure_map": [32, 33], "region_of_interest_structure_map": [32, 33], "3369219": [32, 33, 39], "2205155": 32, "606": 32, "nonneuron": [32, 33, 39], "h18": [32, 39], "001": [32, 33, 39], "002": [32, 33, 39, 45], "h19": [32, 33, 39], "109": [32, 41], "amygdaloid": 32, "basal": [32, 39], "cerebellum": [32, 37, 39], "cerebr": [32, 35, 37, 38, 39], "claustrum": 32, "hippocampu": [32, 42], "myelencephalon": [32, 33, 39], "pon": [32, 33, 35, 39], "cord": [32, 35], "membership_groupbi": 32, "cluster_annotation_term_set_nam": [32, 33, 34, 36], "02m": 32, "20mmb": 32, "cluster_annotation_term_label": [32, 34, 36], "cluster_annotation_term_set_label": [32, 34, 36], "cluster_annotation_term_nam": [32, 33, 34, 36], "number_of_cel": [32, 34, 36, 37, 38, 41], "cs202210140_494": [32, 34], "ccn202210140_subc": [32, 34], "url_297_0": [32, 34], "7e807a": [32, 34], "cs202210140_495": [32, 34], "url_308_1": [32, 34], "220": [32, 34], "c54945": [32, 34], "cs202210140_496": [32, 34], "url_308_2": [32, 34], "187": [32, 34], "5232b7": [32, 34], "cs202210140_497": [32, 34], "url_308_3": [32, 34], "246": [32, 34, 40], "31beba": [32, 34], "cs202210140_498": [32, 34], "url_308_4": [32, 34], "188": [32, 34], "c8a9bc": [32, 34], "term_set": [32, 33, 34, 35, 36], "unstack": [32, 33, 34, 35, 36, 37], "fillna": [32, 33, 34, 36], "33k": 32, "7kmb": [32, 40], "2461": 32, "amex_153_2461": 32, "amex_153": 32, "excitatori": 32, "vglut1": [32, 33, 34], "vglut2": 32, "2462": 32, "amex_153_2462": 32, "2463": 32, "amex_153_2463": 32, "2464": 32, "amex_153_2464": 32, "2465": 32, "amex_153_2465": 32, "2218": 32, "374b8a": 32, "062463": 32, "003380": 32, "2bdfd1": [32, 33, 34], "2216": 32, "4bcbc6": 32, "2217": 32, "83c943": 32, "2219": 32, "bc4440": 32, "2220": 32, "cb7aba": 32, "82k": 32, "125kmb": 32, "structure_identifi": 32, "structure_symbol": 32, "structure_nam": 32, "a13": 32, "dhba": 32, "10202": 32, "ofci": 32, "cab781": 32, "a14": 32, "10196": 32, "a14r": 32, "rostral": 32, "subdivis": 32, "b8a26d": 32, "10197": 32, "a14c": 32, "a19": 32, "10272": 32, "psc": 32, "peristri": 32, "d14d46": 32, "a1c": 32, "10236": 32, "core": [32, 40], "d670a0": 32, "rsuffix": [32, 33, 37], "_color": [32, 33], "subcluster_color": [32, 33, 34], "supercluster_color": [32, 33, 34], "10x386_2": [32, 33, 39], "catggattctcgacgg": [32, 33, 39], "lktx_210825_01_b01": [32, 33, 39], "cx": [32, 33, 39], "51": [32, 33, 39, 44], "url_312_20": [32, 33], "url_312": [32, 33], "upper": [32, 33, 34], "rhombic": [32, 33, 34], "lip": [32, 33, 34], "4cb941": [32, 33], "97b8c8": [32, 33], "80ba": [32, 33, 34], "5d6cb2": [32, 33], "10x383_5": [32, 33, 39], "tcttgcggtgaattga": [32, 33, 39], "lktx_210818_02_e01": [32, 33, 39], "bs": [32, 33, 39], "94": [32, 33, 39], "ctcatcggtcgagcaa": [32, 33, 39], "url_312_17": [32, 33], "c85e40": [32, 33], "10x378_8": [32, 33, 39], "ttggatgagacaagcc": [32, 33, 39], "lktx_210809_01_h01": [32, 33, 39], "93": [32, 33, 34, 39], "url_312_18": [32, 33], "61c1c2": [32, 33], "517dbe": [32, 33], "10x387_7": [32, 33, 39], "tgaacgtagtattccg": [32, 33, 39], "lktx_210825_02_g01": [32, 33, 39], "url_312_16": [32, 33], "45328f": [32, 33], "vglut3": 32, "da": 32, "hdc": 32, "gly": [32, 36, 45], "196aa5": 32, "2252c2": 32, "22a5bb": 32, "2b39df": 32, "3f38b8": 32, "423b77": 32, "4f90b2": 32, "4fe3ab": 32, "6b0c48": 32, "8bad78": 32, "8c4f7f": 32, "8c7063": 32, "95369c": 32, "c6525e": 32, "ff553d": 32, "ve": 32, "merg": 32, "neurons_subsampl": [32, 33], "non_neurons_subsampl": [32, 33], "n": [32, 34, 36, 37, 38, 39, 40], "303681": 32, "107871": 32, "ll": [32, 33, 39, 40], "focu": 32, "done": [33, 40], "previous": [33, 37], "memembership": 33, "deeper": 33, "dive": 33, "again": 33, "hold": 33, "biotyp": [33, 39], "ensg00000000003": [33, 39], "tspan6": [33, 39], "protein_cod": [33, 39], "tetraspanin": [33, 39], "ensg00000000005": [33, 39], "tnmd": [33, 39], "tenomodulin": [33, 39], "ensg00000000419": [33, 39], "dpm1": [33, 39], "dolichyl": [33, 39], "phosphat": [33, 39], "mannosyltransferas": [33, 39], "subunit": [33, 39], "ensg00000000457": [33, 39], "scyl3": [33, 39], "scy1": [33, 39], "pseudokinas": [33, 39], "ensg00000000460": [33, 39], "c1orf112": [33, 39], "chromosom": [33, 39], "112": [33, 35, 39], "ptprc": [33, 39], "plp1": [33, 39], "aqp4": [33, 39], "ttr": [33, 39], "example_cells_with_gen": 33, "233m": 33, "000000": [33, 35, 41], "652457": 33, "484976": 33, "006844": 33, "348821": 33, "046448": 33, "cell_extended_with_gen": 33, "becaus": 33, "immun": 33, "oligodendrocyt": [33, 34], "astrocyt": 33, "choroid": 33, "plexu": 33, "much": [33, 40], "higher": 33, "relev": 33, "what": [33, 40], "variou": 33, "seven": 33, "vs": 33, "idend": 33, "And": 33, "final": [33, 34, 36, 41], "could": [33, 39], "aren": 33, "shown": [33, 40], "than": [34, 40], "almost": 34, "overload": 34, "while": [34, 36, 40], "string": [34, 35, 36, 