Metadata v2.1: one name per assay; exact float values from the release parquet; no annotation changed

metadata/v2/README.md

@@ -1,6 +1,6 @@
 # SpatialDataAgent-DB sample metadata v2
 
-Schema `sda-sample-metadata-2`, built 2026-11-04 from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
+Schema `sda-sample-metadata-2`, version 2.1 (2026-11-05), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
 No expression, coordinate or image file changes; v2 is a new metadata table that sits next to the release.
 
 ## Files
@@ -122,3 +122,10 @@ repository:
 - `assay_decisions.py`: assay of the "Other" studies;
 - `build_metadata_v2.py`: this table;
 - `qa_full.py`: QA sample and judge.
+
+## Versions
+
+- **2.1** (tag `metadata-v2.1-20261105`): each assay now has one name (for example "Resolve Molecular Cartography"
+  became "Molecular Cartography", and "Visium (FFPE)" became "Visium", since preservation is its own field).
+  `um_per_unit` and `image_um_per_px` are copied exactly from the release parquet. No annotation changed.
+- **2.0** (tag `metadata-v2-20261105`): first release.

metadata/v2/provenance.json

@@ -48,16 +48,38 @@
    "Plant | Musculoskeletal": 10,
    "Spinal cord / nerve | Head & neck / oral": 8,
    "Plant | Heart / vessels": 8
-  }
+  },
+  "tumour_v2_incl_xenograft_disease": 3265,
+  "tumour_regex_only_after_xenograft": 43
  },
  "files": {
-  "README.md": "953c665094dcf4e795517f039a3cd446002379645810928235a41689eb02235f",
+  "README.md": "efd3bd99c80704355adc792817ca771c0219c555ae56e11d6d118bb2d976fd1f",
   "changes_v2.csv": "7901fcd917602f308ea0ca3c8a74c462c473caa2178a33ec5e9c3552498728a5",
   "dropped_disease_terms.csv": "697ecd7701a923e8b7ad2c1309d1064403993c8ac75efdcf7cd61776db159862",
   "qa_v2.json": "3c55068f167fa701729223e2d9c2a082befdba17f6627e610c719efb738927a5",
-  "samples_metadata_v2.csv": "95a88711ac9a260aace525cbef93e26c42519c3b59a39cafe00817ee580ee3ad",
-  "samples_metadata_v2.parquet": "95b33b3bd6f6e764e3dc461b1c2c7bf280d7e69397a9a596224f4ff87fc21bb3",
+  "samples_metadata_v2.csv": "62f36ce967cabb80398f141b8b2beb981ff97a89a14d3a49d7577bb59d28f12e",
+  "samples_metadata_v2.parquet": "702d11d28b5a606b2b0a13510c46a01f3d310c4312727b9bb80007b6ab6b213a",
   "schema_v2.json": "5f4b29aaf5d1d990c45916d2e1922f5da0b484500c55e93d57b62b1b6864b194",
-  "studies_v2.csv": "0f6c97c3ea020dd5bfa87f92398d395736567396ae7351a88957550d372d3c89"
+  "studies_v2.csv": "d8bf238b728f901a917e5a41cadde6cb0797fd5982c369849dcc1cb2e4fb83ad"
+ },
+ "version": "2.1",
+ "changes_from_2.0": "one name per assay (ASSAY_CANON); um_per_unit and image_um_per_px copied exactly from the release parquet; no annotation changed",
+ "sensitivity_balanced_r2_series_units": {
+  "human": {
+   "organ": 0.355,
+   "platform": 0.109,
+   "paper_regex": [
+    0.321,
+    0.125
+   ]
+  },
+  "mouse": {
+   "organ": 0.48,
+   "platform": 0.194,
+   "paper_regex": [
+    0.47,
+    0.179
+   ]
+  }
  }
 }

metadata/v2/samples_metadata_v2.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:95b33b3bd6f6e764e3dc461b1c2c7bf280d7e69397a9a596224f4ff87fc21bb3
-size 820752
+oid sha256:702d11d28b5a606b2b0a13510c46a01f3d310c4312727b9bb80007b6ab6b213a
+size 820621

metadata/v2/studies_v2.csv

@@ -1,9 +1,9 @@
 published_gse,study_title,n_samples,organisms,platforms,assay_names,organs,diseases,disease_statuses,n_with_image,pubmed_ids,split
 GSE111672,Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas,8,Homo sapiens,ST (legacy),ST (legacy),pancreas,pancreatic ductal adenocarcinoma,disease,0,31932730,val
 GSE120374,Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis,317,Mus musculus,ST (legacy),ST (legacy),spinal cord,amyotrophic lateral sclerosis;hereditary motor neuron disease;lateral sclerosis,normal;disease,0,,train
-GSE130682,High-density spatial transcriptomics arrays for in situ tissue profiling,1,Mus musculus,Other,HDST (high-density spatial transcriptomics),brain,,normal,1,31501547,train
+GSE130682,High-density spatial transcriptomics arrays for in situ tissue profiling,1,Mus musculus,Other,HDST,brain,,normal,1,31501547,train
 GSE135805,Spatial Transcriptomics of Human Cardiac Tissue,4,Homo sapiens,ST (legacy),ST (legacy),heart,cardiomyopathy;dilated cardiomyopathy;hypertrophic cardiomyopathy,normal;disease,0,31862877,train
-GSE137986,High spatial resolution multi-omics atlas sequencing of mouse embryos,11,Mus musculus,DBiT-seq,DBiT-seq (or DBiT-derived),embryo (whole),,normal,0,33188776,train
