Publish HistAgent tutorial and Agent Module data

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+chat/spots.jsonl filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,69 @@
+---
+pretty_name: HistAgent tutorial and Chat data
+license: other
+task_categories:
+- image-to-text
+- text-retrieval
+language:
+- en
+---
+
+# HistAgent tutorial and Chat data
+
+This repository contains the public data used by the HistAgent tutorials and
+the configurable Chat example.
+
+## Contents
+
+```text
+HistAgent-data/
+├── tutorials/              # data loaded by the five tutorial notebooks
+├── chat/
+│   ├── spots.jsonl         # 9,150 spatial transcriptomics spot records
+│   ├── config.example.env  # Chat data-path configuration
+│   └── slice_images/       # three RCC tissue images for the slice selector
+└── manifest.json           # byte sizes and SHA-256 checksums
+```
+
+The tutorial files include benchmark summaries, spot-level examples, plotted
+WSI panels, a pretrained ABMIL example and the atlas-retrieval examples.
+
+The Chat JSONL contains ranked genes, cell-state summaries, pathways and
+spatial context for each public demo spot. The tissue images use public study
+accessions as filenames so the Chat server can match them to their slices.
+
+## Download
+
+```python
+from huggingface_hub import snapshot_download
+
+root = snapshot_download(
+    "wli13/HistAgent-data",
+    repo_type="dataset",
+)
+```
+
+Tutorial notebooks expect:
+
+```python
+DATA_DIR = root / "tutorials"
+```
+
+For Chat:
+
+```text
+HISTAGENT_INPUT_JSONL=<root>/chat/spots.jsonl
+HISTAGENT_ATLAS_SQLITE=
+HISTAGENT_SLICE_IMAGE_DIRS=<root>/chat/slice_images
+```
+
+The public Chat bundle does not require the optional full-atlas SQLite file.
+Natural-language retrieval uses the 9,150 rich spot records in `spots.jsonl`.
+
+## Provenance and use
+
+The bundle contains derived research outputs and examples assembled from the
+public studies cited by the HistAgent manuscript. Source-study terms continue
+to apply to the underlying data. HistAgent molecular readouts are predictions
+and must not be treated as measured transcript counts or used for clinical
+decision-making without independent validation.

chat/config.example.env

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+HISTAGENT_INPUT_JSONL=chat/spots.jsonl
+HISTAGENT_ATLAS_SQLITE=
+HISTAGENT_SLICE_IMAGE_DIRS=chat/slice_images

