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Name (Github)StatusTechnology
Author (PR)
Tissue Expert
SpeciesTissueFF/FFPEN samplesN patientsPanelLinkPublicationAnnotation how?Histology
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SEA_AD_dataMergedMERFISHBrianMeganBrain
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STARmap-2018-mouse-cortexMergedSTARmapSebastianMeganBrain
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STARmap_plusMergedSTARmap PLUSFlorianMeganMouseBrainFF203
custom 1022 genes
https://zenodo.org/records/8327576
Code: https://github.com/wanglab-broad/mCNS-atlas
https://www.nature.com/articles/s41586-023-06569-5
Manual. Alignment to CCFv3
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abc_atlas_wmb_thalamusMerged
MERSCOPE/MERFISH
Megan, Thomas
MeganMouse
Brain (thalamus)
FF591
custom 500 gene panel
Data Summary: https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/summary
Data Visualizer: https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore
Data Access Jupyter Notebooks: https://alleninstitute.github.io/abc_atlas_access/intro.html
Spatial visualization: Link
https://www.nature.com/articles/s41586-023-06812-z
Manual. Alignment to CCFv3
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libd_dlpfcMergedVisiumNiklasMeganHuman
Brain (dorosolateral prefrontal cortex)
FF123N/Ahttps://research.libd.org/spatialLIBD/
https://pubmed.ncbi.nlm.nih.gov/33558695/
Manual. Using this web application to visualize cytoarchitecture combined with a dimensionality reduction method, specifically t-SNE, as well as the expression patterns of myelin basic protein (MBP) and PCP4, known WM and L5 marker genes, a single experimenter manually assigned each spot to a cortical layer for each sample for all but 352 out of the 47,681 spots across all samples. These 352 spots were located on small fragments of damaged tissue disconnected from the main tissue section. We added these supervised layer annotations to our sce object and the final version is available for download through the fetch_data function in spatialLIBD
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locus_coeruleusMergedVisiumFlorianMeganBrain
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mouse_brain_sagittal_anteriorMergedVisiumKirtiMeganMouseBrainNo annotation
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mouse_brain_sagittal_posteriorMergedVisiumKirtiMeganMouseBrainNo annotation
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mouse_kidney_coronalMergedVisiumKirtiChristophKidneyNo annotation
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osmfish_SspMergedosmFISHPaulMeganMouseBrainFF1133https://linnarssonlab.org/osmFISH/osmFISH_SScortex_mouse_all_cells.loom
https://www.nature.com/articles/s41592-018-0175-z
Computational
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sotip_simulationMerged-Paul--
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spatialDLPFCMergedVisiumNiklasMeganHuman
Brain (dorosolateral prefrontal cortex)
FF3010N/Ahttps://research.libd.org/spatialLIBD/
https://pubmed.ncbi.nlm.nih.gov/38781370/
No annotation
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stereoseq_developing_Drosophila_embryos_larvae
MergedStereo-SeqQirong Mao
Cross Section
https://db.cngb.org/stomics/datasets/STDS0000060
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stereoseq_mouse_embryoMergedStereo-SeqQirong MaoNaveed/NiklasMouseEmbryoFF53N/Ahttps://ftp.cngb.org/pub/SciRAID/stomics/STDS0000058/stomics/
https://pubmed.ncbi.nlm.nih.gov/35512705/
Computational. Spatially constrained clustering (SCC), which is built on top of the Leiden clustering algorithm, was used.
Separate annotation here https://zenodo.org/records/10516814
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stereoseq_olfactory_bulbMergedStereo-SeqQirong MaoMeganBrain
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visium_breast_cancer_SEDRMergedVisiumPaulHuman
Breast (invasive ductal carcinoma)
FF11N/Ahttps://www.10xgenomics.com/resources/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0
Processed: https://github.com/JinmiaoChenLab/SEDR_analyses/tree/master/data/BRCA1
Manual annotation based on H&E staining
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visium_chicken_heartMergedVisium
Anastasiia Okhtienko
ChristophChickenHeartFF44N/Ahttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149457
https://github.com/madhavmantri/chicken_heart
Data used in this study: https://www.biorxiv.org/content/10.1101/2022.02.28.482296v2.full
https://www.nature.com/articles/s41467-021-21892-z
Seurat clustering with modification(?)