37, 39, 40], "84": [34, 41, 45], "8k": [34, 40], "433kmb": 34, "3308": 34, "cs202210140_3802": 34, "3309": 34, "138": 34, "cs202210140_3803": 34, "3310": 34, "85": 34, "cs202210140_3804": 34, "3311": 34, "cs202210140_3805": 34, "3312": 34, "74": 34, "cs202210140_3806": 34, "readabl": [34, 35, 36, 37], "descript": [34, 35, 36, 37, 38], "among": [34, 35, 36], "finest": [34, 36], "ccn202210140_clu": 34, "intermedi": [34, 35], "ccn202210140_supc": 34, "h": 34, "ccn202210140_neur": 34, "iterrow": [34, 36, 37], "tsindex": [34, 36, 37], "tsrow": [34, 36, 37], "louvain": 34, "independ": 34, "characterist": [34, 36], "belong": [34, 36], "state": 34, "togeth": [34, 36, 37, 41], "anoth": 34, "cytograph": 34, "broader": [34, 36], "character": 34, "lack": 34, "enzym": [34, 36], "superclass": [34, 36], "form": [34, 36], "547k": 34, "87mmb": 34, "parent_term_label": [34, 35, 36], "parent_term_set_label": [34, 35, 36], "term_set_ord": [34, 35, 36], "term_ord": [34, 35, 36], "cs202210140_476": 34, "intratelencephal": 34, "fea7ba": 34, "455006": 34, "cs202210140_477": 34, "426600": 34, "228467": 34, "cs202210140_473": 34, "ee1010": 34, "18856": 34, "cs202210140_474": 34, "corticothalam": 34, "6b": [34, 35], "5ef0f1": 34, "78396": 34, "cs202210140_484": 34, "mge": 34, "interneuron": 34, "dffe66": 34, "222434": 34, "talli": [34, 36], "unlik": 34, "term_cluster_count": [34, 36], "number_of_clust": [34, 36, 37], "cs202210140_1": 34, "cs202210140_10": 34, "cs202210140_100": 34, "cs202210140_1000": 34, "cs202210140_1001": 34, "term_by_label": [34, 36], "term_with_count": [34, 35, 36], "139": 34, "72": 34, "116": 34, "211": 34, "let": [34, 36, 42], "bar": [34, 36], "bar_plot_by_level_and_typ": [34, 36], "idx": [34, 36, 37, 38, 44], "ctype": [34, 36], "enumer": [34, 35, 36, 37, 38, 44, 45], "number_of_": [34, 36], "barh": [34, 36], "set_xscal": [34, 36], "splatter": 34, "largest": [34, 36], "1k": 34, "fuunction": [34, 35, 36, 37], "url_297": 34, "url_308": 34, "nkcell_2_3308": 34, "nkcell_2": 34, "miscellan": 34, "nkcell_2_3309": 34, "nkcell_2_3310": 34, "nkcell_2_3311": 34, "nkcell_2_3312": 34, "f9f9f9": [34, 36], "s_color": [34, 35, 36], "909ff6": 34, "a5b0d9": 34, "3d84ba": 34, "e2ee30": 34, "fefe00": 34, "c25347": 34, "b9bfb4": 34, "6cc93d": 34, "423149": 34, "pair": [34, 36], "axb": [34, 36], "b_name": [34, 36], "term_by_nam": [34, 36], "b_color": [34, 36], "stacked_bar_distribut": [34, 36], "bottom": [34, 36], "i": [34, 35, 36, 37, 45], "col": [34, 36], "left": [34, 35, 36, 37], "arrai": [34, 35, 36, 40], "legend": [34, 36], "bbox_to_anchor": [34, 36], "ipykernel_15202": 34, "1772253940": [34, 36], "sunburst": [34, 36], "diagram": [34, 36], "inherit": [34, 36], "ring": [34, 36], "outer": [34, 36], "angl": [34, 36, 41], "proport": [34, 36], "lvl": [34, 36], "pie": [34, 36], "rotatelabel": [34, 36], "labeldist": [34, 36], "025": [34, 36], "radiu": [34, 36], "wedgeprop": [34, 36], "dict": [34, 36, 40], "width": [34, 36], "edgecolor": [34, 36], "startangl": [34, 36], "els": [34, 35, 36, 40, 44], "informat": 35, "onlin": 35, "applic": 35, "multiscal": 35, "openli": 35, "asset": 35, "request": [35, 39, 40], "simpleitk": [35, 40, 41], "sitk": [35, 41], "There": [35, 40, 42, 45], "volumetr": 35, "allenccfv3": 35, "average_template_10": [35, 40], "construct": 35, "shape": 35, "intens": 35, "1675": 35, "specim": 35, "annotation_10": [35, 40], "heirach": 35, "partonomi": 35, "annotation_boundary_10": [35, 40], "mask": 35, "boundari": 35, "compress": 35, "nifti": 35, "nii": [35, 40, 41], "gz": [35, 40, 41], "average_template_imag": [35, 41], "readimag": [35, 41], "average_template_arrai": [35, 41], "getarrayviewfromimag": [35, 41], "annotation_imag": [35, 41], "annotation_arrai": [35, 41], "annotation_boundary_imag": [35, 41], "annotation_boundary_arrai": [35, 41], "image_info": [35, 41], "img": [35, 41], "getsiz": [35, 41], "getspac": [35, 41], "mm": [35, 41], "getdirect": [35, 41], "getorigin": [35, 41], "1320": 35, "800": 35, "1140": 35, "micromet": 35, "asl": 35, "superior": 35, "inferior": 35, "dorsal": 35, "ventral": 35, "third": 35, "right": 35, "009999999776482582": [35, 41], "695000171661377": 35, "349999904632568": 35, "21999979019165": 35, "voxel_volum": 35, "2e": 35, "00e": 35, "sanm": 35, "plot_sect": [35, 37, 38, 41, 42, 44, 45], "greys_r": [35, 41], "off": 35, "zindex": [35, 41], "720": 35, "zslice": 35, "transpos": 35, "average_templ": 35, "grei": [35, 41], "tile": 35, "parcellation_index": [35, 41, 45], "688": 35, "voxel_count": 35, "volume_mm3": 35, "987": 35, "allenccf": 35, "997": 35, "3564320": 35, "564320": 35, "63": 35, "68": 35, "256520": 35, "657": 35, "667": 35, "232608": 35, "1288": 35, "526157192": 35, "371584": 35, "1289": 35, "526157196": 35, "112222": 35, "135": 35, "405256": 35, "499566": 35, "148": [35, 37], "153": 35, "461680": 35, "159": 35, "164": 35, "432": 