Incorporate Scientist feedback.

Update WHB_notebooks.md
Update WHB-10Xv3.md
Update WHB-10X-clustering.md
Update WHB-taxonomy.md
Update WHB-10X-clustering.md
updated Jupyter notebooks
updated part 2 with new genes

descriptions/WHB-10X-clustering.md

@@ -1,33 +1,34 @@
-# Clustering analysis of whole human brain 10X single cell transcriptomes
+# Clustering analysis of whole human brain 10X single nucleus transcriptomes
 
-Clustering analysis of over 3 million single cell transcriptomes spanning the
-whole adult human brain, resulting in a set of 461 clusters and 3313
-subclusters.
+Clustering analysis of over 3 million single nucleus transcriptomes spanning
+the whole adult human brain, resulting in a set of 461 clusters and 3313
+subclusters. The dataset linked below contains metadata on all cells and geens
+in the WHB dataset.
 
 Full details on the dataset can be found in [Siletti et al. 2023](https://www.science.org/doi/10.1126/science.add7046).
 
 The associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:
 
-| Component | Current Version                                                                                                                                              | Size     |
-|---|--------------------------------------------------------------------------------------------------------------------------------------------------------------|----------|
-| Metadata | [s3://allen-brain-cell-atlas/metadata/WHB-10Xv3/20240330](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-10Xv3/20240330/) | 862.1 MB |
+| Component              | Current Version                                                                                                                                              | Size     |
+|------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|----------|
+| Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/WHB-10Xv3/20240330](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-10Xv3/20240330/) | 862.1 MB |
 
 Data is being share under the CC BY NC 4.0 license.
 
 Related resources :
-* Human brain single cell transcriptomes ([WHB-10Xv3](WHB-10Xv3.md))
+* Human brain single nucleus transcriptomes ([WHB-10Xv3](WHB-10Xv3.md))
 * Whole human brain taxonomy of cell types ([WHB-taxonomy](WHB-taxonomy.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the manifest.json file to 
   facilitate data download and usage.
-* [**10x scRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
-  learn about the  whole human brain taxonomy through some example use cases
-  and visualization.
+* [**10x snRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
+  learn about the whole human brain taxonomy through some example use cases and
+  visualization.
 * [**Accessing 10X gene expression data**](../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb):
   learn how to load individual genes from the 10X expression data.
-* **10x scRNA-seq gene expression data**
-  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): learn about the 10x dataset through some example use
-    cases and visualization of cells.
-  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): Explore the whole brain data through visualization and
+* **10x snRNA-seq gene expression data**
+  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): understand the basic structure of the data and metadata,
+    and visualize brain region and cell type annotations in a UMAP.
+  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore the whole brain data through visualization and
     analyses of a set of genes of interest.

descriptions/WHB-10Xv3.md

@@ -1,7 +1,8 @@
-# Human brain 10Xv3 single cell transcriptomes
+# Human brain 10Xv3 single nucleus transcriptomes
 
-This dataset consists of over three million single cells containing two million
-neurons from 100 locations across the forebrain, midbrain, and hindbrain.
+This dataset consists of nuclei extracted from over three million single cells
+(approximately two million neurons and one million non-neurons) from 100
+locations across the forebrain, midbrain, and hindbrain.
 
 Full details on the dataset can be found in [Siletti et al. 2023](https://www.science.org/doi/10.1126/science.add7046).
 
@@ -14,21 +15,21 @@ a AWS Public Dataset:
 
 Data is being share under the CC BY NC 4.0 license.
 
-Related resources :
-* Clustering analysis of over 3 million single cell transcriptomes spanning the
+Related resources:
+* Clustering analysis of over 3 million single nucleus transcriptomes spanning the
   whole adult human brain ([WHB-10X-clustering](WHB-10X-clustering.md))
 * Whole human brain taxonomy of cell types ([WHB-taxonomy](WHB-taxonomy.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the manifest.json file to
   facilitate data download and usage.
 * [**10x scRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
-  learn about the  whole human brain taxonomy through some example use cases
-  and visualization.
+  learn about the whole human brain taxonomy through some example use cases and
+  visualization.
 * [**Accessing 10X gene expression data**](../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb):
   learn how to load individual genes from the 10X expression data.
 * **10x scRNA-seq gene expression data**
-  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): learn about the 10x dataset through some example use
-    cases and visualization of cells.
-  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): Explore the whole brain data through visualization and
-    analyses of a set of genes of interest.
+  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): understand the basic structure of the data and metadata,
+    and visualize brain region and cell type annotations in a UMAP.
+  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore the whole brain data through visualization and
+    analyses of a set of genes of interest.

descriptions/WHB-taxonomy.md

@@ -1,34 +1,34 @@
 # Human brain taxonomy of cell types
 
 The data presented here from [Siletti et al. 2023](https://www.science.org/doi/10.1126/science.add7046),
-consists of over three million single cells and two million neurons from 100
-locations across the forebrain, midbrain, and hindbrain. The integrated 
-transcriptomic taxonomy contains 31 superclusters, 461 clusters, and 3313
-subclusters.
+consists of nuclei collect from over three million single cells (apprixmately
+two million neurons and one million non-neurons) from 100 locations across the
+forebrain, midbrain, and hindbrain. The integrated transcriptomic taxonomy
+contains 31 superclusters, 461 clusters, and 3313 subclusters.
 