+GSE137986,High spatial resolution multi-omics atlas sequencing of mouse embryos,11,Mus musculus,DBiT-seq,DBiT-seq,embryo (whole),,normal,0,33188776,train
 GSE144239,Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST],16,Homo sapiens,ST (legacy);Visium,ST (legacy);Visium,skin,squamous cell carcinoma,disease,16,32579974;38037084;41872488,train
 GSE147747,Molecular Atlas of the Adult Mouse Brain,75,Mus musculus,ST (legacy),ST (legacy),brain,,normal,75,32637622,train
 GSE148612,Neuroinflammatory astrocyte subtypes in the mouse brain,6,Mus musculus,Visium,Visium,brain,,normal;perturbation,6,34413515,test
@@ -97,8 +97,8 @@ GSE202623,Spatial Transcriptomics correlated Electron Microscopy [MERFISH],3,Mus
 GSE203424,INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease,12,Mus musculus,Visium,Visium,brain,Alzheimer disease,perturbation;disease;normal,12,36448627,train
 GSE203552,Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma,4,Homo sapiens,Visium,Visium,brain,primary central nervous system lymphoma,disease,4,36153593,test
 GSE203612,Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment,12,Homo sapiens,Visium,Visium,breast;stomach;liver;ovary;pancreas;uterus;other,breast carcinoma;cancer;hepatocellular carcinoma;ovarian carcinoma;pancreatic ductal adenocarcinoma;endometrial carcinoma;melanoma,disease,12,35931863,train
-GSE205054,Spatial epigenome-transcriptome co-profiling of mammalian tissues [RNA-Seq],4,Mus musculus,DBiT-seq,DBiT-seq (or DBiT-derived),brain;embryo (whole),,normal,0,36922587;39870864,train
-GSE205055,Spatial epigenome-transcriptome co-profiling of mammalian tissues,7,Homo sapiens;Mus musculus,DBiT-seq,DBiT-seq (or DBiT-derived),brain,,normal,0,36922587;39870864,train
+GSE205054,Spatial epigenome-transcriptome co-profiling of mammalian tissues [RNA-Seq],4,Mus musculus,DBiT-seq,DBiT-seq,brain;embryo (whole),,normal,0,36922587;39870864,train
+GSE205055,Spatial epigenome-transcriptome co-profiling of mammalian tissues,7,Homo sapiens;Mus musculus,DBiT-seq,DBiT-seq,brain,,normal,0,36922587;39870864,train
 GSE205307,Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy,2,Mus musculus,Visium,Visium,unknown,cancer,disease,2,38424167,test
 GSE205707,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,14,Mus musculus;Canis lupus familiaris,Visium,Visium,skeletal muscle,,perturbation,6,,val
 GSE206245,Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma,17,Homo sapiens,Visium;ST (legacy),Visium;ST (legacy),airway;stomach,nasopharyngeal carcinoma;gastric cancer;carcinoma;epithelial neoplasm,disease,14,39231979,train
@@ -109,7 +109,7 @@ GSE206787,Spatiotemporal signaling underlies progressive vascular rarefaction in
 GSE206790,Profibrotic subsets of SPP1+ macrophages and POSTN+ fibroblasts contribute to fibrotic scarring in acne keloidalis,1,Homo sapiens,Visium,Visium,skin,acne,disease,1,38218364,train
 GSE207205,Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection [Spatial transcriptomics],8,Homo sapiens,Visium,Visium,thymus,,normal,8,36741401,train
 GSE207546,Choroid plexus mast cells drive tumor-associated hydrocephalus,3,Mus musculus,Visium,Visium,brain,neoplasm;hydrocephalus,disease,3,38056463,train
-GSE207843,Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue,18,Mus musculus,DBiT-seq,DBiT-seq (or DBiT-derived),spleen;heart;liver;kidney;brain;pancreas,,normal,0,36934108,train
+GSE207843,Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue,18,Mus musculus,DBiT-seq,DBiT-seq,spleen;heart;liver;kidney;brain;pancreas,,normal,0,36934108,train
 GSE208253,Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response,12,Homo sapiens,Visium,Visium,oral cavity,oral cavity squamous cell carcinoma,disease,12,37596273,train
 GSE208747,Decoding spatial gene activity changes in multiple sclerosis lesion progression,26,Homo sapiens,Visium,Visium,brain,multiple sclerosis,disease;normal,26,39501035,test
 GSE209583,"Spatial transcriptomics analysis of wild type, 5XFAD mice, 5XFAD mice treated with either vehicle or human neural stem cells (hNSC)",14,Mus musculus,Visium,Visium,brain,Alzheimer disease,disease;normal,14,38155736,train
@@ -127,7 +127,7 @@ GSE212526,Spatial transcriptomics analysis of soft tissue sarcomas.,4,Homo sapie
