rc/1.3.0

_toc.yml

@@ -56,6 +56,7 @@ parts:
         - file: descriptions/HMBA-10XMultiome-BG-Aligned
         - file: descriptions/HMBA-10XMultiome-BG
         - file: descriptions/HMBA-Spatial-BG
+        - file: descriptions/HMBA-Macaque-PatchSeq-BG
 
   - caption: NOTEBOOKS
     chapters:
@@ -109,6 +110,7 @@ parts:
         - file: notebooks/hmba_bg_10X_snRNASeq_tutorial
         - file: notebooks/hmba_bg_spatial_slabs_and_taxonomy
         - file: notebooks/hmba_bg_spatial_genes
+        - file: notebooks/hmba_bg_macaque_patchseq
 
   - caption: ADDITIONAL RESOURCES
     chapters:

descriptions/HMBA-10XMultiome-BG-Aligned.md

@@ -13,7 +13,7 @@ page.
 These data from the basis of the cross species [Basal Ganglia (BG) taxonomy](HMBA-BG-taxonomy-CCN20250428.md).
 
 For more information on the dataset, please refer to the following webpage:
-[Mammalian Basal Ganglia Consensus Cell Type Atlas](https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/).
+[Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia).
 
 The expression matrices and associated metadata are hosted on AWS S3 bucket as
 a AWS Public Dataset:
@@ -26,12 +26,14 @@ a AWS Public Dataset:
 Data is being shared under the CC BY NC 4.0 license.
 
 Related resources:
+* Single cell transcriptomes for each individual species in the
+  HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
 * Taxonomy and Clustering analysis of ~2 million single cell
   transcriptomes from the aligned dataset.
   ([HMBA-BG-taxonomy-CCN20250428](HMBA-BG-taxonomy-CCN20250428.md))
-* Single cell transcriptomes for each individual species in the
-  HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
 * Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
+([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb):
@@ -51,3 +53,5 @@ Associated notebooks:
 [*notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb*]
 * [**Spatial transcriptomic gene expression**](../notebooks/hmba_bg_spatial_genes.ipynb):
   Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]

descriptions/HMBA-10XMultiome-BG.md

@@ -15,7 +15,7 @@ this includes:
 This release also includes data for running [MapMyCells](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells) for each of the currently released species using the associated [taxonomy](HMBA-BG-taxonomy-CCN20250428.md).
 
 For more information on the dataset, please refer to the following webpage:
-[Mammalian Basal Ganglia Consensus Cell Type Atlas](HMBA-BG-taxonomy-CCN20250428.md).
+[Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia).
 
 The expression matrices and associated metadata are hosted in a AWS S3 bucket
 as a AWS Public Dataset:
@@ -35,6 +35,8 @@ Related resources:
 * ~2 million single cell transcriptomes with aligned genes across species.
   ([HMBA-10XMultiome-BG-Aligned](HMBA-10XMultiome-BG-Aligned.md))
 * Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
+([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb):
@@ -53,4 +55,6 @@ Associated notebooks:
   cases and visualization.
 [*notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb*]
 * [**Spatial transcriptomic gene expression**](../notebooks/hmba_bg_spatial_genes.ipynb):
-  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]

descriptions/HMBA-BG-taxonomy-CCN20250428.md

@@ -27,7 +27,7 @@ previously published taxonomies, and self-projection, ensuring the accuracy and
 robustness of each level in the taxonomic hierarchy across all the species.
 
 For more information on the dataset, please refer to the following webpage:
-[Mammalian Basal Ganglia Consensus Cell Type Atlas](https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/).
+[Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia).
 