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Immunity 55, 527–541.e5 (2022).","Biological category":"Immune microenvironment","Biological target":"RCC TLS regions","Marker reference":"Meylan et al. 29-gene TLS imprint","Markers used":"IGHA1;IGHG1;IGHG2;IGHG3;IGHG4;IGHM;IGKC;IGLC1;JCHAIN;CD79A;FCRL5;MZB1;SSR4;XBP1;TRBC2;IL7R;CXCL12;LUM;C1QA;C7;CD52;APOE;PTGDS;PIM2;DERL3","Measured ST AUPRC":0.6079634933642918,"HistAgent AUPRC":0.743032435032611,"STPath AUPRC":0.1807023284665895,"OmiCLIP AUPRC":0.2178663241938052},{"Section":"GSE213688_GSM6592052","GEO Series":"GSE213688","GEO Sample":"GSM6592052","Repository accession":"GSM6592052","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Immune microenvironment","Biological target":"Breast TIL / lymphoid compartment","Marker reference":"Published positive T-cell marker component from the breast-cancer TME classifier","Markers used":"CD3D;CD3E;CD3G","Measured ST AUPRC":0.3951369146823507,"HistAgent AUPRC":0.6256978419174334,"STPath AUPRC":0.4058741116540961,"OmiCLIP AUPRC":0.5275338195208694},{"Section":"GSE213688_GSM6592054","GEO Series":"GSE213688","GEO Sample":"GSM6592054","Repository accession":"GSM6592054","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Immune microenvironment","Biological target":"Breast TIL / lymphoid compartment","Marker reference":"Published positive T-cell marker component from the breast-cancer TME classifier","Markers used":"CD3D;CD3E;CD3G","Measured ST AUPRC":0.5434819308805219,"HistAgent AUPRC":0.7927631563791024,"STPath AUPRC":0.472038698059974,"OmiCLIP AUPRC":0.4350745140974631},{"Section":"Human_Prostate_Erickson_08102022_Visium_Patient_1_H2_1","GEO Series":"","GEO Sample":"","Repository accession":"10.17632/svw96g68dv.1 | Patient_1_H2_1","Species":"Human","Organ":"Prostate","Study":"Erickson 2022","Study reference":"Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Prostate stromal compartment","Marker reference":"Composite of the published fibroblast and pericyte marker sets","Markers used":"DCN;LUM;PTN;IGF1;APOD;COL1A2;FBLN1;MEG3;CXCL12;RGS5;ACTA2;MYH11;MT1M;FRZB;MT1A;NDUFA4L2;PPP1R14A;MYLK;PHLDA1","Measured ST AUPRC":0.6454658467418909,"HistAgent AUPRC":0.8098626740035776,"STPath AUPRC":0.282197274269499,"OmiCLIP AUPRC":0.7325925302433924},{"Section":"Human_Prostate_Erickson_08102022_Visium_Patient_1_H2_2","GEO Series":"","GEO Sample":"","Repository accession":"10.17632/svw96g68dv.1 | Patient_1_H2_2","Species":"Human","Organ":"Prostate","Study":"Erickson 2022","Study reference":"Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Prostate stromal compartment","Marker reference":"Composite of the published fibroblast and pericyte marker sets","Markers used":"DCN;LUM;PTN;IGF1;APOD;COL1A2;FBLN1;MEG3;CXCL12;RGS5;ACTA2;MYH11;MT1M;FRZB;MT1A;NDUFA4L2;PPP1R14A;MYLK;PHLDA1","Measured ST AUPRC":0.6813464403017034,"HistAgent AUPRC":0.9479273231153827,"STPath AUPRC":0.479604656611474,"OmiCLIP AUPRC":0.9707621359391516},{"Section":"Human_Prostate_Erickson_08102022_Visium_Patient_1_V1_2","GEO Series":"","GEO Sample":"","Repository accession":"10.17632/svw96g68dv.1 | Patient_1_V1_2","Species":"Human","Organ":"Prostate","Study":"Erickson 2022","Study reference":"Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Prostate stromal compartment","Marker reference":"Composite of the published fibroblast and pericyte marker sets","Markers used":"DCN;LUM;PTN;IGF1;APOD;COL1A2;FBLN1;MEG3;CXCL12;RGS5;ACTA2;MYH11;MT1M;FRZB;MT1A;NDUFA4L2;PPP1R14A;MYLK;PHLDA1","Measured ST AUPRC":0.66351131103667,"HistAgent AUPRC":0.9305924296175988,"STPath AUPRC":0.5802491516471776,"OmiCLIP AUPRC":0.9325284677790344},{"Section":"GSE213688_GSM6592049","GEO Series":"GSE213688","GEO Sample":"GSM6592049","Repository accession":"GSM6592049","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Breast CAF / stromal compartment","Marker reference":"Published positive CAF marker component from the breast-cancer TME classifier","Markers used":"PDGFRB;PDGFRA;PDPN;DCN;COL1A1;COL1A2;FAP;THY1;CXCL12;MCAM;ACTA2;MYLK;MYL9;TAGLN;CALD1;CAV1;MEF2C;NOTCH3;RGS5","Measured ST AUPRC":0.3215091704522756,"HistAgent AUPRC":0.583980156300487,"STPath AUPRC":0.4479413445180808,"OmiCLIP AUPRC":0.6594440217800369},{"Section":"GSE213688_GSM6592051","GEO Series":"GSE213688","GEO Sample":"GSM6592051","Repository accession":"GSM6592051","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Breast CAF / stromal compartment","Marker reference":"Published positive CAF marker component from the breast-cancer TME classifier","Markers used":"PDGFRB;PDGFRA;PDPN;DCN;COL1A1;COL1A2;FAP;THY1;CXCL12;MCAM;ACTA2;MYLK;MYL9;TAGLN;CALD1;CAV1;MEF2C;NOTCH3;RGS5","Measured ST AUPRC":0.6348500639395558,"HistAgent AUPRC":0.9473764516398884,"STPath AUPRC":0.8107071158270132,"OmiCLIP AUPRC":0.9768425227145556},{"Section":"GSE213688_GSM6592052","GEO Series":"GSE213688","GEO Sample":"GSM6592052","Repository accession":"GSM6592052","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Stromal / fibrotic microenvironment","Biological target":"Breast CAF / stromal compartment","Marker reference":"Published positive CAF marker component from the breast-cancer TME classifier","Markers used":"PDGFRB;PDGFRA;PDPN;DCN;COL1A1;COL1A2;FAP;THY1;CXCL12;MCAM;ACTA2;MYLK;MYL9;TAGLN;CALD1;CAV1;MEF2C;NOTCH3;RGS5","Measured ST AUPRC":0.2765661952275118,"HistAgent AUPRC":0.625497347313072,"STPath AUPRC":0.3441745655825215,"OmiCLIP AUPRC":0.5049590252663657},{"Section":"GSE193460_GSM5808054","GEO Series":"GSE193460","GEO Sample":"GSM5808054","Repository accession":"GSM5808054","Species":"Mouse","Organ":"Lung","Study":"Dhainaut 2022","Study reference":"Dhainaut, M. et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 185, 1223–1239.e20 (2022).","Biological category":"Tumour / epithelial state","Biological target":"WPRE-positive lung tumour","Marker reference":"Krt8, Krt18 and Epcam explicitly reported as tumour-lesion-enriched keratin and epithelial genes","Markers used":"Krt8;Krt18;Epcam","Measured ST AUPRC":0.8524757119378117,"HistAgent AUPRC":0.6417219014323887,"STPath AUPRC":0.2707631686069724,"OmiCLIP AUPRC":0.2415083998999807},{"Section":"GSE193460_GSM5808055","GEO Series":"GSE193460","GEO Sample":"GSM5808055","Repository accession":"GSM5808055","Species":"Mouse","Organ":"Lung","Study":"Dhainaut 2022","Study reference":"Dhainaut, M. et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 185, 1223–1239.e20 (2022).","Biological category":"Tumour / epithelial state","Biological target":"WPRE-positive lung tumour","Marker reference":"Krt8, Krt18 and Epcam explicitly reported as tumour-lesion-enriched keratin and epithelial genes","Markers used":"Krt8;Krt18;Epcam","Measured ST AUPRC":0.8400711324733409,"HistAgent AUPRC":0.7381596410816733,"STPath AUPRC":0.3076329103976639,"OmiCLIP AUPRC":0.3421999888767961},{"Section":"GSE193460_GSM5808056","GEO Series":"GSE193460","GEO Sample":"GSM5808056","Repository accession":"GSM5808056","Species":"Mouse","Organ":"Lung","Study":"Dhainaut 2022","Study reference":"Dhainaut, M. et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 185, 1223–1239.e20 (2022).","Biological category":"Tumour / epithelial state","Biological target":"WPRE-positive lung tumour","Marker reference":"Krt8, Krt18 and Epcam explicitly reported as tumour-lesion-enriched keratin and epithelial genes","Markers used":"Krt8;Krt18;Epcam","Measured ST AUPRC":0.8854232391771233,"HistAgent AUPRC":0.7389527199351767,"STPath AUPRC":0.3772879429817578,"OmiCLIP AUPRC":0.4196074185968733},{"Section":"GSE193460_GSM5808057","GEO Series":"GSE193460","GEO Sample":"GSM5808057","Repository accession":"GSM5808057","Species":"Mouse","Organ":"Lung","Study":"Dhainaut 2022","Study reference":"Dhainaut, M. et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 185, 1223–1239.e20 (2022).","Biological category":"Tumour / epithelial state","Biological target":"WPRE-positive lung tumour","Marker reference":"Krt8, Krt18 and Epcam explicitly reported as tumour-lesion-enriched keratin and epithelial genes","Markers used":"Krt8;Krt18;Epcam","Measured ST AUPRC":0.7733351798223841,"HistAgent AUPRC":0.613434083356211,"STPath AUPRC":0.1536836783276255,"OmiCLIP AUPRC":0.1674456799998194},{"Section":"Human_Prostate_Erickson_08102022_Visium_Patient_1_H2_1","GEO Series":"","GEO Sample":"","Repository accession":"10.17632/svw96g68dv.1 | Patient_1_H2_1","Species":"Human","Organ":"Prostate","Study":"Erickson 2022","Study reference":"Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).","Biological category":"Tumour / epithelial state","Biological target":"Prostate malignant versus benign epithelium","Marker reference":"Externally validated eight-gene Prostate Tumor Gene Signature","Markers used":"PCA3;AMACR;ERG;CACNA1D;FABP5;COL9A2;PHGR1;GCNT1","Measured ST AUPRC":0.4164578606076237,"HistAgent AUPRC":0.4686630883446406,"STPath AUPRC":0.2210123522927035,"OmiCLIP AUPRC":0.1880900866299258},{"Section":"Human_Prostate_Erickson_08102022_Visium_Patient_1_H2_2","GEO Series":"","GEO Sample":"","Repository accession":"10.17632/svw96g68dv.1 | Patient_1_H2_2","Species":"Human","Organ":"Prostate","Study":"Erickson 2022","Study reference":"Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).","Biological category":"Tumour / epithelial state","Biological target":"Prostate malignant versus benign epithelium","Marker reference":"Externally validated eight-gene Prostate Tumor Gene Signature","Markers used":"PCA3;AMACR;ERG;CACNA1D;FABP5;COL9A2;PHGR1;GCNT1","Measured ST AUPRC":0.205095885676921,"HistAgent AUPRC":0.1184270240263498,"STPath AUPRC":0.0138738497517259,"OmiCLIP AUPRC":0.0224560601682868},{"Section":"GSE213688_GSM6592054","GEO Series":"GSE213688","GEO Sample":"GSM6592054","Repository accession":"GSM6592054","Species":"Human","Organ":"Breast","Study":"Coutant 2023","Study reference":"Coutant, A. et al. Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes. Laboratory Investigation 103, 100258 (2023).","Biological category":"Tumour / epithelial state","Biological target":"Breast normal epithelium","Marker reference":"Fixed human breast epithelial-component panel","Markers used":"EPCAM;KRT8;KRT18;CLDN4;DSC2;ELF3;SFN;ITGB4;ITGB6;KRT6A;KRT7;LAD1;LAMA3;LAMB3;SLPI;ST14;TGFA;SCEL;PTGES;SH2D3A;AP1M2;MPZL2;EHF;G0S2;LSR;S100A14","Measured ST AUPRC":0.9197102175039256,"HistAgent AUPRC":0.917191345687214,"STPath AUPRC":0.8298331726268193,"OmiCLIP AUPRC":0.570400072514115},{"Section":"Human_Brain_Maynard_02082021_Visium_151508","GEO Series":"","GEO Sample":"","Repository accession":"spatialLIBD sample 151508","Species":"Human","Organ":"Brain","Study":"Maynard 2021","Study reference":"Maynard, K. R. et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436 (2021).","Biological category":"Tissue anatomy","Biological target":"DLPFC white matter","Marker reference":"Independent known myelin transcript panel","Markers used":"CNP;PLP1;MAG;CLDN11","Measured ST AUPRC":0.3492274803091549,"HistAgent AUPRC":0.9001070361140725,"STPath AUPRC":0.0823911116714834,"OmiCLIP AUPRC":0.0274460610864636},{"Section":"Human_Brain_Maynard_02082021_Visium_151673","GEO Series":"","GEO Sample":"","Repository accession":"spatialLIBD sample 151673","Species":"Human","Organ":"Brain","Study":"Maynard 2021","Study reference":"Maynard, K. R. et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436 (2021).","Biological category":"Tissue anatomy","Biological target":"DLPFC white matter","Marker reference":"Independent known myelin transcript panel","Markers used":"CNP;PLP1;MAG;CLDN11","Measured ST AUPRC":0.8902736507070603,"HistAgent AUPRC":0.9400415547487908,"STPath AUPRC":0.65332741739147,"OmiCLIP AUPRC":0.5481470299952124},{"Section":"Human_Brain_Maynard_02082021_Visium_151674","GEO Series":"","GEO Sample":"","Repository accession":"spatialLIBD sample 151674","Species":"Human","Organ":"Brain","Study":"Maynard 2021","Study reference":"Maynard, K. R. et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436 (2021).","Biological category":"Tissue anatomy","Biological target":"DLPFC white matter","Marker reference":"Independent known myelin transcript panel","Markers used":"CNP;PLP1;MAG;CLDN11","Measured ST AUPRC":0.9288673654333514,"HistAgent AUPRC":0.985623975605608,"STPath AUPRC":0.3869527187536975,"OmiCLIP AUPRC":0.107501458121605},{"Section":"Human_Brain_Maynard_02082021_Visium_151675","GEO Series":"","GEO Sample":"","Repository accession":"spatialLIBD sample 151675","Species":"Human","Organ":"Brain","Study":"Maynard 2021","Study reference":"Maynard, K. R. et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436 (2021).","Biological category":"Tissue anatomy","Biological target":"DLPFC white matter","Marker reference":"Independent known myelin transcript panel","Markers used":"CNP;PLP1;MAG;CLDN11","Measured ST AUPRC":0.9185675368671627,"HistAgent AUPRC":0.9767052573788167,"STPath AUPRC":0.3614549083298954,"OmiCLIP AUPRC":0.1116136491866433},{"Section":"Human_Brain_Maynard_02082021_Visium_151676","GEO Series":"","GEO Sample":"","Repository accession":"spatialLIBD sample 151676","Species":"Human","Organ":"Brain","Study":"Maynard 2021","Study reference":"Maynard, K. R. et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436 (2021).","Biological category":"Tissue anatomy","Biological target":"DLPFC white matter","Marker reference":"Independent known myelin transcript panel","Markers used":"CNP;PLP1;MAG;CLDN11","Measured ST AUPRC":0.9094454317369068,"HistAgent AUPRC":0.9620889465504032,"STPath AUPRC":0.3111667645885169,"OmiCLIP AUPRC":0.0933240826363496},{"Section":"Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1","GEO Series":"","GEO Sample":"","Repository accession":"10.5281/zenodo.10698931 | mMAMP/MA | V1_Mouse_Brain_Sagittal_Anterior","Species":"Mouse","Organ":"Brain","Study":"GraphST annotation / BenchmarkST redistribution","Study reference":"Long, Y. et al. Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Nature Communications 14, 1155 (2023).","Biological category":"Tissue anatomy","Biological target":"Mouse corpus callosum","Marker reference":"Independent mouse CNS spatial-atlas fibre-tract marker set","Markers used":"Mbp;Cldn11;Mal","Measured ST AUPRC":0.2554053194765088,"HistAgent AUPRC":0.167256027008141,"STPath AUPRC":0.057485448721897,"OmiCLIP AUPRC":0.032293986636971},{"Section":"Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1","GEO Series":"","GEO Sample":"","Repository accession":"10.5281/zenodo.10698931 | mMAMP/MA | V1_Mouse_Brain_Sagittal_Anterior","Species":"Mouse","Organ":"Brain","Study":"GraphST annotation / BenchmarkST redistribution","Study reference":"Long, Y. et al. Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Nature Communications 14, 1155 (2023).","Biological category":"Tissue anatomy","Biological target":"Mouse cerebral cortex","Marker reference":"Shi et al., Nature 2023, Supplementary Table 5, https://doi.org/10.1038/s41586-023-06569-5","Markers used":"Nrgn;Slc17a7;Satb2;Cck;Pde1a","Measured ST AUPRC":0.8924834974292258,"HistAgent AUPRC":0.938707474286144,"STPath AUPRC":0.5436933678760899,"OmiCLIP AUPRC":0.5233846614069615},{"Section":"Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1","GEO Series":"","GEO Sample":"","Repository accession":"10.5281/zenodo.10698931 | mMAMP/MA | V1_Mouse_Brain_Sagittal_Anterior","Species":"Mouse","Organ":"Brain","Study":"GraphST annotation / BenchmarkST redistribution","Study reference":"Long, Y. et al. Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Nature Communications 14, 1155 (2023).","Biological category":"Tissue anatomy","Biological target":"Mouse olfactory bulb","Marker reference":"Independent mouse CNS spatial-atlas OB_1 and OB_2 marker union","Markers used":"Gad1;Gng4;Meis2;Pbx3;Synpr;Th;Cdhr1;Kctd12","Measured ST AUPRC":0.880638410686903,"HistAgent AUPRC":0.9323627885250688,"STPath AUPRC":0.1970722768966918,"OmiCLIP AUPRC":0.5515111615495936},{"Section":"Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1","GEO Series":"","GEO Sample":"","Repository accession":"10.5281/zenodo.10698931 | mMAMP/MA | V1_Mouse_Brain_Sagittal_Anterior","Species":"Mouse","Organ":"Brain","Study":"GraphST annotation / BenchmarkST redistribution","Study reference":"Long, Y. et al. Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Nature Communications 14, 1155 (2023).","Biological category":"Tissue anatomy","Biological target":"Mouse striatum","Marker reference":"Independent mouse CNS spatial-atlas STR marker set","Markers used":"Ppp1r1b;Gpr88;Scn4b;Rgs9;Penk","Measured ST AUPRC":0.831030303064979,"HistAgent AUPRC":0.7523077852481168,"STPath AUPRC":0.2408224764271848,"OmiCLIP AUPRC":0.3496659242761692}]

tutorials/fig3b.json

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tutorials/fig3d.json

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tutorials/fig4c_brca.json

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tutorials/fig4d_summary.json

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tutorials/fig5_query_sets.json

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tutorials/fig5_summary.json

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tutorials/figure3_examples.json

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+  "source": "frozen 135-slide downstream evaluation manifests"
+}

tutorials/figure3_examples.npz

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tutorials/figure3b_rank_metrics_per_section.csv

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+GSE203612_GSM6177607,human,stomach,HistAgent,2624,0.5332368863352095,0.4658820019895153
+GSE203612_GSM6177607,human,stomach,OmiCLIP,2624,0.2065963753387534,0.10080007749030338
+GSE203612_GSM6177607,human,stomach,STPath,2624,0.24571731029810298,0.14530965381679384
+GSE251950_GSM7990473,human,stomach,HistAgent,3834,0.40964542599315995,0.33388029322883944
+GSE251950_GSM7990473,human,stomach,OmiCLIP,3834,0.13593492837852977,0.05738356924560805
+GSE251950_GSM7990473,human,stomach,STPath,3834,0.1783488137737567,0.0821926433397657
+GSE251950_GSM7990475,human,stomach,HistAgent,3043,0.727702924745317,0.6921730172243891
+GSE251950_GSM7990475,human,stomach,OmiCLIP,3043,0.26552744002628986,0.16061308654241027
+GSE251950_GSM7990475,human,stomach,STPath,3043,0.3546434439697666,0.2133558634960975
+GSE251950_GSM7990477,human,stomach,HistAgent,3577,0.7130388593793682,0.6716589840987068
+GSE251950_GSM7990477,human,stomach,OmiCLIP,3577,0.2597428012300811,0.16693483356717126
+GSE251950_GSM7990477,human,stomach,STPath,3577,0.30775510204081635,0.16335918017151516
+GSE251950_GSM7990478,human,stomach,HistAgent,2426,0.657182648962481,0.592868729955765
+GSE251950_GSM7990478,human,stomach,OmiCLIP,2426,0.29434670502183785,0.16583891553781438
+GSE251950_GSM7990478,human,stomach,STPath,2426,0.4013129045271965,0.2565438308962555
+GSE251950_GSM7990479,human,stomach,HistAgent,2483,0.5436035872628991,0.47264373741006377
+GSE251950_GSM7990479,human,stomach,OmiCLIP,2483,0.2437781434471786,0.12780288990019367
+GSE251950_GSM7990479,human,stomach,STPath,2483,0.27709099738456505,0.1309237443072011
+GSE251950_GSM7990480,human,stomach,HistAgent,1882,0.6585653560042508,0.6046910191799857
+GSE251950_GSM7990480,human,stomach,OmiCLIP,1882,0.26663124335812965,0.14892213463551734
+GSE251950_GSM7990480,human,stomach,STPath,1882,0.29914984059511157,0.17122117195282943
+GSE251950_GSM7990481,human,stomach,HistAgent,3037,0.5688982349008691,0.5067959655002705
+GSE251950_GSM7990481,human,stomach,OmiCLIP,3037,0.17544097544426823,0.06412658097496501
+GSE251950_GSM7990481,human,stomach,STPath,3037,0.2170412388621147,0.09935744135639395
+GSE251950_GSM7990482,human,stomach,HistAgent,3491,0.6953022056717274,0.6530107848236227
+GSE251950_GSM7990482,human,stomach,OmiCLIP,3491,0.23759954167860212,0.1260509388083288
+GSE251950_GSM7990482,human,stomach,STPath,3491,0.3106330564308221,0.18445393741523647
+GSE203424_GSM6171787,mouse,brain,HistAgent,3126,0.805866922584773,0.7813958295187617
+GSE203424_GSM6171787,mouse,brain,OmiCLIP,3126,0.5564555342290467,0.46851976575380766
+GSE203424_GSM6171787,mouse,brain,STPath,3126,0.23932821497120924,0.08298926117280495
+GSE209583_GSM6380085,mouse,brain,HistAgent,2732,0.6363909224011712,0.5671768789458372
+GSE209583_GSM6380085,mouse,brain,OmiCLIP,2732,0.44756954612005856,0.3413651282554176
+GSE209583_GSM6380085,mouse,brain,STPath,2732,0.24699853587115664,0.10471877238455893
+GSE209583_GSM6380090,mouse,brain,HistAgent,1723,0.3113150146224004,0.22171921315842838
+GSE209583_GSM6380090,mouse,brain,OmiCLIP,1723,0.23477239988561166,0.13640424547414498
+GSE209583_GSM6380090,mouse,brain,STPath,1723,0.1315155497387547,0.042822767237415654
+GSE217058_GSM6704284,mouse,brain,HistAgent,2108,0.6801542253419822,0.6292137391733963
+GSE217058_GSM6704284,mouse,brain,OmiCLIP,2108,0.49415315278293487,0.39729131594353884
+GSE217058_GSM6704284,mouse,brain,STPath,2108,0.24069569137468802,0.09069345904645185
+GSE217058_GSM6704287,mouse,brain,HistAgent,3128,0.5794166016591372,0.5062001723645065
+GSE217058_GSM6704287,mouse,brain,OmiCLIP,3128,0.43017899607974996,0.3173038602642303
+GSE217058_GSM6704287,mouse,brain,STPath,3128,0.2333658037977984,0.0918743869429774
+GSE222410_GSM6922991,mouse,brain,HistAgent,1967,0.7917031011692933,0.7630246490171377
+GSE222410_GSM6922991,mouse,brain,OmiCLIP,1967,0.5510015251652263,0.4683122279871444
+GSE222410_GSM6922991,mouse,brain,STPath,1967,0.26193187595322825,0.10139687749237809
+GSE222981_GSM6937701,mouse,brain,HistAgent,2962,0.8115192437542202,0.7890939570579621
+GSE222981_GSM6937701,mouse,brain,OmiCLIP,2962,0.5698717083051992,0.47641208780392735
+GSE222981_GSM6937701,mouse,brain,STPath,2962,0.22912896691424714,0.09436430322391359
+GSE223066_GSM6939167,mouse,brain,HistAgent,2778,0.78207343412527,0.7524806293647837
+GSE223066_GSM6939167,mouse,brain,OmiCLIP,2778,0.5741612670986321,0.4878956737790361
+GSE223066_GSM6939167,mouse,brain,STPath,2778,0.3024838012958963,0.12333586504633992
+GSE232910_GSM7392320,mouse,brain,HistAgent,3601,0.4551407194730381,0.3663697527204554
+GSE232910_GSM7392320,mouse,brain,OmiCLIP,3601,0.3136626730414074,0.20881947473204357
+GSE232910_GSM7392320,mouse,brain,STPath,3601,0.18246666208772652,0.06413984715567747
+Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1,mouse,brain,HistAgent,2695,0.8043933209647496,0.778992165774839
+Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1,mouse,brain,OmiCLIP,2695,0.5584192949907236,0.47532272192304653
+Mouse_Brain_10X_06232020_Visium_Sagittal_Anterior_Section_1,mouse,brain,STPath,2695,0.20684972170686458,0.07739316821011309
+GSE169749_GSM5213483,mouse,colon,HistAgent,2604,0.7851766513056836,0.7548790949872539
+GSE169749_GSM5213483,mouse,colon,OmiCLIP,2604,0.12100614439324117,0.05032511778145553
+GSE169749_GSM5213483,mouse,colon,STPath,2604,0.15311059907834104,0.06630444524574441
+GSE169749_GSM5213484,mouse,colon,HistAgent,3630,0.7813884297520661,0.7506644852626186
+GSE169749_GSM5213484,mouse,colon,OmiCLIP,3630,0.1242038567493113,0.057880621814612905
+GSE169749_GSM5213484,mouse,colon,STPath,3630,0.14932782369146008,0.05847935675247923
+GSE190595_GSM5726156,mouse,colon,HistAgent,3934,0.7004652294778743,0.6504980374230303
+GSE190595_GSM5726156,mouse,colon,OmiCLIP,3934,0.09037177254486259,0.025567670714438703
+GSE190595_GSM5726156,mouse,colon,STPath,3934,0.13244123787169146,0.04481450880984998
+GSE190595_GSM5726157,mouse,colon,HistAgent,3547,0.7207330138144913,0.6752844030125356
+GSE190595_GSM5726157,mouse,colon,OmiCLIP,3547,0.08696363123766564,0.022688194353057783
+GSE190595_GSM5726157,mouse,colon,STPath,3547,0.09189173949816748,0.0201854149588939
+GSE211895_GSM6505142,mouse,colon,HistAgent,1378,0.6233671988388969,0.5478580689772589
+GSE211895_GSM6505142,mouse,colon,OmiCLIP,1378,0.22702467343976782,0.12204431946679568
+GSE211895_GSM6505142,mouse,colon,STPath,1378,0.2960087082728592,0.1445298125708359
+GSE211895_GSM6505143,mouse,colon,HistAgent,1372,0.7034402332361516,0.6501076655179662
+GSE211895_GSM6505143,mouse,colon,OmiCLIP,1372,0.26565597667638485,0.15976649058886008
+GSE211895_GSM6505143,mouse,colon,STPath,1372,0.3069533527696793,0.15523431388308884
+GSE211895_GSM6505144,mouse,colon,HistAgent,1982,0.7909485368314834,0.759525217440445
+GSE211895_GSM6505144,mouse,colon,OmiCLIP,1982,0.2889303733602422,0.16519471981669542
+GSE211895_GSM6505144,mouse,colon,STPath,1982,0.28168516649848635,0.12847554155099827
+GSE211895_GSM6505145,mouse,colon,HistAgent,1909,0.7864745940282871,0.7538705222960865
+GSE211895_GSM6505145,mouse,colon,OmiCLIP,1909,0.266799371398638,0.15766078024357075
+GSE211895_GSM6505145,mouse,colon,STPath,1909,0.31104243059193293,0.1657559009417287
+GSE235742_GSM7508784,mouse,colon,HistAgent,640,0.77534375,0.7454366511883453
+GSE235742_GSM7508784,mouse,colon,OmiCLIP,640,0.1695625,0.08860232011668144