35, "000432": 35, "697783214": 35, "697": 35, "783214": 35, "simplif": 35, "heirarchi": [35, 36], "parcellation_term_set": [35, 40], "parcellation_terminology_label": 35, "ontolog": 35, "2017": [35, 40], "orga": 35, "cate": 35, "divi": 35, "stru": 35, "sub": [35, 39], "substructur": [35, 41, 45], "hex": 35, "triplet": 35, "rgb": 35, "parcellation_term": [35, 40], "1631": 35, "graph_ord": 35, "red": 35, "green": 35, "blue": 35, "parent_identifi": 35, "ffffff": [35, 41], "mba": 35, "255": 35, "bfdae3": [35, 41], "191": 35, "218": 35, "227": [35, 40], "567": [35, 40], "ch": 35, "cerebrum": 35, "b0f0ff": 35, "240": [35, 40], "b0ffb8": 35, "184": 35, "695": 35, "ctxpl": 35, "cortic": [35, 37, 42], "plate": [35, 42], "70ff70": 35, "memership": 35, "parcellation_term_set_membership": [35, 40], "1293": 35, "parcellation_term_label": 35, "parcellation_term_set_label": 35, "1009": 35, "73": [35, 41], "315": 35, "parcellation_annot": [35, 41, 45], "parcellation_to_parcellation_term_membership": [35, 40], "3440": 35, "parcellation_label": 35, "parcellation_term_nam": 35, "parcellation_term_acronym": 35, "parcellation_term_set_nam": 35, "70ff71": [35, 41], "113": 35, "268f45": 35, "38": [35, 37, 38, 40, 42, 44], "143": [35, 36], "3435": 35, "v4": 35, "aaaaaa": 35, "170": 35, "fourth": 35, "ventricl": 35, "unassign": [35, 41], "367": [35, 40], "3436": 35, "885": 35, "3437": 35, "v4r": 35, "recess": 35, "886": 35, "3438": 35, "canal": 35, "369": [35, 40], "3439": 35, "887": 35, "term_parcellation_count": 35, "number_of_parcel": 35, "687": 35, "597": 35, "241": [35, 40], "313": 35, "59": [35, 36, 41, 42], "10703": 35, "10704": 35, "1072": 35, "1074": 35, "998": 35, "term_voxel_count": 35, "sum": [35, 36], "ca1": [35, 41], "000006": 35, "1051": [35, 37], "000004": 35, "ca3": 35, "000002": 35, "545": 35, "inner": [35, 41, 45], "506056786": 35, "506": 35, "056786": 35, "449681182": 35, "449": 35, "681182": 35, "123282624": 35, "123": 35, "282624": 35, "973876": 35, "frp1": 35, "valid": [35, 40], "alist": 35, "aa": 35, "vlist": 35, "parcellation_term_with_count": [35, 40], "distribut": 35, "tmv": [35, 41], "m6b": [35, 41], "lfb": [35, 41], "cst": [35, 41], "int": [35, 39, 41], "psv": [35, 41], "1323": 35, "ipn": 35, "ipi": 35, "1324": 35, "ipdm": 35, "1325": 35, "ipdl": 35, "1326": 35, "iprl": 35, "1327": 35, "pag": [35, 39, 41], "su3": 35, "tuberomammillari": 35, "mouth": 35, "bundl": 35, "corticospin": 35, "intern": 35, "capsul": 35, "princip": [35, 37], "sensori": 35, "interpeduncular": 35, "dorsomedi": 35, "dorsolater": 35, "rostrolater": 35, "periaqueduct": 35, "supraoculomotor": 35, "organ_color": 35, "category_color": 35, "division_color": 35, "structure_color": 35, "substructure_color": 35, "e64438": [35, 41], "ff4c3e": [35, 41], "188064": [35, 41], "cccccc": [35, 41], "ff9b88": [35, 41], "ffae6f": [35, 41], "ff64ff": 35, "ffa6ff": 35, "ff90ff": 35, "channel": 35, "230": 35, "204": 35, "parcellation_to_parcellation_term_membership_acronym": [35, 40, 41, 45], "parcellation_to_parcellation_term_membership_nam": [35, 40], "parcellation_to_parcellation_term_membership_color": [35, 40, 41, 45], "parcellation_to_parcellation_term_membership_": 35, "sshape": 35, "uint8": 35, "temp": 35, "flat": [35, 45], "represnt": [36, 37], "727": 36, "cs20230722_0001": 36, "740": 36, "cs20230722_0010": 36, "1053": 36, "cs20230722_0100": 36, "1000": [36, 42], "cs20230722_1000": 36, "1001": 36, "96": [36, 40], "cs20230722_1001": 36, "ccn20230722_neur": 36, "ccn20230722_cla": 36, "ccn20230722_subc": 36, "ccn20230722_supt": 36, "definitio": 36, "ccn20230722_clu": 36, "synthes": 36, "primarili": 36, "categor": 36, "cs20230722_neur_glut": 36, "cs20230722_neur_na": 36, "na": 36, "cs20230722_neur_gaba": 36, "cs20230722_neur_dopa": 36, "particular": 36, "0001": 36, "cla": 36, "epd": 36, "car3": 36, "glut_1": [36, 41, 42], "instead": 36, "cs20230722_supt_0001": 36, "cs20230722_clus_000": 36, "find": [36, 39, 44], "term_name_count": 36, "usage_count": 36, "name_clash_term": 36, "382": 36, "1583": 36, "cs20230722_clus_0001": 36, "00664e": 36, "1584": 36, "cs20230722_clus_0002": 36, "0002": 36, "5c79cc": 36, "1585": 36, "cs20230722_clus_0003": 36, "0003": 36, "86ff4d": 36, "1586": 36, "cs20230722_clus_0004": 36, "0004": 36, "cc563d": 36, "128": [36, 37], "4262": 36, "129": [36, 37], "3222": 36, "130": [36, 37], "12216": 36, "9334": 36, "cs20230722_clus_0005": 36, "131": 36, "0005": 36, "1056": 36, "e7ff26": 36, "cs20230722_clas_01": 36, "402": 36, "cs20230722_clas_02": 36, "83": 36, "cs20230722_clas_03": 36, "cs20230722_clas_04": 36, "cs20230722_clas_05": 36, "105": 36, "term_cell_count": 36, "1095484": 36, "310198": 36, "4767": 36, "84352": 36, "107502": 36, "2561": 36, "2054137": 36, "127": 36, "1089152": 36, "1991": 36, "834601": 36, "9396": 36, "62": [36, 39], "8989": 36, "datafarm": 36, "600": 