 The associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:
 
-| Component | Current Version | Size   |
-|---|--|--------|
-| Metadata | [s3://allen-brain-cell-atlas/metadata/WHB-taxonomy/20240330/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-taxonomy/20240330/) | 1.6 MB |
+| Component              | Current Version | Size   |
+|------------------------|--|--------|
+| Cell taxonomy metadata | [s3://allen-brain-cell-atlas/metadata/WHB-taxonomy/20240330/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-taxonomy/20240330/) | 1.6 MB |
 
 Data is being shared under the CC BY NC 4.0 license.
 
 Related resources :
-* Human brain single cell transcriptomes ([WHB-10Xv3](WHB-10Xv3.md))
-* Clustering analysis of over 3 million single cell transcriptomes spanning the
+* Human brain single nucleus transcriptomes ([WHB-10Xv3](WHB-10Xv3.md))
+* Clustering analysis of over 3 million single nucleus transcriptomes spanning the
   whole adult human brain ([WHB-10X-clustering](WHB-10X-clustering.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the manifest.json file to
   facilitate data download and usage.
-* [**10x scRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
-  learn about the  whole human brain taxonomy through some example use cases
-  and visualization.
+* [**10x snRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
+  learn about the whole human brain taxonomy through some example use cases and
+  visualization.
 * [**Accessing 10X gene expression data**](../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb):
   learn how to load individual genes from the 10X expression data.
-* **10x scRNA-seq gene expression data**
-  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): learn about the 10x dataset through some example use
-    cases and visualization of cells.
-  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): Explore the whole brain data through visualization and
-    analyses of a set of genes of interest.
+* **10x snRNA-seq gene expression data**
+  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): understand the basic structure of the data and metadata,
+    and visualize brain region and cell type annotations in a UMAP.
+  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore the whole brain data through visualization and
+    analyses of a set of genes of interest.

descriptions/WHB_notebooks.md

@@ -4,10 +4,9 @@
   learn about the whole human brain taxonomy through some example use cases and
   visualization.
 [*notebooks/WHB_cluster_annotation_tutorial.ipynb*]
-* [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): learn about the 10x dataset through some example use cases
-  and visualization of cells.
+* [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): understand the basic structure of the data and metadata,
+  and visualize brain region and cell type annotations in a UMAP.
 [*notebooks/10x_snRNASeq_tutorial_part_1.ipynb*]
-* [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore
-  the whole brain data through visualization and analyses of a set of genes of
-  interest.
-[*notebooks/10x_snRNASeq_tutorial_part_2.ipynb*]
+* [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore the whole brain data through visualization and
+  analyses of a set of genes of interest.
+[*notebooks/10x_snRNASeq_tutorial_part_2.ipynb*]

intro.md

@@ -7,7 +7,12 @@ insights to the ABC Atlas, this groundbreaking platform will keep growing,
 opening up endless possibilities for groundbreaking discoveries and
 breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can
 gain new insights into the brain’s complex workings, advancing our
-understanding of this amazing organ in ways we never thought possible.
+understanding of this amazing organ in ways we never thought possible. The
+ABC Atlas can be accessed at [here](https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas)
+and is the primary method of interacting with these data. Any questions or
+issues associated with the ABC Atlas are best directed to the [Allen Institute
+Commnituy Forum](https://community.brain-map.org/). This repository is intended
+for users who wish to download the ABC Atlas data and processes it locally.
 
 Data associated with the ABC Atlas is hosted on Amazon Web Services (AWS) in an
 S3 bucket as a AWS Public Dataset, [arn:aws:s3:::allen-brain-cell-atlas](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html).
@@ -55,7 +60,7 @@ Available notebooks:
 ## Release Notes
 * **[Spring 2024 Public Beta (version 20240330)]**
   * Added Whole Human Brain transcriptomic, taxonomy and clustering datasets
-    from Siletti et al. 2022 to the ABC Atlas.
+    from Siletti et al. 2023 to the ABC Atlas.
   * Added new AbcProjectCache python class to facilitate data download and
     usage.
     * Added file hashes to the manifest.json to facilitate data integrity

notebooks/10x_snRNASeq_tutorial_part_2a.ipynb

@@ -438,38 +438,38 @@
      "output_type": "stream",
      "text": [
       "WMB-10XMulti\n",
-      " - time taken:  1.2555350000000018\n",
+      " - time taken:  0.1000140000000016\n",
       "WMB-10Xv2-CTXsp\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.74G/1.74G [05:46<00:00, 5.02MMB/s]\n"
+      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|██████████| 1.74G/1.74G [01:09<00:00, 24.9MMB/s]   \n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  1.9390729999999934\n",
+      " - time taken:  2.0210620000000006\n",
       "WMB-10Xv2-HPF\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-HPF-log2.h5ad: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 6.10G/6.10G [30:31<00:00, 3.33MMB/s]\n"
+      "WMB-10Xv2-HPF-log2.h5ad: 100%|██████████| 6.10G/6.10G [04:48<00:00, 21.2MMB/s]    \n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  7.567903999999999\n",
-      "total time taken:  325.37152000000003\n"
+      " - time taken:  6.7627419999999745\n",
+      "total time taken:  140.118578\n"
      ]
     }
    ],
@@ -554,7 +554,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,