 GSE212706,Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [spatial trascriptomics],6,Mus musculus,Visium,Visium,breast,breast neoplasm;cancer,disease;normal,6,,train
 GSE212903,Spatial transcriptomics of the mouse brain across three age groups,6,Mus musculus,Visium,Visium,brain,,normal,6,37591239,train
 GSE213216,A single-cell transcriptomic analysis of endometriosis,2,Homo sapiens,Visium,Visium,other;peritoneum,endometriosis,disease,2,36624343;38370978,train
-GSE213264,High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq,18,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),spleen;colon;small intestine;kidney;tonsil;thymus;skin;brain,glioblastoma,normal;disease,0,36823353;39095360,train
+GSE213264,High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq,18,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq,spleen;colon;small intestine;kidney;tonsil;thymus;skin;brain,glioblastoma,normal;disease,0,36823353;39095360,train
 GSE213286,Craters on the melanoma surface serve as hubs for CD8+ T cells,1,Danio rerio,Slide-seq,Slide-seq,skin,melanoma,disease,0,41109214,train
 GSE213306,Spatial transcriptomic analysis of human oligodendrocyte development across gestational weeks 10 to 24,8,Homo sapiens,Visium,Visium,brain,,normal,0,41509247,train
 GSE213388,Periportal macrophages protect against commensal-driven liver inflammation [spatial transcriptomics],4,Mus musculus,Visium,Visium,liver,,normal,4,38658756,val
@@ -197,7 +197,7 @@ GSE226663,"Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single
 GSE226760,The Triptryium wilfordii derivative celastrol has anti-fibrotic effects in systemic sclerosis [Spatial Transcriptomics],8,Mus musculus,Visium,Visium,skin,systemic sclerosis;skin disorder;scleroderma,normal;disease,8,37328193,train
 GSE226997,Visium Spatial transcriptomics analysis of human primary colorectal cancer,4,Homo sapiens,Visium,Visium,colon,colorectal cancer,disease,4,38446659,train
 GSE227019,Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics,3,Homo sapiens,Visium,Visium,ovary,ovarian cancer,disease,3,36882687,test
-GSE227046,High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing,7,Mus musculus,Other;Visium,ISS (Cartana / in situ sequencing);Visium,kidney,,normal;perturbation,1,38360882,train
+GSE227046,High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing,7,Mus musculus,Other;Visium,ISS (Cartana);Visium,kidney,,normal;perturbation,1,38360882,train
 GSE227332,The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Thymus Visium],6,Mus musculus,Visium,Visium,thymus,,normal;perturbation,6,37948511,test
 GSE227598,Time-series spatial transcriptomic analysis of murine colon undergoing AOM-DSS tumorigenesis with and without LXR activation,5,Mus musculus,Visium,Visium,colon,,normal;disease,5,39567700,train
 GSE227742,Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation,4,Mus musculus,Visium,Visium,small intestine,,normal;perturbation,4,39567700,train
@@ -343,7 +343,7 @@ GSE251693,Double-negative B cells and DNASE1L3 colocalise with microbiota in gut
 GSE251926,Open-ST: High-resolution spatial transcriptomics in 3D,19,Homo sapiens,Other,Open-ST,lymph node,head and neck squamous cell carcinoma,disease,0,38917789,train
 GSE251938,Single-cell and In Situ Spatial Transcriptomics of Marjolin ulcers,1,Homo sapiens,Xenium,Xenium,skin,ulcer disease;burn,disease,1,39128494,train
 GSE251950,Spatial transcriptomics of gastric cancers (Visium 10X platform),10,Homo sapiens,Visium,Visium,stomach;unknown,gastric cancer,disease,10,39580151,train
-GSE252090,Spatial single cell RNA profiles from medulloblastoma Group 3/4 tumors with oncogene aberrations,23,Homo sapiens,Molecular Cartography,Resolve Molecular Cartography,brain,medulloblastoma,disease,0,40335697,val
+GSE252090,Spatial single cell RNA profiles from medulloblastoma Group 3/4 tumors with oncogene aberrations,23,Homo sapiens,Molecular Cartography,Molecular Cartography,brain,medulloblastoma,disease,0,40335697,val
 GSE252108,Dissecting the intra- and intertumoral heterogeneity of adrenocortical carcinoma by single-cell multi-omics analyses [I],2,Homo sapiens,Visium,Visium,adrenal gland,adrenal cortex carcinoma,disease,0,,train
 GSE252113,Dissecting the intra- and intertumoral heterogeneity of adrenocortical carcinoma by single-cell multi-omics analyses,5,Homo sapiens,Visium,Visium,adrenal gland,adrenal cortex carcinoma,disease;normal,5,,train