 The associated metadata is hosted in a AWS S3 bucket as a AWS Public Dataset:
 
@@ -44,6 +44,8 @@ Related resources :
 * Single cell transcriptomes for each individual species in the
   HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
 * Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
+([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))
 
 Associated notebooks:
 * [**Getting started**](../notebooks/getting_started.ipynb):
@@ -63,3 +65,5 @@ Associated notebooks:
 [*notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb*]
 * [**Spatial transcriptomic gene expression**](../notebooks/hmba_bg_spatial_genes.ipynb):
   Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]

descriptions/HMBA-BG_dataset.md

@@ -6,4 +6,6 @@
   ([HMBA-10XMultiome-BG-Aligned](HMBA-10XMultiome-BG-Aligned.md))
 * Single cell transcriptomes for each individual species in the
   HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
-* Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+* Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
+([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))

descriptions/HMBA-BG_notebooks.md

@@ -11,4 +11,6 @@
   cases and visualization.
 [*notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb*]
 * [**Spatial transcriptomic gene expression**](../notebooks/hmba_bg_spatial_genes.ipynb):
-  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]

descriptions/HMBA-Macaque-PatchSeq-BG.md

@@ -0,0 +1,48 @@
+# Human-Mammalian Brain - Basal Ganglia: Macaque Patch-seq cells multimodal data
+
+Data and metadata for the Patch-seq component of the Human and Mammalian Brain Atlas - Basal Ganglia (HMBA-BG) dataset. 
+
+The basal ganglia (BG) constitute a system of interconnected brain structures that play a crucial role in motor control, learning, behavior, and emotion. These structures are implicated in numerous disorders affecting human health, including Parkinson’s disease, Huntington’s disease, and substance abuse disorders. Despite their importance, little is known about the cellular-level functional properties of the BG in humans and translationally relevant primate species. To address this gap, we performed Patch-seq experiments – integrating patch clamp electrophysiology with single cell RNA-sequencing anchored in the high-resolution, cross-species HMBA consensus basal ganglia cell type taxonomy. This approach enables us to reveal the morpho-electric properties of transcriptomically-defined striatal cell types in primates. Following electrophysiological characterization, nuclei were aspirated for RNA sequencing (SMART-Seq v4), and transcriptomic profiles were mapped to the consensus taxonomy. Each sample was assigned spatial coordinates within an anatomical reference, and cells with high-quality fills and mappings were subsequently reconstructed to obtain morphological features. The data derive from macaque (Macaca mulatta and Macaca nemestrina) striatal tissue obtained through a Tissue Distribution Program. These data are directly comparable to mouse basal ganglia datasets collected using the same protocols.  
+
+Patch-seq samples were mapped to striatal neuronal types using the Hierarchical Approximate Nearest Neighbor (HANN) method implemented in the [Allen Institute MapMyCells package](https://brain-map.org/bkp/analyze/mapmycells), excluding non-neuronal types. After applying quality control to the mapping results, 717 macaque samples were retained. For more information on the taxonomy, please refer to the following webpage: [Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia). Additionally, you can see the associated notebooks linked at the end of this page. 
+
+The expression matrices and associated metadata are hosted on AWS S3 bucket as
+a AWS Public Dataset:
+
+| Component | Current Version | Size    |
+|---|--|---------|
+| Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/HMBA-Macaque-PatchSeq/20260228/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/HMBA-Macaque-PatchSeq/20260228/) | 60.8 MB |
+| Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-Macaque-PatchSeq/20260228/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-Macaque-PatchSeq/20260228/) | 4.5 MB |
+
+Data is being shared under the CC BY NC 4.0 license.
+
+Related resources:
+* ~2 million single cell transcriptomes with aligned genes across species.
+  ([HMBA-10XMultiome-BG-Aligned](HMBA-10XMultiome-BG-Aligned.md))
+* Single cell transcriptomes for each individual species in the
+  HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
+* Taxonomy and Clustering analysis of ~2 million single cell
+  transcriptomes from the aligned dataset.
+  ([HMBA-BG-taxonomy-CCN20250428](HMBA-BG-taxonomy-CCN20250428.md))
+* Spatial transcriptomic data for three species and donors ([HMBA-Spatial-BG](HMBA-Spatial-BG.md))
+
+Associated notebooks:
+* [**Getting started**](../notebooks/getting_started.ipynb):
+  Learn how to use the ABCProjectCache object to facilitate data download and
+  usage.
+* [**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 clustering analysis and annotation**](../notebooks/hmba_bg_clustering_analysis_and_annotation.ipynb):
+  Learn about the HMBA-BG data/metadata structure and taxonomy through example use cases and
+  visualization.
+[*notebooks/hmba_bg_clustering_analysis_and_annotation.ipynb*]
+* [**10X scRNA-seq gene expression**](../notebooks/hmba_bg_10X_snRNASeq_tutorial.ipynb):
+  Interact with HMBA-BG 10X-Aligned gene expression data. [*notebooks/hmba_bg_10X_snRNASeq_tutorial.ipynb*]
+* [**Spatial transcriptomic slab coordinates and annotation**](../notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb):
+  Learn about the HMBA-BG spatial data/metadata structure and mapping to the BG taxonomy through example use
+  cases and visualization.
+[*notebooks/hmba_bg_spatial_slabs_and_taxonomy.ipynb*]
+* [**Spatial transcriptomic gene expression**](../notebooks/hmba_bg_spatial_genes.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_spatial_genes.ipynb*]
+* [**Macaque Patch-Seq notebooks**](../notebooks/hmba_bg_macaque_patchseq.ipynb):
+  Interact with HMBA-BG spatial transcriptomic gene expression data. [*notebooks/hmba_bg_macaque_patchseq.ipynb*]