Note: Maybe re-annotation is needed. Current anatomical annotation is taken from Seurat clustering.
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xenium-breast-cancerMergedXeniumFlorianHumanBreastFFPE11
Xenium Human Breast Gene Expression Panel v1 (280 genes) with 100 additional custom genes (hBreast_v1_AddOn100g)
https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-with-custom-add-on-panel-1-standard
Manual. From Gen Bio: Xenium breast cancer data were annotated using the matched histopathology (H&E) image provided along with the dataset. The data were annotated for eight region types: ductal carcinoma in-situ (DCIS), invasive tumor, normal ducts, immune cells, cysts, blood vessels, adipose tissue, and stroma. 10x: The ground truth annotations were manually identified and verified with expert pathologists who observed that regions were either morphologically distinct or were surrounded by a unique microenvironment in the histology images
Separate annotation here https://zenodo.org/records/10516814
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xenium-mouse-brain-SergioSalasMergedXeniumSebastianMeganMouse
Brain (coronal section)
FF11
Xenium Mouse Brain Gene Expression Panel v1 (247 genes)
Temp: https://drive.google.com/file/d/1mEMfxIRVXJ-XBfKyK3kxRU0k3I6sQINY/view?usp=drive_link
Original: https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-replicates-1-standard
https://www.nature.com/articles/s41592-025-02617-2
Manual. The dataset underwent manual annotation using the mouse coronal P56 sample from Allen Brain Atlas [PMID:32386544] to specify anatomical regions [PMID:40082609].
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slideseq2_olfactory_bulbPullSlide-seqV2PaulMeganMouse
Brain (olfactory bulb)
FF2020N/Ahttps://db.cngb.org/stomics/datasets/STDS0000172/summary
https://www.nature.com/articles/s41593-022-01030-8
Manual. Annotated by the authors based on the expression of marker genes.
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merfish_aging_mouse_brainON HOLDMERFISHPaulMeganBrainhttps://cellxgene.cziscience.com/collections/31937775-0602-4e52-a799-b6acdd2bac2e
Dataset includes two conditions. Inflam vs aging. Should however not affect anatomical domains . Counts not available
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data_barseq2_mouse_viscortexON HOLDBARseq2PaulMeganBrain
Counts not available
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her2st-breast-cancerPullSTSebastianBreast
Need to check-in with Sebastian
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visium_hd_cancer_colonMergedVisium HDPaulAminHuman
Colon (colorectal cancer)
FFPE11N/Ahttps://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc
https://www.biorxiv.org/content/10.1101/2024.06.04.597233v1
Manual. Pathologist annotation based on HE, refined by marker genes. Tumor:EPCAM,Vessel:VWF,Muscle:MYL9
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merfish_devheartMergedMERFISHKirtiChristophHuman
Heart (developing)
FF42238https://datadryad.org/stash/dataset/doi:10.5061/dryad.w0vt4b8vp
https://www.nature.com/articles/s41586-024-07171-z
Computational. Cellular communities were identified based on k-means clustering of relative cellular composition within 150 um of each cell.
GT not based on expression, but cell labels
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stereoseq_liverMergedStereo-SeqKirtiNaveedMouseLiverFF6?N/Ahttps://db.cngb.org/stomics/lista/spatial/
https://www.nature.com/articles/s41588-024-01709-7
Computational. The ground truth annotations were computationally identified where zonation layers were annotated based on the differences between the scores of pericentral and periportal hepatocyte landmark genes.
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cosmx_lungMerged
CosMx (prototype instrament)
KirtiHuman
Lung (NSCLC)
FFPE58960https://staging.nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/
https://www.nature.com/articles/s41587-022-01483-z

Computational. The frequency of each cell type among its 200 closest neighbors was clustered using Mclust.
Separate pathologist annotation https://zenodo.org/records/10516814
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cosmx_liverMergedCosMxKirtiNaveedHuman
Liver (Normal and HCC)
FFPE22
Human Universal Cell Characterization Panel 1000 plex
https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/human-liver-rna-ffpe-dataset/
Computational. The frequency of each cell type among its 200 closest neighbors was clustered using Mclust.
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