Add initial notebook example and jupyter-book pages.

_toc.yml

@@ -19,6 +19,7 @@ parts:
       - file: descriptions/WMB-10X
       - file: descriptions/WMB-taxonomy
       - file: descriptions/MERFISH-C57BL6J-638850
+      - file: descriptions/MERFISH-C57BL6J-638850-imputed
       - file: descriptions/WMB-neighborhoods
       - file: descriptions/Allen-CCF-2020
       - file: descriptions/MERFISH-C57BL6J-638850-CCF
@@ -49,6 +50,7 @@ parts:
           - file: notebooks/merfish_tutorial_part_1
           - file: notebooks/merfish_tutorial_part_2a
           - file: notebooks/merfish_tutorial_part_2b
+          - file: descriptions/merfish_imputed_genes_example.ipynb
       - file: notebooks/cluster_groups_and_embeddings_tutorial
       - file: notebooks/cluster_neighborhood_gallery
       - file: notebooks/ccf_and_parcellation_annotation_tutorial

descriptions/MERFISH-C57BL6J-638850-CCF.md

@@ -25,6 +25,7 @@ Related resources :
 * Whole mouse brain clustering ([WMB-10X](WMB-10X.md))
 * Whole mouse brain mouse taxonomy of cell types ([WMB-taxonomy](WMB-taxonomy.md))
 * Whole mouse brain MERFISH spatial transcriptomics dataset ([MERFISH-C57BL6J-638850](MERFISH-C57BL6J-638850.md))
+* Imputed, whole mouse brain MERFISH spatial transcriptomics dataset ([MERFISH-C57BL6J-638850-imputed](MERFISH-C57BL6J-638850-imputed.md))
 * Allen CCFv3 with a simplified 5-level anatomical hierarchy ([Allen-CCF-2020](Allen-CCF-2020.md))
 
 Associated notebooks:
@@ -39,6 +40,8 @@ Associated notebooks:
     example use cases in part 2b.
   * [**Part 2b**](../notebooks/merfish_tutorial_part_2b.ipynb): Explore the whole brain data through visualization and
     analyses of a set of genes of interest.
+  * [**MERFISH imputed genes**](../notebooks/merfish_tutorial_part_1.ipynb):
+    Learn about the using the imputed genes of the MERFISH dataset.
 * [**Allen CCFv3 parcellation and annotation**](../notebooks/ccf_and_parcellation_annotation_tutorial.ipynb): learn about the Allen
   CCFv3 and a simplified 5-level anatomical hierarchy through some example use
   cases and visualization.

descriptions/MERFISH-C57BL6J-638850-imputed.md

@@ -0,0 +1,33 @@
+# Imputed gene MERFISH spatial transcriptomics  dataset of a single adult mouse brain
+
+TO FILL IN
+
+The expression matrices and associated metadata is hosted on AWS S3 bucket as a
+AWS Public Dataset:
+
+| Component | Current Version                                                                                                                                                                                                      | Size |
+|---|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---|
+| Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/MERFISH-C57BL6J-638850-imputed/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/MERFISH-C57BL6J-638850/20230830/) | 14.2 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850-imputed/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/MERFISH-C57BL6J-638850/20231215/)                       | 1.81 GB |
+
+Data is being share under the CC BY NC 4.0 license.
+
+Related resources :
+* Whole mouse brain clustering ([WMB-10X](WMB-10X.md))
+* Whole mouse brain mouse taxonomy of cell types ([WMB-taxonomy](WMB-taxonomy.md))
+* Whole mouse brain MERFISH spatial transcriptomics dataset ([MERFISH-C57BL6J-638850](MERFISH-C57BL6J-638850.md))
+
+Associated notebooks:
+* [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the AbcProjectCache to
+  facilitate data download and usage.
+* [**10x scRNA-seq clustering analysis and annotation**](../notebooks/cluster_annotation_tutorial.ipynb): learn about the
+  whole mouse brain taxonomy through some example use cases and visualization.
+* * * **MERFISH whole brain spatial transcriptomics**
+  * [**Part 1**](../notebooks/merfish_tutorial_part_1.ipynb): learn about the MERFISH dataset through some example use
+    cases and visualization for a single brain section.
+  * [**Part 2a**](../notebooks/merfish_tutorial_part_2a.ipynb): learn to access data and prepare for whole brain
+    example use cases in part 2b.
+  * [**Part 2b**](../notebooks/merfish_tutorial_part_2b.ipynb): Explore the whole brain data through visualization and
+    analyses of a set of genes of interest.
+  * [**MERFISH imputed genes**](../notebooks/merfish_tutorial_part_1.ipynb):
+    Learn about the using the imputed genes of the MERFISH dataset.

descriptions/MERFISH-C57BL6J-638850.md

@@ -17,6 +17,7 @@ AWS Public Dataset:
 Data is being share under the CC BY NC 4.0 license.
 
 Related resources :
+* Imputed, whole mouse brain MERFISH spatial transcriptomics dataset ([MERFISH-C57BL6J-638850-imputed](MERFISH-C57BL6J-638850-imputed.md))
 * Whole mouse brain clustering ([WMB-10X](WMB-10X.md))
 * Whole mouse brain mouse taxonomy of cell types ([WMB-taxonomy](WMB-taxonomy.md))
 
@@ -32,3 +33,5 @@ Associated notebooks:
     example use cases in part 2b.
   * [**Part 2b**](../notebooks/merfish_tutorial_part_2b.ipynb): Explore the whole brain data through visualization and
     analyses of a set of genes of interest.
+  * [**MERFISH imputed genes**](../notebooks/merfish_tutorial_part_1.ipynb):
+    Learn about the using the imputed genes of the MERFISH dataset.

descriptions/WMB_dataset.md

@@ -22,4 +22,7 @@
   ([Allen-CCF-2020](Allen-CCF-2020.md))
 * CCF mapped coordinates for cells in the whole brain spatial transcriptomics
   dataset ([MERFISH-C57BL6J-638850-CCF](MERFISH-C57BL6J-638850-CCF.md))
+*  3.9 million cell spatial transcriptomics dataset with ~8000 genes
+   imputed using the 500 genes in the base MERFISH-C57BL6J-638850 dataset
+   [MERFISH-C57BL6J-638850-imputed](MERFISH-C57BL6J-638850-imputed.md).
 

intro.md

@@ -58,6 +58,14 @@ Available notebooks:
   (Kimberly Siletti)**
 
 ## Release Notes
+* **[Summer 2024 Public Beta (version 20240930) ab_atlas_access (v0.2.0)]**
+  * Released ~8k imputed genes for the MERFISH-C57BL6J-638850 dataset.
+  * Added new notebooks and pages for the imputed gene dataset.
+  * Updated cache object for better compatiblity across platforms.
+    * Added automatic unittesting via GitHub Actions.
+    * Modifed cache to autodetect cache type (local or s3) for easier
+      compatiblity with CodeOcean/s3fs-fuse mounts.
+    * Simplified notebooks use of the cache.
 * **[abc_atlas_access (v0.1.2)]**
   * Add matplotlib magic.
   * Fixed bugs in pathlib import in notebooks