36, "34368": [36, 37, 45], "288": [36, 45], "mdrn": [36, 45], "hoxb5": [36, 45], "ebf2": [36, 45], "1102": [36, 45], "gaba_1": [36, 45], "4955": [36, 45], "34372": [36, 37, 45], "285": [36, 45], "lhx1": [36, 45], "1091": [36, 45], "gaba_3": [36, 45], "4901": [36, 45], "34374": [36, 37, 45], "4902": [36, 45], "34376": [36, 37, 45], "4903": [36, 45], "34380": [36, 37, 45], "1095": [36, 45], "gaba_7": [36, 45], "4924": [36, 45], "0096c7": [36, 45], "660038": [36, 45], "5ccca4": [36, 45], "500099": [36, 45], "f20985": [36, 45], "976df9": [36, 45], "0f6627": [36, 45], "2e4799": [36, 45], "15ff00": [36, 45], "ff2b26": [36, 45], "459988": [36, 45], "50": [36, 38, 39, 42], "ipykernel_77026": 36, "cluster_group": 37, "62k": 37, "0kmb": 37, "group_typ": 37, "ccn20230722_hy": [37, 38], "ea": 37, "hypotha": [37, 38], "1404": 37, "ccn20230722_mb": [37, 38], "hb": 37, "1040": 37, "1431": 37, "ccn20230722_nn": [37, 38], "imn": [37, 41, 42], "gc": 37, "nn": [37, 45], "immatur": [37, 38], "granul": [37, 38], "248": 37, "ccn20230722_pallium": [37, 38], "pallium": 37, "de": [37, 38], "517": 37, "ccn20230722_subpallium": [37, 38], "subpallium": 37, "telencephal": [37, 38], "ccn20230722_th": [37, 38], "epi": [37, 40], "epitha": [37, 38], "ccn20230722_wholebrain": [37, 38], "wholebrain": [37, 38], "clust": [37, 38], "dentat": 37, "gyru": 37, "pineal": 37, "gland": 37, "deriv": 37, "development": 37, "hippocamp": 37, "subplat": 37, "preoptic": 37, "epithalamu": 37, "e": [37, 40], "group_membership": 37, "cluster_group_membership": 37, "674k": 37, "78mmb": 37, "cluster_label": 37, "cluster_group_label": [37, 38], "cluster_group_nam": 37, "cs20230722_0128": 37, "cs20230722_0129": 37, "cs20230722_0130": 37, "pca": 37, "preform": 37, "pc": 37, "2d": [37, 41], "dimension_reduct": [37, 38], "68k": 37, "6kmb": 37, "umap20230830": [37, 38, 40], "295448": [37, 38], "186775": [37, 38], "180669": [37, 38], "1418529": [37, 38], "1494801": [37, 38], "611423": [37, 38], "126171": [37, 38, 40], "boolean": 37, "cluster_group_membership_pivot": 37, "conveni": 37, "joined_10x": 37, "glabel": 37, "f5f5f5": [37, 38], "maps_by_group": 37, "mlabel": [37, 38], "coord": [37, 38], "7m": 37, "31mmb": 37, "neighborhoo": 37, "orig": 37, "resus": 37, "neighborhood_exp": 37, "slc17ab": 37, "glutamerg": 37, "begin": 37, "02g": 37, "49": [37, 39, 40], "6mmb": [37, 41, 45], "joined_merfish": 37, "properti": 37, "blist": [37, 38, 44], "bsl": [37, 38, 44], "vv": [37, 38, 44], "subplots_adjust": [37, 38, 44], "wspace": [37, 38, 44], "hspace": [37, 38, 44], "subgroup": 37, "46": [37, 38, 41, 44], "40": [37, 38, 41, 42, 45], "36": [37, 38, 40, 41, 45], "32": [37, 39, 45], "cell_10x": 38, "10x_cell_metadata_with_group_membership": 38, "cell_merfish": 38, "merfish_cell_metadata_with_group_membership": 38, "3938808": [38, 42, 43], "fetch_coord": 38, "52": 38, "44": 38, "60": 38, "amount": 39, "analy": 39, "care": 39, "simplili": 39, "paral": 39, "scale": [39, 41], "leav": 39, "still": 39, "attempt": [39, 40], "too": 39, "anndata_util": 39, "similarli": 39, "piec": 39, "instanti": [39, 40], "705m": 39, "533584": 39, "230048": 39, "moan": 39, "307856": 39, "542040": 39, "mosr": 39, "740066": 39, "186017": 39, "926133": 39, "015151": 39, "pnan": 39, "622083": 39, "561958": 39, "10x194_8": 39, "gaaatgagttcggctg": 39, "lktx_190529_02_h01": 39, "154318": 39, "585480": 39, "3264": 39, "sn": 39, "10x350_4": 39, "tttaccatcgcacgac": 39, "lktx_210421_03_d01": 39, "906175": 39, "914979": 39, "3265": 39, "cbdn": 39, "10x225_1": 39, "agaagcgtccatatgg": 39, "lktx_190913_02_a01": 39, "091915": 39, "212210": 39, "10x221_5": 39, "ttgaacgcagccttct": 39, "lktx_190830_01_e01": 39, "665837": 39, "993120": 39, "stg": 39, "10x385_3": 39, "ctacccagtggcgctt": 39, "lktx_210818_04_c01": 39, "579284": 39, "853419": 39, "gpi": 39, "23m": 39, "17mmb": 39, "ensg00000288638": 39, "al627443": 39, "lncrna": 39, "ensg00000288639": 39, "ac093246": 39, "protein": [39, 42, 45], "ensg00000288642": 39, "cdr1": 39, "cerebellar": 39, "degener": 39, "ensg00000288643": 39, "ac114982": 39, "ensg00000288645": 39, "ac084756": 39, "would": [39, 40], "onc": [39, 40], "uncompress": 39, "avoid": [39, 40], "chunk": 39, "recombin": 39, "output": [39, 40], "gene_nam": 39, "adjust": 39, "addition": [39, 40], "funciton": 39, "31msignatur": 39, "0m": 39, "0mget_gene_data": 39, "34m": 39, "0mabc_atlas_cach": 39, "0mabc_atlas_access": 39, "0mabc_project_cach": 39, "0mabcprojectcach": 39, "0mall_cel": 39, "0mpanda": 39, "0mcore": 39, "0mframe": 39, "0mdatafram": 39, "0mall_gen": 39, "0mselected_gen": 39, "0mlist": 39, "0mstr": 39, "0mdata_typ": 39, "0mchunk_siz": 39, "0mint": 39, "36m8192": 39, "31mdocstr": 39, "mai": [39, 40], "potenti": 39, "instanc": 39, "all_cel": 39, "all_gen": 39, "selected_gen": 39, "data_typ": 39, "kind": [39, 40], "chunk_siz": 39, "8192": 39, "io": 39, "output_gene_data": 39, "31mfile": 39, "31mtype": 39, "hour": 39, "depend": [39, 40, 45], "speed": 39, "gene_data": 39, "ngene_data": 39, "quicker": 39, "roughli": 39, "hand": [39, 42], "complet": [39, 40], "nonneuron_cel": 39, "78g": 39, "0mmb": [39, 40, 41, 45], "133": 39, "182634": 39, "219": 39, "19582499999999": 39, "10x362_3": 39, "tcagtgagtattgacc": 39, "177927": 39, "10x362_5": 39, "tccgtgtgtgaaagtt": 39, "262379": 39, "cacgggtagagcagaa": 39, "240114": 39, "gattcttgtatgtcac": 39, "314513": 39, "10x362_6": 39, "aggacttgtatccttt": 39, "736156": 39, "210833": 39, "587301": 39, "006084": 39, "567961": 39, "119619": 39, "888263": 39, "thu": 39, "recommend": 40, "enviro": 40, "pip": 40, "u": 40, "git": 40, "http": 40, "github": 40, "com": 40, "alleninstitut": 40, "morriscb": 40, "updatejupyterbook": 40, "clone": 40, "revis": 40, "privat": 40, "req": 40, "build": 40, "k_k2xa_5": 40, "command": 40, "blob": 40, "quiet": 40, "checkout": 40, "switch": 40, "branch": 40, "commit": 40, "5cbeb4e1fe7ebb6492696b6dae9a76697b8c4cd0": 40, "25ldone": 40, "25h": 40, "wheel": 40, "pyproject": 40, "toml": 40, "25hrequir": 40, "satisfi": 40, "post1": 40, "boto3": 40, "55": 40, "ghp": 40, "moto": 40, "pydant": 40, "pytest": 40, "scipi": 40, "tqdm": 40, "api": 40, "compat": 40, "h5py": 40, "natsort": 40, "dateutil": 40, "post0": 40, "pytz": 40, "tzdata": 40, "2022": 40, "botocor": 40, "35": [40, 41], "jmespath": 40, "s3transfer": 40, "contourpi": 40, "cycler": 40, "fonttool": 40, "kiwisolv": 40, "pillow": 40, "pypars": 40, "cryptographi": 40, "42": 40, "xmltodict": 40, "werkzeug": 40, "respons": 40, "jinja2": 40, "charset": 40, "idna": 40, "urllib3": 40, "certifi": 40, "extens": 40, "iniconfig": 40, "pluggi": 40, "cffi": 40, "markupsaf": 40, "six": [40, 45], "pyyaml": 40, "pycpars": 40, "filenam": 40, "py3": 40, "whl": 40, "20811": 40, "sha256": 40, "d8098f32f446e44b53e54ad633cdea61188d55b3cc708d45cb702c309ee9224c": 40, "ephem": 40, "c8464kd3": 40, "d8": 40, "c5": 40, "498927e9ff1fdc24cca5fd8a35f6daeb0d2b61623f3ee82a07": 40, "successfulli": 40, "built": 40, "uninstal": 40, "exist": 40, "restart": 40, "kernel": 40, "drop": [40, 41], "menu": 40, "uncom": 40, "get_ipython": 40, "do_shutdown": 40, "setup": 40, "usabl": 40, "just": 40, "list_manifest_file_nam": 40, "load_manifest": 40, "last": 40, "session": 40, "upon": 40, "warn": 40, "thrown": 40, "older": 40, "recent": 40, "stick": 40, "confus": 40, "old": 40, "latest": 40, "load_latest_manifest": 40, "cloud_cach": 40, "outdatedmanifestwarn": 40, "date": 40, "compare_manifest": 40, "onto": 40, "self": 40, "list_all_downloaded_manifest": 40, "If": 40, "want": 40, "msg": 40, "rais": 40, "except": 40, "g": 40, "expression_matrici": 40, "list_directori": 40, "befor": 40, "get_directory_data_s": 40, "get_directory_metadata_s": 40, "65": 40, "guid": 40, "signific": 40, "allen_ccf_list": 40, "get_directory_data": 40, "5m": 40, "8mmb": [40, 45], "4m": 40, "3mmb": [40, 45], "343m": 40, "131k": 40, "838kmb": 40, "861k": 40, "60mmb": 40, "11k": 40, "902k": 40, "30mmb": 40, "21m": 40, "239k": 40, "99mmb": 40, "531k": 40, "41mmb": 40, "without": 40, "get_metadata_path": 40, "30m": 40, "95mmb": 40, "accept": 40, "argment": 40, "32280": 40, "32281": 40, "32282": 40, "32283": 40, "32284": 40, "ensmusg00000095041": 40, "ac149090": 40, "throw": 40, "error": [40, 42, 45], "ambigu": 40, "89": [40, 45], "3m": 40, "03": [40, 42, 45], "keyerror": 40, "traceback": 40, "line": 40, "477": 40, "force_download": 40, "skip_hash_check": 40, "472": 40, "data_path": 40, "_get_local_path": 40, "473": 40, "474": 40, "475": 40, "476": 40, "download_data": 40, "478": 40, "479": 40, "480": 40, "481": 40, "482": 40, "483": 40, "822": 40, "cloudcachebas": 40, "788": 40, "789": 40, "790": 40, "793": 40, "bool": 40, "794": 40, "795": 40, "796": 40, "797": 40, "necessari": 40, "820": 40, "821": 40, "super_attribut": 40, "823": 40, "824": 40, "file_attribut": 40, "825": 40, "395": 40, "basiclocalcach": 40, "366": 40, "368": 40, "test": 40, "393": 40, "394": 40, "_get_file_path": 40, "397": 40, "321": 40, "292": 40, "293": 40, "294": 40, "295": 40, "319": [40, 45], "320": 40, "_manifest": 40, "get_file_attribut": 40, "323": 40, "324": 40, "325": 40, "_file_exist": 40, "326": 40, "local_path": 40, "238": 40, "226": 40, "_create_file_attribut": 40, "remote_path": 40, "files_data": 40, "file_typ": 40, "228": 40, "url": 40, "235": [40, 41, 42], "file_hash": 40, "noqa": 40, "e501": 40, "236": 40, "237": 40, "239": 40, "pleas": 40, "242": 40, "243": 40, "244": 40, "245": [40, 45], "247": 40, "corrupt": 40, "accidenti": 40, "delet": 40, "inividu": 40, "64mmb": 40, "07": [40, 45], "against": 40, "recommened": 40, "overhead": 40, "assum": 40, "46m": 40, "ctcacactcgtagatc": 40, "044_d01": 40, "603476": 40, "148670": 40, "ccgtactcatccaaca": 40, "036_d01": 40, "817812": 40, "366151": 