Add imputed notebook example and jupyter-book pages.

Add correct links for merfish imputed data.
Add imputed gene page.
Update notebook to create gene page.
Update notebooks to new cache and verify they run to completion.
Update for 20240831 release.

Fix gene page name.

_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: notebooks/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

@@ -25,20 +25,23 @@ 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:
 * [**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
+* **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
+  * [**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_imputed_genes_example.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 +1,38 @@
+# Imputed MERFISH spatial transcriptomics of a single adult mouse brain
+
+The MERFISH spatial transcriptomics dataset ([MERFISH-C57BL6J-638850](MERFISH-C57BL6J-638850.md)) was mapped
+to the whole mouse brain taxonomy ([WMB-taxonomy](WMB-taxonomy.md)) using a [hierarchical
+correlation method](https://github.com/AllenInstitute/scrattch.mapping). To further integrate the transcriptomics and spatial
+profiles of each cell type, 10Xv3 expression was projected or imputed into the
+MERFISH space. The basic idea is to compute the k-nearest neighbors (KNNs)
+among the 10Xv3 cells for each MERFISH cell and use the average expression of
+these neighbors for each gene as the imputed values. Imputed expression values
+were generated for 8,460 marker genes.  Further details can be found in the
+methods section of [Yao et. al](https://www.nature.com/articles/s41586-023-06812-z).
+
+| Component | Current Version                                                                                                                                                                                                              | Size  |
+|---|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------|
+| Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/MERFISH-C57BL6J-638850-imputed/20240831](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/MERFISH-C57BL6J-638850-imputed/20240831/) | 47 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850-imputed/20240831](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/MERFISH-C57BL6J-638850-imputed/20240831/)                       | 1 MB  |
+
+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_imputed_genes_example.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))
 
@@ -25,10 +26,12 @@ Associated notebooks:
   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
+* **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
+  * [**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_imputed_genes_example.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).