+GSE235742_GSM7508784,mouse,colon,STPath,640,0.20434375000000005,0.0814918680980558
+GSE235742_GSM7508785,mouse,colon,HistAgent,572,0.7575524475524475,0.7221397172098571
+GSE235742_GSM7508785,mouse,colon,OmiCLIP,572,0.17097902097902098,0.08691079141925724
+GSE235742_GSM7508785,mouse,colon,STPath,572,0.20727272727272728,0.08510138320960763
+GSE188888_GSM5691527,mouse,heart,HistAgent,1374,0.8848471615720526,0.8755722932388118
+GSE188888_GSM5691527,mouse,heart,OmiCLIP,1374,0.5846724890829694,0.5172793827120789
+GSE188888_GSM5691527,mouse,heart,STPath,1374,0.2903056768558952,0.10118455554411011
+GSE188888_GSM5691529,mouse,heart,HistAgent,2095,0.8764295942720765,0.8659230020000793
+GSE188888_GSM5691529,mouse,heart,OmiCLIP,2095,0.5737183770883055,0.520996860462366
+GSE188888_GSM5691529,mouse,heart,STPath,2095,0.1872840095465394,0.040511466514140115
+GSE206787_GSM7898096,mouse,heart,HistAgent,591,0.8757698815566837,0.8660533706621728
+GSE206787_GSM7898096,mouse,heart,OmiCLIP,591,0.4748900169204737,0.3764779512737772
+GSE206787_GSM7898096,mouse,heart,STPath,591,0.35038917089678506,0.1995275773283393
+GSE206787_GSM7898098,mouse,heart,HistAgent,1245,0.7692530120481927,0.739669657943503
+GSE206787_GSM7898098,mouse,heart,OmiCLIP,1245,0.44173493975903616,0.34514182088752776
+GSE206787_GSM7898098,mouse,heart,STPath,1245,0.36583132530120477,0.19791586647596768
+GSE206787_GSM7898099,mouse,heart,HistAgent,948,0.6570253164556961,0.6076964544406595
+GSE206787_GSM7898099,mouse,heart,OmiCLIP,948,0.3213291139240506,0.231100008734203
+GSE206787_GSM7898099,mouse,heart,STPath,948,0.3260970464135021,0.1795585944740026
+GSE214611_GSM6613077,mouse,heart,HistAgent,1917,0.7900573813249869,0.7608674845663933
+GSE214611_GSM6613077,mouse,heart,OmiCLIP,1917,0.5813875847678664,0.5269096416126466
+GSE214611_GSM6613077,mouse,heart,STPath,1917,0.17346896191966615,0.044222727868039866
+GSE214611_GSM6613079,mouse,heart,HistAgent,3123,0.7984166256648157,0.7699777883784252
+GSE214611_GSM6613079,mouse,heart,OmiCLIP,3123,0.5712760557000384,0.533380773654127
+GSE214611_GSM6613079,mouse,heart,STPath,3123,0.12407581827979663,0.025288279144794843
+GSE214611_GSM6613080,mouse,heart,HistAgent,3540,0.829542372881356,0.8093444987028909
+GSE214611_GSM6613080,mouse,heart,OmiCLIP,3540,0.5911581920903954,0.54457256638523
+GSE214611_GSM6613080,mouse,heart,STPath,3540,0.11161581920903957,0.019771268771903956
+GSE214611_GSM6613082,mouse,heart,HistAgent,2468,0.8286046256953874,0.8071209510452683
+GSE214611_GSM6613082,mouse,heart,OmiCLIP,2468,0.5973347496605196,0.5554896013391818
+GSE214611_GSM6613082,mouse,heart,STPath,2468,0.1079392439441062,0.022651719350427688
+GSE214611_GSM6613086,mouse,heart,HistAgent,2438,0.7816010878415088,0.7490536957351399
+GSE214611_GSM6613086,mouse,heart,OmiCLIP,2438,0.5419888199197509,0.4554187241469301
+GSE214611_GSM6613086,mouse,heart,STPath,2438,0.2156392761883068,0.09286283468349413
+GSE193460_GSM5808054,mouse,lung,HistAgent,1906,0.7278174186778593,0.6898241151324328
+GSE193460_GSM5808054,mouse,lung,OmiCLIP,1906,0.3898950682056664,0.29626870886910006
+GSE193460_GSM5808054,mouse,lung,STPath,1906,0.2524554039874082,0.09386643310942214
+GSE193460_GSM5808055,mouse,lung,HistAgent,1931,0.7122157283420878,0.6719059832529989
+GSE193460_GSM5808055,mouse,lung,OmiCLIP,1931,0.3605400606643487,0.2645583655472764
+GSE193460_GSM5808055,mouse,lung,STPath,1931,0.2523629503588074,0.09932019915302596
+GSE193460_GSM5808056,mouse,lung,HistAgent,1244,0.717508038585209,0.6741096774785673
+GSE193460_GSM5808056,mouse,lung,OmiCLIP,1244,0.32453376205787776,0.20885643012929178
+GSE193460_GSM5808056,mouse,lung,STPath,1244,0.2526688102893891,0.09947609076988516
+GSE193460_GSM5808057,mouse,lung,HistAgent,2546,0.623503534956795,0.5741612329270477
+GSE193460_GSM5808057,mouse,lung,OmiCLIP,2546,0.2824037706205813,0.17467810362860228
+GSE193460_GSM5808057,mouse,lung,STPath,2546,0.20545954438334638,0.08798394840414525
+GSE202322_GSM6108348,mouse,lung,HistAgent,2486,0.7100884955752212,0.6699823802735687
+GSE202322_GSM6108348,mouse,lung,OmiCLIP,2486,0.4783668543845535,0.41084589751827527
+GSE202322_GSM6108348,mouse,lung,STPath,2486,0.15985518905872886,0.04845437796717613
+GSE202322_GSM6108349,mouse,lung,HistAgent,2520,0.6566825396825398,0.6079632564815471
+GSE202322_GSM6108349,mouse,lung,OmiCLIP,2520,0.4056269841269841,0.3324802347527251
+GSE202322_GSM6108349,mouse,lung,STPath,2520,0.15796825396825398,0.05064026314057487
+GSE202322_GSM6108350,mouse,lung,HistAgent,2847,0.6879381805409203,0.6433537516873186
+GSE202322_GSM6108350,mouse,lung,OmiCLIP,2847,0.37071303126097643,0.24307448472673554
+GSE202322_GSM6108350,mouse,lung,STPath,2847,0.20465753424657532,0.06469952963453651
+GSE202322_GSM6108351,mouse,lung,HistAgent,2969,0.6590175890483323,0.6193104490978668
+GSE202322_GSM6108351,mouse,lung,OmiCLIP,2969,0.36741055752399926,0.2635314633183078
+GSE202322_GSM6108351,mouse,lung,STPath,2969,0.15828194279080388,0.046052494264676516
+GSE225766_GSM7055901,mouse,muscle,HistAgent,1493,0.8668720696584059,0.855160873533169
+GSE225766_GSM7055901,mouse,muscle,OmiCLIP,1493,0.6085063630274615,0.5516169964696814
+GSE225766_GSM7055901,mouse,muscle,STPath,1493,0.11458807769591428,0.025167294702785767
+GSE225766_GSM7055902,mouse,muscle,HistAgent,1438,0.8626008344923506,0.8507905503012896
+GSE225766_GSM7055902,mouse,muscle,OmiCLIP,1438,0.6092489568845618,0.5576100309193244
+GSE225766_GSM7055902,mouse,muscle,STPath,1438,0.11564673157162726,0.02686767316927757
+GSE225766_GSM7055903,mouse,muscle,HistAgent,1064,0.8274812030075188,0.811435372212454
+GSE225766_GSM7055903,mouse,muscle,OmiCLIP,1064,0.5407330827067669,0.4942651767687779
+GSE225766_GSM7055903,mouse,muscle,STPath,1064,0.21321428571428572,0.07019215200610442
+GSE225766_GSM7055904,mouse,muscle,HistAgent,959,0.814786235662148,0.7966406690573892
+GSE225766_GSM7055904,mouse,muscle,OmiCLIP,959,0.5272367049009384,0.4831840651866402
+GSE225766_GSM7055904,mouse,muscle,STPath,959,0.2069864442127216,0.06511685817499027
+GSE225766_GSM7055907,mouse,muscle,HistAgent,1155,0.809044733044733,0.7895478962225463
+GSE225766_GSM7055907,mouse,muscle,OmiCLIP,1155,0.5473939393939394,0.49192281278277206
+GSE225766_GSM7055907,mouse,muscle,STPath,1155,0.205029341029341,0.06745606005878681
+GSE225766_GSM7055908,mouse,muscle,HistAgent,1136,0.8125,0.7928853877057288
+GSE225766_GSM7055908,mouse,muscle,OmiCLIP,1136,0.5331338028169014,0.48266384275412383
+GSE225766_GSM7055908,mouse,muscle,STPath,1136,0.21647887323943663,0.0744539415348703
+GSE225766_GSM7230944,mouse,muscle,HistAgent,1854,0.7783387270765911,0.7503004564537429
+GSE225766_GSM7230944,mouse,muscle,OmiCLIP,1854,0.431715210355987,0.3568309790065493
+GSE225766_GSM7230944,mouse,muscle,STPath,1854,0.17778856526429343,0.05278926880468212
+GSE225766_GSM7230945,mouse,muscle,HistAgent,2283,0.7900043802014892,0.7649056566059753
+GSE225766_GSM7230945,mouse,muscle,OmiCLIP,2283,0.42477441962330265,0.3457914487161736
+GSE225766_GSM7230945,mouse,muscle,STPath,2283,0.19342969776609722,0.06232449401369469
+GSE200720_GSM6042726,mouse,spleen,HistAgent,2774,0.7558687815428984,0.7181114161420628
+GSE200720_GSM6042726,mouse,spleen,OmiCLIP,2774,0.3590338860850757,0.2666404646549832
+GSE200720_GSM6042726,mouse,spleen,STPath,2774,0.24611391492429704,0.11619601557574116
+GSE200720_GSM6042728,mouse,spleen,HistAgent,2659,0.7628206092515984,0.7308157721269629
+GSE200720_GSM6042728,mouse,spleen,OmiCLIP,2659,0.36479879654005254,0.2711724847430337
+GSE200720_GSM6042728,mouse,spleen,STPath,2659,0.2610831139526138,0.132579475413467
+GSE200720_GSM6042730,mouse,spleen,HistAgent,2254,0.6765738971173754,0.6340647887702814
+GSE200720_GSM6042730,mouse,spleen,OmiCLIP,2254,0.3216506836848452,0.23121955908921524
+GSE200720_GSM6042730,mouse,spleen,STPath,2254,0.23450930539439857,0.11557562802188484
+GSE254652_GSM8047864,mouse,spleen,HistAgent,2207,0.5850566379700952,0.5307099105110262
+GSE254652_GSM8047864,mouse,spleen,OmiCLIP,2207,0.3177979157227005,0.2310649431282929
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tutorials/figure5_embedding_queries.json

@@ -0,0 +1,118 @@
+{
+  "query_order": [
+    "breast_tumor",
+    "heart_muscle"
+  ],
+  "queries": {
+    "breast_tumor": {
+      "display_query": "breast epithelial tumor states",
+      "canonical_embedding_text": "Cell type: Cancer cell; Luminal progenitor cell.",
+      "source_spot_id": "GSE210616_GSM6433591\tGSE210616_GSM6433591_AACGTGCGAAAGTCTC-1"
+    },
+    "heart_muscle": {
+      "display_query": "heart spots with active muscle pathways",
+      "canonical_embedding_text": "Cell type: Fibroblast; Cardiomyocyte.",
+      "source_spot_id": "Human_Heart_Kuppe_10082022_Visium_Visium_14_CK292\tHuman_Heart_Kuppe_10082022_Visium_Visium_14_CK292_CCAGCCTGGACCAATA-1"
+    }
+  },
+  "image_query": {
+    "display_query": "Human cortical H&E query",
+    "local_image_file": "figure5_he_query_brain_local.png",
+    "context_image_file": "figure5_he_query_brain_context.png",
+    "source_slice_id": "Human_Brain_Maynard_02082021_Visium_151671",
+    "source_spot_id": "Human_Brain_Maynard_02082021_Visium_151671\tHuman_Brain_Maynard_02082021_Visium_151671_CAACGACCCGTTTACA-1",
+    "species": "human",
+    "organ": "brain",
+    "spot_diameter_um": 55,
+    "context_diameter_um": 220,
+    "microns_per_pixel": 0.8594,
+    "input_mode": "paired_fov",
+    "predicted_genes": [
+      "MT3",
+      "FTH1",
+      "CST3",
+      "GAPDH",
+      "NRGN",
+      "TMSB10",
+      "SNAP25",
+      "TUBA1B",
+      "NDUFA4",
+      "CLU",
+      "CALM2",
+      "CALM1",
+      "COX6C",
+      "CKB",
+      "GNAS",
+      "TMSB4X",
+      "CCK",
+      "OLFM1",
+      "SELENOW",
+      "MTRNR2L12",
+      "COX6A1",
+      "UCHL1",
+      "VSNL1",
+      "ACTB",
+      "YWHAH",
+      "PPIA",
+      "SPARCL1",
+      "UBB",
+      "STMN1",
+      "COX4I1",
+      "CALM3",
+      "RTN3",
+      "NEFL",
+      "RTN1",
+      "ATP5F1E",
+      "ITM2B",
+      "PEBP1",
+      "MTRNR2L8",
+      "CHN1",
+      "EEF1A1",
+      "HSP90AA1",
+      "ATP1B1",
+      "HSP90AB1",
+      "MAP1B",
+      "HSPA8",
+      "FTL",
+      "SYT1",
+      "GPM6A",
+      "HINT1",
+      "COX5B"
+    ],
+    "example_results": [
+      {
+        "relevance": 0.98,
+        "slice_id": "Human_Brain_Maynard_02082021_Visium_151672",
+        "cell_type": "Astrocyte",
+        "matched_genes": "MT3, FTH1, CST3, GAPDH, NRGN, TMSB10, SNAP25, TUBA1B"
+      },
+      {
+        "relevance": 0.9658,
+        "slice_id": "Human_Brain_Maynard_02082021_Visium_151674",
+        "cell_type": "Neuron",
+        "matched_genes": "MT3, FTH1, GAPDH, NRGN, TMSB10, SNAP25, TUBA1B, NDUFA4"
+      },
+      {
+        "relevance": 0.9618,
+        "slice_id": "Human_Brain_Maynard_02082021_Visium_151676",
+        "cell_type": "Astrocyte",
+        "matched_genes": "MT3, FTH1, CST3, GAPDH, NRGN, TMSB10, SNAP25, TUBA1B"
+      },
+      {
+        "relevance": 0.9603,
+        "slice_id": "Human_Brain_Louise_02152023_Visium_Br6522_ant",
+        "cell_type": "Astrocyte",
+        "matched_genes": "MT3, FTH1, CST3, GAPDH, NRGN, TMSB10, SNAP25, TUBA1B"
+      },
+      {
+        "relevance": 0.9594,
+        "slice_id": "Human_Brain_Louise_02152023_Visium_Br6522_mid",
+        "cell_type": "Excitatory neuron",
+        "matched_genes": "MT3, FTH1, CST3, GAPDH, NRGN, TMSB10, SNAP25, TUBA1B"
+      }
+    ],
+    "retrieval_note": "The image query uses a 55 μm spot view and a 220 μm context view with species=human and organ=brain."
+  },
+  "source": "representative spatial atlas locations",
+  "production_note": "The downloadable notebook uses a compact reproducible subset."
+}