 GSE252176,Multi-Omics molecular subtyping based on commensal microbiome predicts molecular characteristics and therapeutic response in Triple-Negative Breast Cancer [Spatial Transcriptome seq],4,Homo sapiens,Visium,Visium,breast,triple-negative breast carcinoma,disease,4,38730464,val
@@ -514,7 +514,7 @@ GSE274572,Delineation of a thrombin receptor-stimulated vascular smooth muscle c
 GSE274605,Molecular signatures of altered energy metabolism and circadian rhythm perturbations in a model of synucleinopathy,8,Mus musculus,Visium,Visium,brain,synucleinopathy;Parkinson disease,disease,8,41736854,train
 GSE274617,Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity [MERFISH],1,Mus musculus,MERFISH/MERSCOPE,MERSCOPE,pancreas,cancer,disease,0,41758082,train
 GSE274623,Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PM],8,Homo sapiens,Xenium,Xenium,peritoneum,cancer,disease,8,,train
-GSE274641,Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues,9,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),embryo (whole);lymph node;brain,lymph node disorder;lymphoma;diffuse large B-cell lymphoma,normal;disease,0,39353436,train
+GSE274641,Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues,9,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq,embryo (whole);lymph node;brain,lymph node disorder;lymphoma;diffuse large B-cell lymphoma,normal;disease,0,39353436,train
 GSE274657,Spatial transcriptomics for platinum-resistant high-grade serous ovarian carcinoma,4,Homo sapiens,Visium,Visium,ovary,ovarian carcinoma,disease,4,40883550,train
 GSE274665,Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer (Spatial Transcriptomics),4,Homo sapiens,Visium,Visium,pancreas,pancreatic ductal adenocarcinoma,disease,4,39627211,train
 GSE274673,Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PDAC],6,Homo sapiens,Xenium,Xenium,pancreas,pancreatic ductal adenocarcinoma,disease,6,,train
@@ -563,7 +563,7 @@ GSE278766,Comparison of CosMx and GeoMx profiling performed on the same human ki
 GSE278848,Visium Spatial Transcriptomics of the Human Hypothalamus,9,Homo sapiens,Visium,Visium,brain,,normal,0,39910307,test
 GSE278936,Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer,52,Homo sapiens,Visium,Visium,prostate;liver;meninges;lymph node;heart,benign prostatic hyperplasia;prostate cancer;metastatic prostate carcinoma;metastatic malignant neoplasm in the liver,disease,52,39550375,train
 GSE278969,Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [xenium],8,Homo sapiens,Xenium,Xenium,other,arthritic joint disease,disease,0,40601776,train
-GSE279181,Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics],18,Homo sapiens,Visium,10x Visium,brain,multiple sclerosis,normal;disease,18,39501036,train
+GSE279181,Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics],18,Homo sapiens,Visium,Visium,brain,multiple sclerosis,normal;disease,18,39501036,train
 GSE279255,Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted,1,Mus musculus,Visium HD,Visium HD,small intestine,infectious disease,disease,1,39843748,train
 GSE279273,Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory [Spatial Transcriptomics],2,Mus musculus,Visium,Visium,brain,,perturbation,2,38260257,train
 GSE279405,Spatial transcriptomical analysis of livers from patients with COVID19,3,Homo sapiens,Visium,Visium,liver,COVID-19,disease,3,39709771,train
@@ -602,7 +602,7 @@ GSE282059,"Nanostring CosMx 6,000-plex RNA profiling of human kidney nephrectomy
 GSE282123,"Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Xenium]",7,Homo sapiens,Xenium,Xenium,colon,ulcerative colitis;colitis,disease,7,42262875,val
 GSE282124,"Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Merscope]",1,Homo sapiens,MERFISH/MERSCOPE,MERSCOPE,colon,ulcerative colitis,disease,0,42262875,train
 GSE282203,Spatial transcriptomics identifies regional disruptions in brain rhythmic gene expression in a mouse model of Alzheimer’s disease,65,Mus musculus,Visium,Visium,brain,Alzheimer disease,disease;normal,65,41659563,train
-GSE282302,In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Spatial Transcriptomics],105,Homo sapiens,Visium,Visium (FFPE),pancreas,pancreatic ductal adenocarcinoma,disease,105,41533516,train
+GSE282302,In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Spatial Transcriptomics],105,Homo sapiens,Visium,Visium,pancreas,pancreatic ductal adenocarcinoma,disease,105,41533516,train