descriptions/HMBA-Spatial-BG.md

@@ -12,7 +12,7 @@ enabling spatial profiling of hundreds of genes for each cell, and the mapping t
 
 These data form the basis of the cross species [Basal Ganglia (BG) taxonomy](HMBA-BG-taxonomy-CCN20250428.md).
 
-For more information on the taxonomy, please refer to the following webpage: [Mammalian Basal Ganglia Consensus Cell Type Atlas](https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/). Additionally, you can see the associated notebooks linked at the end of this page.
+For more information on the taxonomy, please refer to the following webpage: [Human and Mammalian Brain Atlas Release: Basal Ganglia](https://brain-map.org/consortia/hmba/hmba-release-basal-ganglia).. Additionally, you can see the associated notebooks linked at the end of this page.
 
 The expression matrices and associated metadata are hosted on AWS S3 bucket as
 a AWS Public Dataset. We'll describe each component below.
@@ -40,9 +40,9 @@ different tables, see the the spatial notebooks linked below. For the metadata,
 of quality control and other metrics is available. You can find descriptions of the columns on the Resources page under [Supplemental Metadata Descriptions](../docs/supplemental_metadata_descriptions/README.md).
 | Component | Current Version | Size    |
 |---|--|---------|
-| Human: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-H22.30.001-BG/20250930/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-MERSCOPE-H22.30.001-BG/20250930/) | 2.4 GB |
-| Macaque: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-QM23.50.001-BG/20250630](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-MERSCOPE-QM23.50.001-BG/20250630/) | 1.4 GB |
-| Marmoset: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-Xenium-CJ23.56.004-BG/20250630/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-Xenium-CJ23.56.004-BG/20250630/) | 762.8 MB |
+| Human: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-H22.30.001-BG/20260228/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-MERSCOPE-H22.30.001-BG/20260228/) | 4.2 GB |
+| Macaque: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-QM23.50.001-BG/20250630](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-MERSCOPE-QM23.50.001-BG/20250630/) | 2.5 GB |
+| Marmoset: Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/HMBA-Xenium-CJ23.56.004-BG/20250630/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/HMBA-Xenium-CJ23.56.004-BG/20250630/) | 1.2 GB |
 
 The links below contain geojson files that define the manually drawn polygons that represent anatomical annotation of select basal ganglia regions. These are used and tutorialized in the spatial notebooks linked at the bottom of this page. Please note that these polygons are not derived from registration to the Harmonized Ontology of Mammalian Brain Anatomy (HOMBA). They should instead be used as cellular groupings to orient the user in the anatomical context of the spatial transcriptomics data.”
 | Component | Current Version | Size    |
@@ -63,6 +63,8 @@ Related resources:
   ([HMBA-10XMultiome-BG-Aligned](HMBA-10XMultiome-BG-Aligned.md))
 * Single cell transcriptomes for each individual species in the
   HMBA-BG dataset.([HMBA-10XMultiome-BG](HMBA-10XMultiome-BG.md))
+* 717 Macaque Patch-Seq cells with summary electro-physiology and morphology features.
+([HMBA-Macaque-PatchSeq-BG](HMBA-Macaque-PatchSeq-BG.md))
 
 
 Associated notebooks: