update data and notebooks to reflect updated neurotransmitter assigne…

…ment and subtype colors
AllenInstitute · Nov 9, 2023 · ecd8032 · ecd8032
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diff --git a/descriptions/MERFISH-C57BL6J-638850-CCF.md b/descriptions/MERFISH-C57BL6J-638850-CCF.md
@@ -11,7 +11,7 @@ Global and section-wise mappings from each of these registration steps were pres
 | Component | Current Version | Size |
 |---|--|---|
 | Image Volumes | [s3://allen-brain-cell-atlas/image_volumes/MERFISH-C57BL6J-638850-CCF/20230630](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#image_volumes/MERFISH-C57BL6J-638850-CCF/20230630/) | 115.4 MB |
-| Metadata | [s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/MERFISH-C57BL6J-638850-CCF/20230830/) | 2.14 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850-CCF/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/MERFISH-C57BL6J-638850-CCF/20231215/) | 2.01 GB |
 
 Data is being share under the CC BY NC 4.0 license.
 

diff --git a/descriptions/MERFISH-C57BL6J-638850.md b/descriptions/MERFISH-C57BL6J-638850.md
@@ -7,7 +7,7 @@ The expression matrices and associated metadata is hosted on AWS S3 bucket as a
 | Component | Current Version | Size |
 |---|--|---|
 | Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/MERFISH-C57BL6J-638850/20230830](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-638850/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/MERFISH-C57BL6J-638850/20230830/) | 2.11 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850/20231215](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.
 

diff --git a/descriptions/WMB-10X.md b/descriptions/WMB-10X.md
@@ -7,7 +7,7 @@ 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/WMB-10X/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-10X/20230830/) | 2.33 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/WMB-10X/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-10X/20231215/) | 2.39 GB |
 
 Data is being share under the CC BY NC 4.0 license.
 

diff --git a/descriptions/WMB-neighborhoods.md b/descriptions/WMB-neighborhoods.md
@@ -6,7 +6,7 @@ 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/WMB-neighborhoods/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-neighborhoods/20230830/) | 5.2 MB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/WMB-neighborhoods/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-neighborhoods/20231215/) | 3.00 GB |
 
 Data is being share under the CC BY NC 4.0 license.
 

diff --git a/descriptions/WMB-taxonomy.md b/descriptions/WMB-taxonomy.md
@@ -2,13 +2,13 @@
 
 The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. The integrated transcriptomic taxonomy contains 5,322 clusters that are organized in a hierarchical manner with nested groupings of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 types/clusters. The scRNA-seq data reveal transcriptome-wide gene expression and co-expression patterns for each cell type. The anatomical location of each cell type has been annotated using a comprehensive brain-wide MERFISH dataset with a total of ~4 million segmented and QC-passed cells, probed with a 500-gene panel and registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3). The MERFISH data not only provide accurate spatial annotation of cell types at subclass, supertype and cluster levels, but also reveal fine-resolution spatial distinctions or gradients for cell types. The combination of scRNA-seq and MERFISH data reveals a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type, as well as unique features of cell type organization in different brain regions. 
 
-A detailed cell type [annotation table](https://allen-brain-cell-atlas.s3-us-west-2.amazonaws.com/metadata/WMB-taxonomy/20230830/cl.df_CCN202307220.xlsx) is also provided along with data downloads detailing information about the hierarchical membership, anatomical annotation, neurotransmitter type, cell type marker genes, transcription factor and neuropeptide markers, and other metadata types for each cluster.
+A detailed cell type [annotation table](https://allen-brain-cell-atlas.s3-us-west-2.amazonaws.com/metadata/WMB-taxonomy/20231215/cl.df_CCN202307220.xlsx) is also provided along with data downloads detailing information about the hierarchical membership, anatomical annotation, neurotransmitter type, cell type marker genes, transcription factor and neuropeptide markers, and other metadata types for each cluster.
 
 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/WMB-taxonomy/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-taxonomy/20230830/) | 5.2 MB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/WMB-taxonomy/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WMB-taxonomy/20231215/) | 0.01 GB |
 
 Data is being share under the CC BY NC 4.0 license.
 

diff --git a/descriptions/Zhuang-ABCA-1.md b/descriptions/Zhuang-ABCA-1.md
@@ -7,7 +7,7 @@ The expression matrices and associated metadata is hosted on AWS S3 bucket as a
 | Component | Current Version | Size |
 |---|--|---|
 | Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/Zhuang-ABCA-1/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-1/20230830/) | 3.09 GB |
-| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-1/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-1/20230830/) | 1.33 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-1/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-1/20231215/) | 1.33 GB |
 | CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-1-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-1-CCF/20230830/) | 0.21 GB |
 
 Data is being share under the CC BY 4.0 license.

diff --git a/descriptions/Zhuang-ABCA-2.md b/descriptions/Zhuang-ABCA-2.md
@@ -7,7 +7,7 @@ The expression matrices and associated metadata is hosted on AWS S3 bucket as a
 | Component | Current Version | Size |
 |---|--|---|
 | Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/Zhuang-ABCA-2/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-2/20230830/) | 1.30 GB |
-| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-2/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-2/20230830/) | 0.57 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-2/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-2/20231215/) | 0.57 GB |
 | CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-2-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-2-CCF/20230830/) | 0.08 GB |
 
 Data is being share under the CC BY 4.0 license.