 GSE282547,Spatial transcriptomic analysis of developing hearts at embryonic and neonatal stages,17,Mus musculus,Visium;Slide-seq,Visium;Slide-seq,heart,,normal;perturbation,8,42141139,train
 GSE282635,Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics [Spatial Transcriptomics],1,Homo sapiens,Visium,Visium,heart,cardiomyopathy,disease,1,40184463,train
 GSE282639,Ectopic expression of MUC5B in the respiratory bronchiole initiates ER stress in the IPF lung,43,Homo sapiens,CosMx,CosMx,lung,idiopathic pulmonary fibrosis,normal;disease,0,41091081,train
@@ -619,7 +619,7 @@ GSE283227,CDK12/13 inactivation triggers STING-mediated antitumor immunity in pr
 GSE283269,Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts,6,Homo sapiens,Visium,Visium,blood vessel,,normal;disease,6,40076574,test
 GSE283283,Spatiotemporal transcriptomic niches of complement pathway and serine protease inhibitor activation in aging and infection,168,Mus musculus,Visium;Stereo-seq,Visium;Stereo-seq,brain;kidney;lung;spleen;heart;liver,cerebral malaria,normal;disease,153,,test
 GSE283302,Spatial Transcriptomic Profiling of the Mouse Adrenal Gland and Adjacent Adipose Tissue,1,Mus musculus,Visium,Visium,adrenal gland,,normal,1,41442035,train
-GSE283333,Comprehensive immune profiling reveals IFN-γ signaling in T cells mediates parasite phagocytosis in a rodent malaria model : Spatial transcriptomics data,2,Mus musculus,BMK S1000,BMK S1000,lung,malaria,normal;disease,2,,train
+GSE283333,Comprehensive immune profiling reveals IFN-γ signaling in T cells mediates parasite phagocytosis in a rodent malaria model : Spatial transcriptomics data,2,Mus musculus,BMK S1000,BMKMANU S1000,lung,malaria,normal;disease,2,,train
 GSE283411,Clonal lineage tracing and transcriptomics of cortical progenitor populations reveal maintenance of differentiation potential.,2,Mus musculus,Slide-seq,Curio Seeker,brain,,normal,0,39952245,train
 GSE283412,Integrated Methylation and Spatial Transcriptomic Profiling of Metaplastic Breast Cancer to Investigate Intra-tumoral Heterogeneity.,8,Homo sapiens,Visium,Visium,breast,breast cancer,disease,8,40790295,train
 GSE283418,Spatial molecular profiling of amygdalar neurons enables precision pharmacology against pain unpleasantness,10,Mus musculus,Molecular Cartography,Molecular Cartography,brain,,normal,0,,train
@@ -628,7 +628,7 @@ GSE283497,Genetically Engineered Brain Organoids Recapitulate Spatial and Develo
 GSE283832,"A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [Xenium Spatial_Transcriptomics]",7,Homo sapiens,Xenium,Xenium,brain,"atypical teratoid rhabdoid tumor, SHH-activated;atypical teratoid rhabdoid tumor, TYR-activated;atypical teratoid rhabdoid tumor, MYC-activated",disease,0,40726147,train
 GSE283863,Cranial radiotherapy profoundly affects glia without inducing widespread cellular senescence,1,Mus musculus,CosMx,CosMx,brain,,perturbation,0,40518745,train
 GSE283872,Prior High Fiber Intake Impinges on the Cellular Responses of Mesenteric Adipose and Intestinal Tissues to Subsequent High Fat Feeding [Spatial Transcriptomics],4,Mus musculus,Stereo-seq,Stereo-seq,small intestine,,perturbation,0,41520334,test
-GSE283883,Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip,1,Mus musculus,Other,"other (named, not in list)",liver,,normal,0,,train
+GSE283883,Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip,1,Mus musculus,Other,"other (named in GEO, not in list)",liver,,normal,0,,train
 GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,35,Homo sapiens,Visium,Visium,colon;small intestine;rectum;other,Crohn disease;inflammatory bowel disease;intestinal disorder,disease;normal,35,41224999,test
 GSE283959,Spatially resolved chimeric analysis reveals extracellular CKB-mediated ATP uptake at the glioma-astrocyte invasive front,4,Mus musculus,Visium,Visium,brain,glioblastoma;glioma,disease,4,40991701,train
 GSE283967,Multi-modal refinement of the human heart atlas during the first gestational trimester,3,Homo sapiens,Visium,Visium,heart,,normal,3,39927812,train
@@ -943,7 +943,7 @@ GSE307990,Spatial and single cell transcriptomics in the human Entorhinal Cortex
 GSE308146,Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - CosMx Data,4,Homo sapiens,CosMx,CosMx,unknown;other,cancer,disease;normal,0,41266321,train
 GSE308147,Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - MERSCOPE Data,2,Homo sapiens,MERFISH/MERSCOPE,MERSCOPE,breast;lung,cancer,disease;normal,0,41266321,train
