Overview of datasets on S3 bucket

[rcannood]

As part of the HCA OP 2026 Spatial Hackathon, a bunch of datasets were uploaded to the S3 bucket.

@arl94 As not to lose track of what was created by whom, would it be possible to give an overview of everything in the bucket?

For example:

---

path: s3://hca-op-spatial/datasets/gt_annotated_data/Human_Breast_Biomarkers_S1_Bot_outs_Aligned.zarr/
technology: ...
available annotations: (which ground truth info there is)
source: (where the data came from)
submitter: (who uploaded the data)
...? anything else

---

path: s3://hca-op-spatial/datasets/gt_annotated_data/WTA_Preview_FFPE_Breast_Cancer_Aligned_subset.zarr/

---

path: s3://hca-op-spatial/datasets/gt_annotated_data/WTA_Preview_FFPE_Breast_Cancer_Aligned.zarr/

---

path: s3://hca-op-spatial/datasets/gt_annotated_data/Xenium_Prime_Cervical_Cancer_FFPE_Aligned.zarr/

---

path: s3://hca-op-spatial/datasets/gt_annotated_data/Xenium_V1_hLiver_nondiseased_section_FFPE_outs_Aligned.zarr/

---

path: s3://hca-op-spatial/datasets/10X_Hackathon_data_3D/xenium_hcervical_cancer_3d/

---

path: s3://hca-op-spatial/datasets/10X_Hackathon_data_3D/xenium_mbrain_3d/

---

path: s3://hca-op-spatial/datasets/MERSCOPE_data/BreastCancerTMA/

---

path: s3://hca-op-spatial/datasets/multimodal_data/Breast_L1_IHC.zarr/

---

path: s3://hca-op-spatial/datasets/multimodal_data/Xenium_V1_Human_Kidney_FFPE_1500x1500_XeniumSpace.zarr/

---

path: s3://hca-op-spatial/datasets/Xenium_V1_Human_Kidney_FFPE.zarr/Xenium_V1_Human_Kidney_FFPE_20260518_V2.zarr/

---

Is anything missing?

[arl94]

Template
Path: s3://hca-op-spatial/datasets/{path}
Technology: ...
Available annotations: (which ground truth info there is)
Source: (where the data came from)
Submitter: (who uploaded the data)

1a. Xenium V1 Human Breast Cancer
Description: Xenium v1 Human Breast FFPE with Biomarkers & Housekeeping Genes Custom Panel, from same tissue block as sample 1, cropped subsection of sample 2
Path: s3://hca-op-spatial/datasets/gt_annotated_data/Human_Breast_Biomarkers_S1_Bot_outs_Aligned.zarr/
Technology: Xenium V1
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-biomarkers
Submitter: H&E annotations performed by @caner-ercan, alignments and mapping to Xenium performed by @arl94

1b. Xenium V1 Human Breast Cancer Subset
Description: Xenium v1 Human Breast FFPE with Biomarkers & Housekeeping Genes Custom Panel, from same tissue block as sample 1, cropped subsection of sample 1a
Path: @yhtgrace
Technology: Xenium V1
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-biomarkers
Submitter: @yhtgrace

2a. WTA Human Breast Cancer
Description: Preview Data - Atera In Situ Gene Expression, FFPE Human Breast Cancer, from same tissue block as sample 1, cropped subsection of sample 1
Path: s3://hca-op-spatial/datasets/gt_annotated_data/WTA_Preview_FFPE_Breast_Cancer_Aligned.zarr/
Technology: Atera Whole Transcriptome Assay
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/atera-wta-ffpe-human-breast-cancer
Submitter: H&E annotations performed by @caner-ercan, alignments and mapping to Xenium performed by @arl94

2b. WTA Human Breast Cancer Subset
Description: Preview Dat - Atera In Situ Gene Expression, FFPE Human Breast Cancer, from same tissue block as sample 1, cropped subsection of sample 2a
Path: s3://hca-op-spatial/datasets/gt_annotated_data/WTA_Preview_FFPE_Breast_Cancer_Aligned_subset.zarr/
Technology: Atera Whole Transcriptome Assay
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/atera-wta-ffpe-human-breast-cancer
Submitter: @yhtgrace