tutorials/figure5_embedding_subset.npz

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+oid sha256:1ff266f29c6902a99aa645825469b167c4975a24800a5c60b751d6577ef029f2
+size 416526

tutorials/quickstart_expression_maps.json

@@ -0,0 +1,547 @@
+{
+  "sections": {
+    "GSE251950_GSM7990478": {
+      "species": "human",
+      "organ": "stomach",
+      "gene": "IGKC",
+      "pcc": 0.7527607948227797
+    },
+    "GSE213688_GSM6592052": {
+      "species": "human",
+      "organ": "breast",
+      "gene": "COL1A1",
+      "pcc": 0.7454216685394932
+    },
+    "GSE202322_GSM6108350": {
+      "species": "mouse",
+      "organ": "lung",
+      "gene": "Sftpc",
+      "pcc": 0.8505840779355743
+    },
+    "GSE254652_GSM8047883": {
+      "species": "mouse",
+      "organ": "spleen",
+      "gene": "Cd74",
+      "pcc": 0.8713135092638626
+    },
+    "GSE175540_GSM5924038": {
+      "species": "human",
+      "organ": "kidney",
+      "gene": "DCN",
+      "pcc": 0.7306821327167066
+    }
+  },
+  "rank_examples": {
+    "GSE251950_GSM7990478": {
+      "barcode": "GSE251950_GSM7990478_ATATCGTTCCTCGAAC-1",
+      "predicted_top50": [
+        "MYL9",
+        "TAGLN",
+        "DES",
+        "FLNA",
+        "ACTA2",
+        "TPM2",
+        "ACTG2",
+        "MYLK",
+        "CNN1",
+        "FTL",
+        "IGFBP7",
+        "FTH1",
+        "MGP",
+        "LGALS1",
+        "SELENOM",
+        "S100A6",
+        "HSPB1",
+        "A2M",
+        "CD81",
+        "CST3",
+        "IFITM3",
+        "UBC",
+        "CD74",
+        "PSAP",
+        "SPARC",
+        "PFN1",
+        "CTSD",
+        "TIMP1",
+        "SERF2",
+        "SPARCL1",
+        "ITM2B",
+        "CD63",
+        "UBB",
+        "IGFBP4",
+        "GSTP1",
+        "HLA-DRA",
+        "IGKC",
+        "HLA-A",
+        "HLA-C",
+        "S100A11",
+        "IGHG4",
+        "IGHG1",
+        "APOE",
+        "KRT8",
+        "KRT18",
+        "H19"
+      ],
+      "measured_top50": [
+        "MYL9",
+        "TAGLN",
+        "MGP",
+        "FTL",
+        "TPM2",
+        "S100A6",
+        "FLNA",
+        "HLA-A",
+        "ACTA2",
+        "CD74",
+        "DES",
+        "IGKC",
+        "IGFBP7",
+        "MYH11",
+        "SERF2",
+        "FTH1",
+        "KRT18",
+        "H19",
+        "KRT8",
+        "APOE",
+        "CTSD",
+        "TIMP1",
+        "ACTG2",
+        "GSTP1",
+        "PFN1",
+        "A2M",
+        "CD81",
+        "COL3A1",
+        "IFITM3",
+        "LGALS1",
+        "SELENOW",
+        "UBB",
+        "C3",
+        "CD63",
+        "COL1A2",
+        "CST3",
+        "EIF1",
+        "HLA-DRA",
+        "IGFBP4",
+        "MYL6",
+        "SELENOM",
+        "SMTN",
+        "SPARC",
+        "SPARCL1",
+        "COX4I1",
+        "EEF1D",
+        "FN1",
+        "HSPB1",
+        "ITM2B",
+        "PSAP"
+      ],
+      "spot_hit_rate_at_50": 0.78,
+      "spot_ap_at_50": 0.7025268346762492
+    },
+    "GSE213688_GSM6592052": {
+      "barcode": "GSE213688_GSM6592052_GCCCGTTCACACAATT-1",
+      "predicted_top50": [
+        "MGP",
+        "COL6A2",
+        "FTL",
+        "FTH1",
+        "COL1A1",
+        "S100A6",
+        "COL1A2",
+        "SPARC",
+        "LGALS1",
+        "VIM",
+        "S100A11",
+        "FN1",
+        "COL3A1",
+        "KRT8",
+        "PFN1",
+        "TAGLN",
+        "ACTN4",
+        "SERF2",
+        "ANXA2",
+        "KRT6B",
+        "HSP90AA1",
+        "MYL9",
+        "BGN",
+        "MYH9",
+        "HLA-A",
+        "MT2A",
+        "FLNA",
+        "KRT14",
+        "LMNA",
+        "EIF1",
+        "MMP7",
+        "KRT7",
+        "EEF2",
+        "TAGLN2",
+        "NME2",
+        "CCND1",
+        "KRT5",
+        "ATP5F1E",
+        "EEF1G",
+        "HLA-C",
+        "EIF4A1",
+        "POSTN",
+        "KRT81"
+      ],
+      "measured_top50": [
+        "KRT17",
+        "COL1A1",
+        "COL1A2",
+        "MGP",
+        "KRT14",
+        "MYL9",
+        "FTH1",
+        "LGALS1",
+        "SPARC",
+        "KRT5",
+        "VIM",
+        "FTL",
+        "TAGLN2",
+        "KRT19",
+        "S100A6",
+        "KRT7",
+        "LMNA",
+        "KRT81",
+        "MALAT1",
+        "EEF1G",
+        "COL3A1",
+        "TAGLN",
+        "CCN2",
+        "MT2A",
+        "ACTN4",
+        "HLA-B",
+        "MYH9",
+        "FN1",
+        "MYL6",
+        "CCND1",
+        "ANXA2",
+        "COL6A2",
+        "HSP90AA1",
+        "EIF4A1",
+        "NME2",
+        "MMP7",
+        "EEF2",
+        "KRT8",
+        "HLA-A",
+        "PMEPA1",
+        "CALD1",
+        "H3F3B",
+        "KRT6B",
+        "TUBA1B",
+        "BGN",
+        "FLNA",
+        "PFN1",
+        "ATP5F1E",
+        "EIF1",
+        "S100A10"
+      ],
+      "spot_hit_rate_at_50": 0.78,
+      "spot_ap_at_50": 0.7379452182647038
+    },
+    "GSE202322_GSM6108350": {
+      "barcode": "GSE202322_GSM6108350_ACCGACTGAGTCCCAC-1",
+      "predicted_top50": [
+        "FTH1",
+        "MGP",
+        "PSAP",
+        "S100A6",
+        "CD74",
+        "CTSB",
+        "APOE",
+        "CST3",
+        "ITM2B",
+        "CTSD",
+        "VIM",
+        "C1QA",
+        "LGALS1",
+        "IFITM3",
+        "CRIP1",
+        "PFN1",
+        "SERF2",
+        "EIF1",
+        "CTSS",
+        "C1QB",
+        "SH3BGRL3",
+        "OAZ1",