 GSE308148,Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - Xenium Data,8,Homo sapiens,Xenium,Xenium,breast;lung;unknown,cancer,disease;normal,7,41266321,train
-GSE308167,Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus,3,Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),lymph node,B-cell chronic lymphocytic leukemia;diffuse large B-cell lymphoma,not stated;disease,0,41540123,train
+GSE308167,Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus,3,Homo sapiens,DBiT-seq,DBiT-seq,lymph node,B-cell chronic lymphocytic leukemia;diffuse large B-cell lymphoma,not stated;disease,0,41540123,train
 GSE308260,Spatial transcriptomics for intrathoracic adhesion in mice,1,Mus musculus,Visium,Visium,lung,,perturbation,1,42230567,train
 GSE308275,Integrated single-cell and spatial transcriptomics of ovarian immune landscape reveal role of distinct macrophages in classic galactosemia associated with premature ovarian insufficiency,2,Homo sapiens,Visium,Visium,ovary,,normal,2,42226209,train
 GSE308486,Novel biomarker for prostatic ductal adenocarcinoma identified using spatial transcriptomic analysis,6,Homo sapiens,Visium,Visium,prostate,adenocarcinoma,disease,6,,train
@@ -961,7 +961,7 @@ GSE309522,Eosinophils enhance granuloma-mediated control of persistent Salmonell
 GSE309565,Morphological and Functional Diversity of Spatially Resolved Vestibular Ganglion Neuron Cell Types,2,Mus musculus,Visium HD,Visium HD,head and neck,,normal;perturbation,2,,test
 GSE309857,Microglial TDP-43 mediates myelin refinement and represses Tyrobp cryptic exon inclusion in mice [Spatial Transcriptomics],4,Mus musculus,Visium,Visium,brain,,perturbation;normal,0,42420559,train
 GSE310073,Immunotolerant Oligomer Scaffolds Promote Regenerative Remodeling and Improved Muscle Structure and Function After Volumetric Muscle Loss,6,Rattus norvegicus,Visium,Visium,skeletal muscle,,perturbation,6,41796221,train
-GSE310116,Mucosal vaccination transcends pathogen boundaries to protect from diverse respiratory threats,4,Mus musculus,Slide-seq,"Curio Trekker (single-cell, Slide-seq beads)",lung,,perturbation;normal,0,41712698,train
+GSE310116,Mucosal vaccination transcends pathogen boundaries to protect from diverse respiratory threats,4,Mus musculus,Slide-seq,Curio Trekker,lung,,perturbation;normal,0,41712698,train
 GSE310129,Spatial transcriptome sequencing of chicken and duck beaks,3,Anas platyrhynchos;Gallus gallus,Stereo-seq,Stereo-seq,head and neck,,normal,0,,train
 GSE310162,Heterogeneity in B- and epithelial-cell senescence in the pathogenesis of COPD/emphysema [Xenium],22,Homo sapiens,Xenium,Xenium,lung,pulmonary emphysema,normal;disease,22,,train
 GSE310351,Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation,6,Homo sapiens,Visium,Visium,blood vessel,,disease,6,41569144,train
@@ -975,7 +975,7 @@ GSE310658,Xenium In Situ analysis of mouse skin mock-treated or treated with Ssp
 GSE310797,Single cell and Spatial RNA-seq in Oral Squamous Cell Carcinoma with Different Stage,3,Homo sapiens,Visium,Visium,oral cavity,oral cavity squamous cell carcinoma,disease,0,41851114,train
 GSE310921,Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses,8,Mus musculus;Homo sapiens,Visium,Visium,skeletal muscle,,normal;perturbation,8,,train
 GSE311123,Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone,1,Homo sapiens,Visium,Visium,bone,bone giant cell tumor;giant cell tumor,disease,1,41872383,val
-GSE311199,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,7,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),brain;embryo (whole);skin,melanoma,normal;disease,0,42641604,train
+GSE311199,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,7,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq,brain;embryo (whole);skin,melanoma,normal;disease,0,42641604,train
 GSE311294,Collagen Alignment and Spatial Transcriptomics Analysis (CASTA) reveals gene programs associated with collagen alignmet in colorectal cancer,5,Homo sapiens,Visium,Visium,colon,colorectal cancer,disease,5,,train
 GSE311369,A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [RGC_CrossSection],1,Mus musculus,Xenium,Xenium,eye,,normal,1,41452983,train
 GSE311383,High-resolution spatial transcriptomics of human liver with VisiumHD,3,Homo sapiens,Visium HD,Visium HD,liver,,normal,3,42342734,train