3a. Xenium Prime 5K Human Cervical Cancer
Description: FFPE Human Cervical Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes, from same tissue block as sample 4
Path: s3://hca-op-spatial/datasets/gt_annotated_data/Xenium_Prime_Cervical_Cancer_FFPE_Aligned.zarr/
Technology: Xenium Prime 5K
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/xenium-prime-ffpe-human-cervical-cancer
Submitter: H&E annotations performed by @caner-ercan, alignments and mapping to Xenium performed by @arl94

3b. Xenium Prime 5K Human Cervical Cancer Subset
Description: FFPE Human Cervical Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes, from same tissue block as sample 4, cropped subsection of sample 3a
Path: @yhtgrace
Technology: Xenium Prime 5K
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/xenium-prime-ffpe-human-cervical-cancer
Submitter: @yhtgrace

3c. 3D Z-stack for Xenium Prime 5K Human Cervical Cancer
Description: 3D raw z-stack internal data from 10X Genomics for FFPE Human Cervical Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes, corresponds to sample 3a
Path: s3://hca-op-spatial/datasets/10X_Hackathon_data_3D/xenium_hcervical_cancer_3d/
Technology: Xenium Prime 5K
Source: 10X Genomics (internal)
Submitter: @arl94

4a. WTA Human Cervical Cancer
Description: Preview Data - Atera In Situ Gene Expression, FFPE Human Cervical Cancer, from same tissue block as sample 3
Path: s3://hca-op-spatial/datasets/gt_annotated_data/WTA_Preview_FFPE_Cervical_Cancer_Aligned.zarr/
Technology: Atera Whole Transcriptome Assay
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/atera-wta-ffpe-human-cervical-cancer
Submitter: H&E annotations performed by @caner-ercan, alignments and mapping to Xenium performed by @arl94

4b. WTA Human Cervical Cancer Subset
Description: Preview Data - Atera In Situ Gene Expression, FFPE Human Cervical Cancer, from same tissue block as sample 3, cropped subsection of sample 4a
Path: @yhtgrace
Technology: Atera Whole Transcriptome Assay
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: https://www.10xgenomics.com/datasets/atera-wta-ffpe-human-cervical-cancer
Submitter: @yhtgrace

5. Human Liver Nondiseased
Description: @caner-ercan
Path: s3://hca-op-spatial/datasets/gt_annotated_data/Xenium_V1_hLiver_nondiseased_section_FFPE_outs_Aligned.zarr/
Technology: Xenium V1
Available annotations: Histoplus Cell Annotations (sdata.tables["table"].obs["histoplus_cell_class"])
Source: @caner-ercan
Submitter: H&E annotations performed by @caner-ercan, alignments and mapping to Xenium performed by @arl94

6a. Xenium Prime Mouse Brain
Description: 3D raw z-stack internal data from 10X Genomics for FFPE Human Cervical Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes
Path: s3://hca-op-spatial/datasets/Xenium_Prime_Mouse_Brain_Coronal_FF.zarr/
Technology: Xenium Prime
Source: http://10xgenomics.com/datasets/xenium-prime-fresh-frozen-mouse-brain
Submitter: @arl94

6b. 3D Z-stack for Xenium Prime Mouse Brain
Description: 3D raw z-stack internal data from 10X Genomics for FFPE Human Cervical Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes, corresponds to Xenium sample 6a
Path: s3://hca-op-spatial/datasets/10X_Hackathon_data_3D/xenium_mbrain_3d/
Technology: Xenium Prime
Source: 10X Genomics (internal)
Submitter: @arl94

7. Multimodal Human Breast Cancer
Description: Xenium V1 Human Breast Cancer with 280 gene panel and IHC labels for CD8+, PanCK+, double-positive, and double-negative cells
Path: s3://hca-op-spatial/datasets/multimodal_data/Breast_L1_IHC.zarr/
Technology: Xenium V1
Available annotations: Immunohistochemistry (IHC) dervied Cell Annotations (sdata.tables["table"].obs["IHC"])
Source: @caner-ercan
Submitter: IHC labeling obtained by @senbaikang, alignments and preparations by @arl94

8a. Multimodal Renal Cell Carcinoma (Kidney)
Description: Xenium In Situ Gene and Protein Expression data for FFPE Human Renal Cell Carcinoma
Path: s3://hca-op-spatial/datasets/multimodal_data/Xenium_V1_Human_Kidney_FFPE.zarr/
Technology: Xenium In Situ
Available annotations: Protein-dervied cell annotations (sdata.tables["table"].obs["cell_labels"]), quantified protein information (sdata.tables["protein"]), aligned H&E images (see source link)
Available scRNA reference: work in progress (potential sources may be: https://www.nature.com/articles/s42003-024-06478-x or https://www.pnas.org/doi/10.1073/pnas.2103240118)
Source: https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma
Submitter: @arl94