40, "agcggtccatgggaac": 40, "037_a01": 40, "798783": 40, "577992": 40, "gatgaggcatgttccc": 40, "037_b01": 40, "188138": 40, "892220": 40, "tagtggtaggcgacat": 40, "715829": 40, "606307": 40, "126166": 40, "tttgttgtccgacata": 40, "290_b01": 40, "042111": 40, "349521": 40, "126167": 40, "tttgttgtcgtctacc": 40, "294_b05": 40, "630137": 40, "033476": 40, "126168": 40, "tttgttgtcgttcctg": 40, "463_a05": 40, "848272": 40, "645908": 40, "126169": 40, "tttgttgtcgttgcct": 40, "621_a02": 40, "982306": 40, "718120": 40, "126170": 40, "tttgttgtctttcgat": 40, "574_a02": 40, "292696": 40, "804039": 40, "41": 40, "2k": 40, "606kmb": 40, "177k": 40, "27mmb": 40, "628": 40, "04kmb": 40, "114k": 40, "956kmb": 40, "137k": 40, "908kmb": 40, "680k": 40, "71mmb": 40, "3k": 40, "8kmb": 40, "parcellation_to_parcellation_term_membership_blu": 40, "4k": [40, 42], "232kmb": 40, "5k": 40, "432kmb": 40, "parcellation_to_parcellation_term_membership_green": 40, "234kmb": 40, "315kmb": 40, "parcellation_to_parcellation_term_membership_r": 40, "0k": 40, "215kmb": 40, "micron": [41, 42], "plane": 41, "init": 41, "ant": 41, "establish": 41, "5d": 41, "multi": 41, "symmetr": 41, "diffeomorph": 41, "finer": 41, "x_section": 41, "y_section": 41, "z_section": 41, "average_correlation_scor": [41, 42], "1019171907102340387": [41, 42], "37": [41, 42], "1408": [41, 42], "596276": [41, 42], "226245": [41, 42], "148963": [41, 42], "dg": [41, 42], "038": [41, 42], "pir": [41, 42], "ex": [41, 42], "0141": [41, 42], "imn_2": [41, 42], "0515": [41, 42], "16f2f2": [41, 42], "3d53cc": [41, 42], "cc7a3d": [41, 42], "73ffbf": [41, 42], "1104095349101460194": [41, 42], "4218": [41, 42], "641180": [41, 42], "064889": [41, 42], "309543": [41, 42], "pg": [41, 42], "trn": [41, 42], "lrn": [41, 42], "fat2": [41, 42], "0953": [41, 42], "4199": [41, 42], "6b5ca5": [41, 42], "9b7acc": [41, 42], "990041": [41, 42], "663d63": [41, 42], "1017092617101450577": [41, 42], "763531": [41, 42], "792921": [41, 42], "189973": [41, 42], "1018093344101130233": [41, 42], "558073": [41, 42], "195950": [41, 42], "868655": [41, 42], "1019171912201610094": [41, 42], "591009": [41, 42], "635732": [41, 42], "995842": [41, 42], "reconstructed_coord": 41, "reconstructed_coordin": 41, "x_reconstruct": 41, "y_reconstruct": 41, "z_reconstruct": 41, "256m": 41, "1019171911101460569": 41, "143894": 41, "890964": 41, "945": 41, "1019171911101550321": 41, "188673": 41, "962972": 41, "1019171911100841066": 41, "859447": 41, "908534": 41, "893": 41, "1019171911101400425": 41, "952014": 41, "564086": 41, "842": 41, "1019171911101380264": 41, "803546": 41, "221688": 41, "cell_join": 41, "255606": 41, "007680": 41, "1160": 41, "036436": 41, "264429": 41, "564": 41, "784270": 41, "007646": 41, "761": 41, "161528": 41, "719814": 41, "718": 41, "618763": 41, "847877": 41, "ccf_coord": 41, "ccf_coordin": [41, 45], "x_ccf": [41, 45], "y_ccf": [41, 45], "z_ccf": [41, 45], "296m": 41, "282330": 41, "987808": 41, "385773": 41, "192214": 41, "002155": 41, "366855": 41, "500341": 41, "750392": 41, "074634": 41, "231647": 41, "544816": 41, "128568": 41, "238502": 41, "135836": 41, "948194": 41, "495417": 41, "445872": 41, "455066": 41, "227966": 41, "133693": 41, "225024": 41, "344912": 41, "989939": 41, "002664": 41, "977068": 41, "398568": 41, "305223": 41, "997138": 41, "798329": 41, "827197": 41, "pcmap": 41, "extent": [41, 42], "bcmap": 41, "alpha": [41, 42], "zorder": 41, "sinc": 41, "spread": 41, "brain_sect": 41, "104572": 41, "32598314": 41, "32656693": 41, "3266852": 41, "16574148": 41, "16579943": 41, "16598123": 41, "parcellation_": [41, 45], "parcellation_organ": 41, "parcellation_categori": 41, "parcellation_divis": 41, "parcellation_structur": 41, "parcellation_substructur": 41, "parcellation_color": [41, 45], "parcellation_organ_color": 41, "parcellation_category_color": 41, "parcellation_division_color": [41, 45], "parcellation_structure_color": [41, 45], "parcellation_substructure_color": [41, 45], "7ed04b": 41, "ffba86": 41, "cbf": 41, "arb": 41, "cell_metadata_with_parcellation_annot": 41, "parcellation_cell_count": 41, "935742": 41, "401346": 41, "383127": 41, "304642": 41, "281852": 41, "274354": 41, "147562": 41, "136569": 41, "133805": 41, "132902": 41, "bfd": 41, "8865": 41, "sss": 41, "7210": 41, "cp": 41, "4715": 41, "4491": 41, "visa": 41, "4462": 41, "3705": 41, "3119": 41, "3000": 41, "2858": 41, "rspv": 41, "2853": 41, "4696": 41, "4404": 41, "132": 41, "mfsbshy": 41, "chpl": 41, "lp": 41, "md": 41, "146": 41, "pou4f1": 41, "sox1": 41, "1067": 41, "851": 41, "pf": 41, "spa": 41, "serpinb7": 41, "1190": 41, "1036": 41, "ld": 41, "am": 41, "mfbc": 41, "007": 41, "121784": 41, "mos2": 41, "12762": 41, "mop2": 41, "10586": 41, "visp2": 41, "9250": 41, "sss2": 41, "7149": 41, "m2": 41, "5203": 41, "bfd2": 41, "5032": 41, "tea2": 41, "4396": 41, "ul2": 