diff --git a/descriptions/Zhuang-ABCA-3.md b/descriptions/Zhuang-ABCA-3.md
@@ -7,7 +7,7 @@ The expression matrices and associated metadata is hosted on AWS S3 bucket as a
 | Component | Current Version | Size |
 |---|--|---|
 | Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/Zhuang-ABCA-3/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-3/20230830/) | 1.69 GB |
-| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-3/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-3/20230830/) | 0.75 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-3/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-3/20231215/) | 0.75 GB |
 | CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-3-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-3-CCF/20230830/) | 0.12 GB |
 
 Data is being share under the CC BY 4.0 license.

diff --git a/descriptions/Zhuang-ABCA-4.md b/descriptions/Zhuang-ABCA-4.md
@@ -7,7 +7,7 @@ The expression matrices and associated metadata is hosted on AWS S3 bucket as a
 | Component | Current Version | Size |
 |---|--|---|
 | Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/Zhuang-ABCA-4/20230830/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/Zhuang-ABCA-4/20230830/) | 0.16 GB |
-| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-4/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-4/20230830/) | 0.08 GB |
+| Metadata | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-4/20231215](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-4/20231215/) | 0.08 GB |
 | CCF Coordinates | [s3://allen-brain-cell-atlas/metadata/Zhuang-ABCA-4-CCF/20230830](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/Zhuang-ABCA-4-CCF/20230830/) | 0.01 GB |
 
 Data is being share under the CC BY 4.0 license.

diff --git a/notebooks/10x_snRNASeq_tutorial_part_1.ipynb b/notebooks/10x_snRNASeq_tutorial_part_1.ipynb
diff --git a/notebooks/10x_snRNASeq_tutorial_part_2a.ipynb b/notebooks/10x_snRNASeq_tutorial_part_2a.ipynb
@@ -41,7 +41,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "version = '20230830'\n",
+    "version = '20231215'\n",
     "download_base = '../../abc_download_root'\n",
     "\n",
     "use_local_cache = False\n",
@@ -454,54 +454,54 @@
      "output_type": "stream",
      "text": [
       "WMB-10XMulti\n",
-      " - time taken:  1.9622096919999983\n",
+      " - time taken:  1.9875723679999986\n",
       "WMB-10Xv2-CTXsp\n",
-      " - time taken:  1.7534853379999973\n",
+      " - time taken:  1.736294100000002\n",
       "WMB-10Xv2-HPF\n",
-      " - time taken:  6.767831976\n",
+      " - time taken:  5.911806116000001\n",
       "WMB-10Xv2-HY\n",
-      " - time taken:  2.9769649340000015\n",
+      " - time taken:  2.839109353999998\n",
       "WMB-10Xv2-Isocortex-1\n",
-      " - time taken:  10.805219346000005\n",
+      " - time taken:  8.228330416999999\n",
       "WMB-10Xv2-Isocortex-2\n",
-      " - time taken:  12.451479411999998\n",
+      " - time taken:  9.044668807999997\n",
       "WMB-10Xv2-Isocortex-3\n",
-      " - time taken:  11.092032212000007\n",
+      " - time taken:  9.986195581999993\n",
       "WMB-10Xv2-Isocortex-4\n",
-      " - time taken:  12.191183033000002\n",
+      " - time taken:  11.247832531\n",
       "WMB-10Xv2-MB\n",
-      " - time taken:  0.9217969590000052\n",
+      " - time taken:  0.8962304950000117\n",
       "WMB-10Xv2-OLF\n",
-      " - time taken:  6.6084268479999935\n",
+      " - time taken:  5.684649880000009\n",
       "WMB-10Xv2-TH\n",
-      " - time taken:  4.5150405959999915\n",
+      " - time taken:  4.081716135999997\n",
       "WMB-10Xv3-CB\n",
-      " - time taken:  7.923351416000003\n",
+      " - time taken:  7.552754073000003\n",
       "WMB-10Xv3-CTXsp\n",
-      " - time taken:  3.9744392829999953\n",
+      " - time taken:  3.717788982000002\n",
       "WMB-10Xv3-HPF\n",
-      " - time taken:  11.715912669999994\n",
+      " - time taken:  9.632554069000008\n",
       "WMB-10Xv3-HY\n",
-      " - time taken:  10.542776168000003\n",
+      " - time taken:  8.718123004000006\n",
       "WMB-10Xv3-Isocortex-1\n",
-      " - time taken:  17.62114658600001\n",
+      " - time taken:  15.792058513\n",
       "WMB-10Xv3-Isocortex-2\n",
-      " - time taken:  11.949673215000018\n",
+      " - time taken:  9.76483662599999\n",
       "WMB-10Xv3-MB\n",
-      " - time taken:  20.26076470999999\n",
+      " - time taken:  18.491481762000006\n",
       "WMB-10Xv3-MY\n",
-      " - time taken:  9.379144964000005\n",
+      " - time taken:  6.938539325000022\n",
       "WMB-10Xv3-OLF\n",
-      " - time taken:  3.1078892949999783\n",
+      " - time taken:  2.9817742030000147\n",
       "WMB-10Xv3-P\n",
-      " - time taken:  6.396515713000014\n",
+      " - time taken:  4.906559042999987\n",
       "WMB-10Xv3-PAL\n",
-      " - time taken:  4.734135684000023\n",
+      " - time taken:  4.105939183000004\n",
       "WMB-10Xv3-STR\n",
-      " - time taken:  20.591621973000002\n",
+      " - time taken:  17.826632974000006\n",
       "WMB-10Xv3-TH\n",
-      " - time taken:  8.585785503000011\n",
-      "total time taken:  213.870688637\n"
+      " - time taken:  7.132106335000003\n",
+      "total time taken:  184.041671802\n"
      ]
     }
    ],