Merge branch 'rc/0.2.0'

Author: morriscb

.github/workflows/abc_atlas_access_ci.yaml

@@ -0,0 +1,26 @@
+name: ci/abc_atlas_access
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+jobs:
+  test:
+    name: ${{ matrix.python-version }}, ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ "macos-latest", "windows-latest", "ubuntu-latest" ]
+        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      - name: Test
+        run: pytest tests

_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).