+        "TYROBP",
+        "COX4I1",
+        "S100A10",
+        "LY6E",
+        "UBB",
+        "C1QC",
+        "ARPC1B",
+        "FCER1G",
+        "H3F3B",
+        "CYBA",
+        "NME2",
+        "H3F3A",
+        "CD52",
+        "CCL5"
+      ],
+      "measured_top50": [
+        "FTH1",
+        "IGKC",
+        "IGHG2B",
+        "MGP",
+        "CD74",
+        "FTL1",
+        "H2-K1",
+        "LY6A",
+        "CD52",
+        "H2-D1",
+        "H2-AA",
+        "H2-AB1",
+        "AW112010",
+        "S100A6",
+        "LYZ2",
+        "IFI27L2A",
+        "PSAP",
+        "H2-EB1",
+        "IFITM3",
+        "CCL5",
+        "CST3",
+        "TYROBP",
+        "ITM2B",
+        "SH3BGRL3",
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+        "NME2",
+        "MYL6",
+        "CTSS",
+        "H3F3B",
+        "LY6E",
+        "C1QA",
+        "LGALS1",
+        "SERF2",
+        "OAZ1",
+        "S100A10",
+        "PFN1",
+        "EEF2",
+        "H3F3A",
+        "NACA",
+        "C1QB",
+        "CYBA",
+        "EIF1",
+        "CTSB",
+        "COX4I1",
+        "CTSD",
+        "FCER1G",
+        "FXYD5"
+      ],
+      "spot_hit_rate_at_50": 0.68,
+      "spot_ap_at_50": 0.6714837840316967
+    },
+    "GSE254652_GSM8047883": {
+      "barcode": "GSE254652_GSM8047883_CTGTTCCAGAAGCTGA-1",
+      "predicted_top50": [
+        "CD74",
+        "IGKC",
+        "PSAP",
+        "IGHM",
+        "CD52",
+        "PFN1",
+        "FTH1",
+        "CYBA",
+        "CORO1A",
+        "CTSB",
+        "LAPTM5",
+        "CD79B",
+        "ARHGDIB",
+        "GNAI2",
+        "COTL1",
+        "SERF2",
+        "ARHGDIA",
+        "CD37",
+        "CNN2",
+        "CSK",
+        "MFGE8",
+        "ANP32B",
+        "POU2AF1",
+        "SERBP1",
+        "PABPC1",
+        "HNRNPA0",
+        "NCL",
+        "RERE",
+        "PPP1CA",
+        "HNRNPUL1",
+        "ARPC3",
+        "SRSF1",
+        "HIST1H2BB",
+        "PCBP2",
+        "HIST1H1E",
+        "EIF3F",
+        "HIST1H2BJ",
+        "TCP1",
+        "HIST1H3D",
+        "HIST1H4H"
+      ],
+      "measured_top50": [
+        "CD74",
+        "IGKC",
+        "IGHM",
+        "HIST1H1C",
+        "HIST1H3C",
+        "CORO1A",
+        "HIST1H3B",
+        "ARHGDIB",
+        "HIST2H2BB",
+        "H2-AA",
+        "PFN1",
+        "CD37",
+        "HIST1H3D",
+        "HIST1H2BJ",
+        "HIST1H1E",
+        "ARPC3",
+        "ATP5E",
+        "NAP1L1",
+        "H2-AB1",
+        "PPP1CA",
+        "ANP32B",
+        "CD79B",
+        "CSK",
+        "TCP1",
+        "SERF2",
+        "FTH1",
+        "POU2AF1",
+        "RERE",
+        "ARHGDIA",
+        "PCBP2",
+        "HNRNPA0",
+        "PSAP",
+        "SRSF1",
+        "PTPRCAP",
+        "CNN2",
+        "NCL",
+        "H2-DMB2",
+        "HIST1H4H",
+        "CTSB",
+        "COTL1",
+        "IGLC1",
+        "PABPC1",
+        "EIF3F",
+        "MZB1",
+        "GNAI2",
+        "HIST1H2BB",
+        "HNRNPUL1",
+        "CD52",
+        "TXN1",
+        "LAPTM5"
+      ],
+      "spot_hit_rate_at_50": 0.74,
+      "spot_ap_at_50": 0.6886899457903327
+    },
+    "GSE175540_GSM5924038": {
+      "barcode": "GSE175540_GSM5924038_TAGGATCTTAACCGCA-1",
+      "predicted_top50": [
+        "UBC",
+        "MT2A",
+        "FTL",
+        "VIM",
+        "IGFBP7",
+        "SPP1",
+        "FTH1",
+        "CD74",
+        "TIMP1",
+        "BGN",
+        "SPARC",
+        "IFITM3",
+        "EEF2",
+        "FN1",
+        "S100A6",
+        "LGALS1",
+        "PFN1",
+        "CD63",
+        "HSPB1",
+        "HTRA1",
+        "COX7C",
+        "OAZ1",
+        "PPDPF",
+        "APP",
+        "COL3A1",
+        "COL1A1",
+        "C3",
+        "MT1E",
+        "CD24",
+        "PABPC1",
+        "COL1A2",
+        "EEF1G",
+        "MT1X",
+        "VEGFA",
+        "CLIC4",
+        "RBM3",
+        "UQCRB",
+        "CCDC91",
+        "EIF4B",
+        "TGFBI",
+        "S100A10",
+        "CP",
+        "CHCHD2",
+        "C1QL1",
+        "BSG",
+        "NDRG1",
+        "ANGPTL4",
+        "PLOD2",
+        "VDAC1",
+        "TM4SF18"
+      ],
+      "measured_top50": [
+        "UBC",
+        "MT2A",
+        "PABPC1",
+        "FTL",
+        "VIM",
+        "SPARC",
+        "MT1E",
+        "SPP1",
+        "FTH1",
+        "COL1A1",
+        "FN1",
+        "IGFBP7",
+        "EEF2",
+        "HSPB1",
+        "S100A10",
+        "CCDC91",
+        "COL1A2",
+        "COL3A1",
+        "CD63",
+        "HTRA1",
+        "TIMP1",
+        "ANGPTL4",
+        "TGFBI",
+        "CHCHD2",
+        "VDAC1",
+        "BSG",
+        "IFITM3",
+        "S100A6",
+        "TM4SF18",
+        "C3",
+        "OAZ1",
+        "APP",
+        "PPDPF",
+        "UQCRB",
+        "HINT1",
+        "BGN",
+        "RBM3",
+        "C1QL1",
+        "CD24",
+        "CD74",
+        "PLOD2",
+        "VEGFA",
+        "CLIC4",
+        "DDIT4",
+        "EEF1G",
+        "PSAP",
+        "CALR",
+        "PFN1",
+        "EIF4B",
+        "ITM2B"
+      ],
+      "spot_hit_rate_at_50": 0.9,
+      "spot_ap_at_50": 0.852577989722228
+    }
+  },
+  "source": "frozen measured-ST and HistAgent expression artifacts; fixed illustrative high-concordance genes; displayed PCC is Pearson correlation; examples are not the cohort metric"
+}