@@ -983,7 +983,7 @@ GSE311609,Single-Cell Spatial Transcriptomics of Archival Human Lung and Breast
 GSE311636,New taxonomy based on individual patient-reported response trajectories defines ulcerative colitis endotypes and reveals vascular inflammation as a mechanism for vedolizumab nonresponse [cosMx],2,Homo sapiens,CosMx,CosMx,rectum,ulcerative colitis,disease,0,,val
 GSE311681,An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis,1,Mus musculus,Xenium,Xenium,liver,cholangitis,disease,1,41963321,train
 GSE311717,Lipid-Associated Macrophage Polarization Drives Chronic Xenograft Fibrosis via APOE-SDC2 Signaling,15,Macaca fascicularis,Visium,Visium,kidney,,disease;perturbation,15,,train
-GSE311781,"Focal white matter lesions drive grey matter inflammation, neuronal dysfunction and synapse loss",10,Rattus norvegicus,DBiT-seq,DBiT-seq (or DBiT-derived),brain,,normal;disease,0,42020752,train
+GSE311781,"Focal white matter lesions drive grey matter inflammation, neuronal dysfunction and synapse loss",10,Rattus norvegicus,DBiT-seq,DBiT-seq,brain,,normal;disease,0,42020752,train
 GSE311783,DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [Spatial Transcriptomics],7,Homo sapiens,Visium,Visium,pancreas,pancreatic ductal adenocarcinoma,disease,7,41707654,train
 GSE311892,The local cellular response to Human Papillomavirus focuses on basal layer restoration as visualized in situ by specific cellular neighborhoods near infected cells,36,Homo sapiens,CosMx,CosMx,other,,disease;normal;not stated,0,41438752,train
 GSE311909,A targetable developmental program co-regulates angiogenesis and immune evasion [Spatial Transcriptomics],2,Homo sapiens,Visium,Visium,skin,melanoma,disease,2,41631877,val
@@ -1067,7 +1067,7 @@ GSE318797,CosMX spatial transcriptomics of mouse subcutaneous EO771 tumors to st
 GSE318867,Vascular STING activation facilitates NK cell anti-tumor immunity in small cell lung cancer [Spatial_Transcriptome],3,Homo sapiens,Visium,Visium,lung,small cell lung carcinoma,disease,3,41791380,train
 GSE319123,Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT,1,Mus musculus,Xenium,Xenium,lung,,perturbation,1,,train
 GSE319236,Spatially resolved maternal and fetal cell contributions to severe Preeclampsia,64,Homo sapiens,Visium,Visium,uterus;placenta,severe pre-eclampsia;preeclampsia,disease,0,,test
-GSE319277,Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT [Spatial Transcriptomics],7,Mus musculus,DBiT-seq,DBiT-seq (or DBiT-derived),lung;liver,,perturbation;disease,0,,train
+GSE319277,Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT [Spatial Transcriptomics],7,Mus musculus,DBiT-seq,DBiT-seq,lung;liver,,perturbation;disease,0,,train
 GSE319536,A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture,22,Homo sapiens,Visium,Visium,bladder,urinary bladder carcinoma,disease,22,,train
 GSE319617,Inference of cell-cell communication in human fetal liver from high definition spatial profiling using Renoir,2,Homo sapiens,Visium HD,Visium HD,liver,,normal,2,42086556,train
 GSE319706,Spatial polarization of endothelial ICAM-1 drives CD8⁺ T cell exclusion in melanoma [Xenium],9,Mus musculus,Xenium,Xenium,skin;other,melanoma,disease,9,,train
@@ -1134,7 +1134,7 @@ GSE327147,MERFISH data on seven mouse brain with Abeta pathology,7,Mus musculus,
 GSE327192,Dendritic cell-mediated antigen presentation regulates tertiary lymphoid structure development in cancer [MERFISH],15,Homo sapiens,MERFISH/MERSCOPE,MERSCOPE,liver;lung,hepatocellular carcinoma;non-small cell lung carcinoma,disease,0,,train
 GSE327284,"Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Spatial data)",2,Mus musculus,Visium HD,Visium HD,brain,traumatic brain injury;vascular disorder,disease,2,42463666,train
 GSE327347,Targeted spatial transcriptomic profiling of pleural mesothelioma using 10x Genomics Xenium,7,Homo sapiens,Xenium,Xenium,lung;other,pleural mesothelioma,disease,7,41319863;42138664,test
-GSE327406,"Spatially resolved, integrated single-cell multiomic profiling of the transcriptome and epigenomic targets in frozen tissue sections",1,Mus musculus,Slide-seq,"Curio Trekker (single-cell, Slide-seq beads)",brain,,normal,0,42371963,train
+GSE327406,"Spatially resolved, integrated single-cell multiomic profiling of the transcriptome and epigenomic targets in frozen tissue sections",1,Mus musculus,Slide-seq,Curio Trekker,brain,,normal,0,42371963,train