41, "3337": 41, "rspagl2": 41, "3142": 41, "acav2": 41, "3085": 41, "resampled_annot": 41, "resampled_annotation_boundari": 41, "resampled_average_templ": 41, "117m": 41, "12m": 41, "55m": 41, "1100": 41, "76": 41, "20000000298023224": 41, "476531505584717": 41, "600000381469727": 41, "435669422149658": 41, "template_slic": 41, "annotation_slic": 41, "boundary_slic": 41, "help": 41, "thick": 42, "cover": 42, "200": 42, "apart": 42, "male": 42, "assai": 42, "merscop": 42, "design": 42, "combinatori": 42, "robust": [42, 45], "quantit": 42, "bind": 42, "dot": 42, "cellpos": 42, "softwar": 42, "dapi": 42, "polyt": 42, "stain": 42, "pupros": 42, "approximatedli": [42, 45], "phyiscal": 42, "hierach": 42, "correl": 42, "564m": 42, "fuction": 42, "5320": 42, "3932069": 42, "5296": 42, "facili": [42, 45], "blank": 42, "codeword": 42, "codebook": 42, "rate": 42, "detect": 42, "531kmb": 42, "550": 42, "transcript_identifi": [42, 43], "ensmusg00000026778": 42, "prkcq": 42, "ensmust00000028118": 42, "kinas": 42, "theta": 42, "18761": 42, "ensmusg00000026837": 42, "col5a1": 42, "ensmust00000028280": 42, "collagen": 42, "v": 42, "12831": 42, "ensmusg00000001985": 42, "grik3": 42, "ensmust00000030676": 42, "glutam": 42, "receptor": [42, 45], "ionotrop": 42, "kainat": 42, "14807": 42, "ensmusg00000039323": 42, "igfbp2": 42, "ensmust00000047328": 42, "insulin": 42, "growth": 42, "16008": 42, "ensmusg00000048387": 42, "osr1": 42, "ensmust00000057021": 42, "odd": 42, "23967": 42, "63g": 42, "4334174": [42, 43], "accessed_on": 42, "pick": [42, 44], "120186": 42, "ensmust00000032710": [42, 43], "ensmust00000045738": [42, 43], "ensmust00000026466": [42, 43], "ensmust00000056442": [42, 43], "ensmust00000085374": [42, 43], "ensmust00000020102": [42, 43], "ensmust00000022100": [42, 43], "ensmust00000021195": [42, 43], "642314999999996": 42, "On": 42, "ipykernel_17089": 42, "2280752953": 42, "muclei": 42, "amydala": 42, "402895000000001": 43, "inlin": 44, "360m": 44, "revers": 44, "aggreg": 44, "class_list": 44, "abl": 44, "recapitul": 44, "088": 44, "083": 44, "rai14": 44, "pdyn": 44, "crh": 44, "258": 44, "nmu": 44, "043": 44, "mi": 44, "frmd7": 44, "047": 44, "sncg": 44, "082": 44, "ebf1": 44, "046": 44, "vip": 44, "103": 44, "pvhd": 44, "dmh": 44, "lhx6": 44, "126": 44, "pvp": 44, "tbx3": 44, "situ": 45, "multiplex": 45, "fluoresc": 45, "hybrid": 45, "specimen": 45, "example_sect": 45, "079": 45, "037": 45, "010": 45, "sdf": 45, "556m": 45, "2846908": 45, "240m": 45, "1227408": 45, "310m": 45, "1585843": 45, "9m": 45, "162578": 45, "subclass_confidence_scor": 45, "cluster_confidence_scor": 45, "high_quality_transf": 45, "182941331246012878296807398333956011710": 45, "089": 45, "704": 45, "682522": 45, "366483": 45, "829530": 45, "969933": 45, "718088": 45, "221260934538535633595532020856387724686": 45, "5243": 45, "667690": 45, "442241": 45, "850554": 45, "22228792606814781533240955623030943708": 45, "14939": 45, "638731": 45, "474328": 45, "888285": 45, "649581": 45, "272043042552227961220474294517855477150": 45, "653425": 45, "433218": 45, "900000": 45, "607080": 45, "110116287883089187971185374239350249328": 45, "5254": 45, "623896": 45, "513574": 45, "999978": 45, "689511": 45, "94310525370042131911495836073267655162": 45, "110": 45, "5255": 45, "997247": 45, "823236": 45, "717769": 45, "971385": 45, "943456": 45, "298798481479578578007190103666214714353": 45, "043871": 45, "706231": 45, "956377": 45, "905493": 45, "330756942354980576352210203729462562749": 45, "5261": 45, "037680": 45, "759890": 45, "811520": 45, "788901": 45, "47305871059582831548494138048361484565": 45, "5252": 45, "044169": 45, "758463": 45, "991924": 45, "634152": 45, "64578198410898899234789748167671783948": 45, "5263": 45, "042301": 45, "589421": 45, "889413": 45, "645770": 45, "049": 45, "lamp5": 45, "0199": 45, "0709": 45, "ccff33": 45, "ff764d": 45, "dc00ff": 45, "998900": 45, "vascular": 45, "331": 45, "1191": 45, "nn_1": 45, "5304": 45, "858881": 45, "82992e": 45, "2f00cc": 45, "bb1fcc": 45, "astro": 45, "epen": 45, "te": 45, "1163": 45, "nn_3": 45, "5225": 45, "594a26": 45, "3dccb1": 45, "a8afa5": 45, "551799": 45, "333": 45, "endo": 45, "1193": 45, "5310": 45, "994567": 45, "00992a": 45, "ffb473": 45, "5311": 45, "cc3d76": 45, "330": 45, "vlmc": 45, "1188": 45, "nn_2": 45, "5301": 45, "653d66": 45, "4d5cff": 45, "79cc5c": 45, "5309": 45, "5c9994": 45, "1187": 45, "66391f": 45, "3b9900": 45, "7k": 45, "632kmb": 45, "ensmusg00000024798": 45, "htr7": 45, "hydroxytryptamin": 45, "serotonin": 45, "15566": 45, "ensmusg00000042385": 45, "gzmk": 45, "granzym": 45, "k": 45, "14945": 45, "ensmusg00000036198": 45, "arhgap36": 45, "gtpase": 45, "activ": 45, "75404": 45, "ensmusg00000028780": 45, "sema3c": 45, "sema": 45, "domain": 45, "immunoglobulin": 45, "ig": 45, "short": 45, "20348": 45, "ensmusg00000015843": 