8b. Multimodal Renal Cell Carcinoma (Kidney) - Subset 1
Description: Xenium In Situ Gene and Protein Expression data for FFPE Human Renal Cell Carcinoma, 1500x1500 micron subset of sample 8a
Path: s3://hca-op-spatial/datasets/multimodal_data/Xenium_V1_Human_Kidney_FFPE_1500x1500_XeniumSpace.zarr/
Technology: Xenium In Situ
Available annotations: Protein-dervied cell annotations (sdata.tables["table"].obs["cell_labels"]), quantified protein information (sdata.tables["protein"]), aligned H&E images (see source link)
Available scRNA reference: work in progress (potential sources may be: https://www.nature.com/articles/s42003-024-06478-x or https://www.pnas.org/doi/10.1073/pnas.2103240118)
Source: https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma
Submitter: @arl94

8c. Multimodal Renal Cell Carcinoma (Kidney) - Subset 2
Description: Xenium In Situ Gene and Protein Expression data for FFPE Human Renal Cell Carcinoma, 1500x1500 pixel subset of sample 8a
Path: s3://hca-op-spatial/datasets/multimodal_data/Xenium_V1_Human_Kidney_FFPE_1500x1500_MorphologySpace.zarr/
Technology: Xenium In Situ
Available annotations: Protein-dervied cell annotations (sdata.tables["table"].obs["cell_labels"]), quantified protein information (sdata.tables["protein"]), aligned H&E images (see source link)
Available scRNA reference: work in progress (potential sources may be: https://www.nature.com/articles/s42003-024-06478-x or https://www.pnas.org/doi/10.1073/pnas.2103240118)
Source: https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma
Submitter: @arl94

9. FFPE Human Pancreas with Xenium Multimodal Cell Segmentation
Description: Xenium In Situ Gene Expression with Cell Segmentation Staining data for adult human pancreatic cancer tissue using the Xenium Human Multi-Tissue and Cancer Panel
Path: s3://hca-op-spatial/datasets/Xenium_V1_human_Pancreas_FFPE.zarr/
Technology: Xenium V1
Source: 10X Genomics (internal)
Submitter: @arl94, at request of Peter Kharchenko

X. Pediatric Lung (Xenium + 50 protein CODEX)
Description: ...
Path: ...
Technology: ...
Available annotations: ...
Matched scRNA path: ...
Source: ...
Submitter: @dariarom94

** Other datasets without details (yet)**
path: s3://hca-op-spatial/datasets/MERSCOPE_data/BreastCancerTMA/

[Fritze]

10. MERSCOPE - Breast cancer TMA
    Description: MERSCOPE data for 5 FFPE cores of a Breast Cancer TMA
    Path raw data: s3://hca-op-spatial/datasets/MERSCOPE_data/BreastCancerTMA/202409242358_240916JHHUBC0005XQ-V2V-HubcTMA-V2-BY_VMSC02511/
    Path spatialdata: s3://hca-op-spatial/datasets/MERSCOPE_data/BreastCancerTMA/spatialdata_zarrs/
    Technology: MERSCOPE (v2 chemistry)
    Available scRNA reference: work in progress (potential source may be: https://academic.oup.com/nargab/article/8/1/lqaf217/8445266)
    Source: https://info.vizgen.com/access-to-merfish-2.0-data-release
    Submitter: @Fritze

11. MERSCOPE - Human brain sample (cortex)
    Description: MERSCOPE data for fresh frozen Human Cortex
    Path raw data: s3://hca-op-spatial/datasets/MERSCOPE_data/HumanBrain/202503211645_HuBrain-FF-22676A1-D2M1769-RC_VMSC16710/
    Path spatialdata: s3://hca-op-spatial/datasets/MERSCOPE_data/HumanBrain/spatialdata_zarrs/
    Technology: MERSCOPE (v2 chemistry)
    Available scRNA reference: work in progress
    Source: https://info.vizgen.com/access-to-merfish-2.0-data-release
    Submitter: @Fritze