 GSE327441,Cellular Signatures of Melanocortin Pathway Genes Across the Locus Coeruleus [Spatial Transcriptomics],4,Homo sapiens,Visium,Visium,brain,,normal,4,41935248,train
 GSE327581,Single-cell spatial transcriptomic profiling of 3xTg-AD mouse brains following fecal microbiota transplantation from stroke and healthy human donors,5,Mus musculus,CosMx,CosMx,brain,cerebrovascular disorder;Alzheimer disease;stroke disorder,disease,0,,train
 GSE327709,Transient cell states encode positional information to direct asymmetric growth [MERFISH],9,Arabidopsis thaliana,MERFISH/MERSCOPE,MERSCOPE,plant,,perturbation,0,42239415,train
@@ -1177,9 +1177,9 @@ GSE333529,A skin–kidney neutrophil axis links UV exposure to renal angiogenesi
 GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,4,Homo sapiens,Visium,Visium,skin,Stevens-Johnson syndrome,disease,4,,train
 GSE333685,Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk,1,Mus musculus,Xenium,Xenium,blood vessel,coronary artery disorder,disease,1,41844614,train
 GSE333693,Rat thymic epithelium-free areas are specialized medullary niches enriched for mature thymocytes and distinct stromal subsets,1,Rattus norvegicus,Stereo-seq,Stereo-seq,thymus,,normal,0,,train
-GSE333735,TGFbeta determines epithelial tissue spacing by regulating mesenchymal condensation,3,Gallus gallus,DBiT-seq,DBiT-seq (or DBiT-derived),lung,,normal,0,42446999,train
+GSE333735,TGFbeta determines epithelial tissue spacing by regulating mesenchymal condensation,3,Gallus gallus,DBiT-seq,DBiT-seq,lung,,normal,0,42446999,train
 GSE333737,MERFISH spatial transcriptomic profiling of extracellular matrix and vascular-associated populations in the adult human pancreas,12,Homo sapiens,MERFISH/MERSCOPE,MERSCOPE,pancreas,diabetes mellitus,normal;disease,0,,train
-GSE333851,Spatial Glyco-Codes Define Human Liver Pathology and Progression,1,Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),liver,hepatocellular carcinoma,disease,0,42465518,train
+GSE333851,Spatial Glyco-Codes Define Human Liver Pathology and Progression,1,Homo sapiens,DBiT-seq,DBiT-seq,liver,hepatocellular carcinoma,disease,0,42465518,train
 GSE334067,Paired mutation calling and spatial transcriptomics identify cellular neighborhoods associated with neoplastic outcomes in mouse colitis,32,Mus musculus,Visium,Visium,colon,colitis,disease,32,42521760,train
 GSE334308,Mapping vascular plasticity in liver fibrogenesis identifies novel fibrosis-associated endothelial cells in early-stage liver disease,2,Homo sapiens,Visium HD,Visium HD,liver,liver disorder,disease,2,,train
 GSE334323,Custom Probe-Based Spatial Transcriptomics Enables Microbiome Detection in FFPE Colorectal Cancer Tissue,6,Homo sapiens,Visium,Visium,colon,adenocarcinoma;colorectal carcinoma,normal;disease,6,,train
@@ -1196,7 +1196,7 @@ GSE335345,"10X Visium spatial transcriptomics of mouse thoracic spine interverte
 GSE335533,Epigenetic reprogramming of CD4⁺ T cell fate by maternal and early-life obesity impairs vaccine responses in the offspring [Spatial Transcriptomics],2,Mus musculus,Visium,Visium,lymph node,,perturbation,2,,train
 GSE335552,An Integrated Spatial Multi-Omics Workflow for Sequential RNA and Protein Profiling in FFPE Tumor Tissue,4,Homo sapiens,Xenium,Xenium,liver,neoplasm,disease;normal,4,,train
 GSE335564,A comparative brain cell atlas of Astyanax mexicanus,1,Astyanax mexicanus,Other,not named in GEO,brain,,normal,0,42395481,train
-GSE335592,CAR-T-drug conjugate against solid tumor,2,Homo sapiens,DBiT-seq,DBiT-seq (or DBiT-derived),lung,neoplasm,disease,0,,val
+GSE335592,CAR-T-drug conjugate against solid tumor,2,Homo sapiens,DBiT-seq,DBiT-seq,lung,neoplasm,disease,0,,val
 GSE335624,Initial OX40–OX40L Signaling Promotes a Skin-Resident Memory T-Cell Reservoir in Atopic Dermatitis,1,Homo sapiens,Xenium,Xenium,skin,atopic eczema;prurigo,disease,1,42638514,train
 GSE335702,Pericyte KATP Channel Hyperactivity Redistributes Cortical Blood Flow in a CADASIL Mouse Model,8,Mus musculus,Visium;Visium HD,Visium;Visium HD,brain;blood vessel,"cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1",disease;normal,8,42547848,train
 GSE335777,Resident tissue macrophages transfer selenium transporter protein to protect pancreatic cancer from ferroptosis,1,Mus musculus,Visium,Visium,pancreas,pancreatic ductal adenocarcinoma,disease,1,,train