45, "rxrg": 45, "retinoid": 45, "gamma": 45, "20183": 45, "per": 45, "subplot_sect": 45, "suptitl": 45, "fontsiz": 45, "sodium": 45, "ino": 45, "216227": 45, "tran": 45, "13162": 45, "vesicular": 45, "22348": 45, "104245": 45, "72961": 45, "15567": 45, "140919": 45, "cell_express": 45, "13g": 45, "182652000000004": 45, "871m": 45, "726561000000004": 45, "16g": 45, "556720999999996": 45, "107m": 45, "8736040000000003": 45, "221m": 45, "1m": 45, "132m": 45, "8m": 45, "902190": 45, "048426": 45, "582962": 45, "906513": 45, "145200": 45, "577602": 45, "906110": 45, "182761": 45, "553731": 45, "904627": 45, "131808": 45, "563525": 45, "907236": 45, "230647": 45, "543048": 45, "681244": 45, "453979": 45, "852027": 45, "676999": 45, "291647": 45, "899531": 45, "1109": 45, "678760": 45, "363282": 45, "894082": 45, "678641": 45, "360346": 45, "901195": 45, "673530": 45, "138034": 45, "897311": 45, "2616328": 45}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"allen": [0, 28, 35], "mous": [0, 1, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 23, 35, 36, 45], "common": [0, 35], "coordin": [0, 2, 35, 41], "framework": [0, 35], "2020": [0, 35], "version": [0, 35], "merfish": [1, 2, 15, 16, 17, 18, 22, 41, 42, 43, 44, 45], "spatial": [1, 15, 16, 17, 18, 19, 22, 23, 29, 32, 42, 43, 44, 45], "transcriptom": [1, 3, 4, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 20, 22, 29, 33, 42, 43, 44, 45], "dataset": [1, 15, 16, 17, 18], "singl": [1, 3, 4, 8, 9, 10, 11, 15, 16, 17, 18, 29, 33], "adult": [1, 8, 13, 15, 16, 17, 18], "brain": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 28, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45], "ccf": [2, 41, 45], "map": [2, 41], "cluster": [3, 8, 12, 25, 34, 36, 37, 45], "analysi": [3, 8, 34, 36], "whole": [3, 6, 7, 8, 9, 10, 11, 13, 14, 19, 20, 22, 23, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45], "human": [3, 4, 5, 6, 7, 32, 33, 34], "10x": [3, 7, 8, 21, 29, 30, 31, 32, 33, 34, 36, 39], "nucleu": [3, 4], "10xv3": [4, 11], "taxonomi": [5, 13, 34, 36], "cell": [5, 6, 8, 9, 10, 11, 13, 14, 19, 20, 23, 28, 29, 32, 33, 34, 36, 38, 41, 42, 45], "type": [5, 6, 13, 14, 20, 38], "atla": [6, 14, 19, 20, 23, 28], "kimberli": 6, "siletti": 6, "scrna": [7, 21], "seq": [7, 21, 29, 30, 31, 32, 33, 34, 36, 39], "gene": [7, 21, 26, 29, 30, 31, 32, 33, 37, 39, 42, 44, 45], "express": [7, 21, 29, 30, 31, 32, 33, 37, 39, 42, 44, 45], "data": [7, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 45], "10xmulti": 9, "10xv2": 10, "group": [12, 37], "neighborhood": [12, 37, 38], "specif": [12, 39], "umap": [12, 29, 32], "embed": [12, 29, 32, 37], "hongkui": [14, 20], "zeng": [14, 20], "zhuang": [15, 16, 17, 18, 19, 23, 45], "abca": [15, 16, 17, 18], "1": [15, 29, 32, 42], "2": [16, 29, 31, 33, 42, 44], "3": 17, "4": 18, "A": [19, 23], "molecularli": [19, 23], "defin": [19, 23], "resolv": [19, 23], "xiaowei": [19, 23, 45], "resourc": 24, "page": 24, "annot": [25, 27, 34, 35, 36, 45], "list": 26, "parcel": [27, 35, 41, 45], "access": [28, 39], "releas": 28, "note": 28, "rna": [29, 30, 31, 32, 33, 34, 36, 39], "part": [29, 30, 31, 32, 33, 42, 43, 44], "overview": [29, 32, 34, 35, 36, 37, 42, 45], "metadata": [29, 32, 40, 42, 45], "matric": [29, 30, 39], "exampl": [29, 30, 33, 34, 35, 36, 37, 42, 45], "us": [29, 30, 33, 34, 35, 36, 37, 40, 42, 45], "case": [29, 30, 33, 34, 35, 36, 37, 42, 45], "canon": [29, 31, 42, 44], "neurotransmitt": [29, 31, 34, 36, 42, 44], "transport": [29, 31, 42, 44], "thalamu": 29, "tachykinin": [29, 31, 42, 44], "tac2": [29, 31, 42, 44], "2a": [30, 43], "2b": [31, 44], "whb": 32, "select": 33, "subclust": 34, "term": [34, 35, 36, 41], "set": [34, 35, 36], "membership": [34, 35, 36, 37], "aggreg": [34, 35, 36, 41], "count": [34, 36], "per": [34, 35, 36], "superclust": 34, "level": [34, 35, 36, 41], "visual": [34, 35, 36, 37, 41], "distribut": [34, 36], "refer": 35, "templat": [35, 41], "anatom": [35, 37, 41], "structur": 35, "voxel": 35, "each": [35, 36], "hierachi": 35, "ccn20230722": 36, "class": 36, "dimens": 37, "reduct": 37, "pivot": 37, "tabl": 37, "context": 37, "galleri": 38, "pallium": 38, "glut": 38, "subpallium": 38, "gaba": 38, "hy": 38, "ea": 38, "th": 38, "epi": 38, "mb": 38, "hb": 38, "cb": 38, "sero": 38, "dopa": 38, "nn": 38, "imn": 38, "gc": 38, "load": 39, "from": 39, "get": 40, "start": 40, "cach": 40, "download": 40, "file": 40, "all": [40, 41], "directori": 40, "individu": 40, "advanc": 40, "option": 40, "forc": 40, "redownload": 40, "skip": 40, "hash": 40, "check": 40, "read": 41, "section": 41, "reconstruct": 41, "reconstruc": 41, "associ": 41, "assign": 41, "differ": 41, "resampl": 41, "boundari": 41, "overlai": 41, "panel": [42, 45], "matrix": [42, 45], "registr": 45}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9, "sphinx": 56}})
\ No newline at end of file