Correction 2026-11-11: 12 samples replaced by re-converted versions (GSE205707 x6, GSE275125 x4, GSM8933093, GSM5643203); 6 samples withdrawn (GSE298115 GSM9008651/GSM9008653, GSE244723 x4) - catalog, metadata v2.2.3, gene index

catalog/atlas-sample-metadata.jsonl

@@ -2929,10 +2929,6 @@
 {"gsm": "GSM7823260", "disease": null, "condition": "Apex resection", "age": null, "sex": null, "donor_id": null, "publication_pmid": "40967223", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
 {"gsm": "GSM7823491", "disease": null, "condition": "wildtype", "age": null, "sex": "female", "donor_id": null, "publication_pmid": "40335695", "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-03T02:24:31.283092+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": {"type": "object_slot"}, "expression_reader": "rds_matrix"}
 {"gsm": "GSM7823492", "disease": null, "condition": "wildtype", "age": null, "sex": "male", "donor_id": null, "publication_pmid": "40335695", "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-03T02:24:31.283092+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": {"type": "object_slot"}, "expression_reader": "rds_matrix"}
-{"gsm": "GSM7825036", "disease": null, "condition": "control", "age": "CS16", "sex": null, "donor_id": null, "publication_pmid": "38011284", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
-{"gsm": "GSM7825037", "disease": null, "condition": "control", "age": "CS16", "sex": null, "donor_id": null, "publication_pmid": "38011284", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
-{"gsm": "GSM7825038", "disease": null, "condition": "control", "age": "CS16", "sex": null, "donor_id": null, "publication_pmid": "38011284", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
-{"gsm": "GSM7825039", "disease": null, "condition": "control", "age": "CS16", "sex": null, "donor_id": null, "publication_pmid": "38011284", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
 {"gsm": "GSM7829909", "disease": null, "condition": "saline control", "age": "6-12 weeks", "sex": null, "donor_id": null, "publication_pmid": "38848213", "publication_doi": null, "counts_ready": "ABSENT", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-02T23:11:24.677275+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "delimited_matrix"}
 {"gsm": "GSM7829910", "disease": null, "condition": "saline control", "age": "6-12 weeks", "sex": null, "donor_id": null, "publication_pmid": "38848213", "publication_doi": null, "counts_ready": "ABSENT", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-02T23:11:24.677275+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "delimited_matrix"}
 {"gsm": "GSM7829911", "disease": null, "condition": "saline control", "age": "6-12 weeks", "sex": null, "donor_id": null, "publication_pmid": "38848213", "publication_doi": null, "counts_ready": "ABSENT", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-02T23:11:24.677275+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "delimited_matrix"}
@@ -7534,8 +7530,6 @@
 {"gsm": "GSM9004713", "disease": null, "condition": null, "age": null, "sex": null, "donor_id": null, "publication_pmid": null, "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-03T01:10:31.467911+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "stereo_gef_bins"}
 {"gsm": "GSM9004714", "disease": null, "condition": null, "age": null, "sex": null, "donor_id": null, "publication_pmid": null, "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-03T01:10:31.467911+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "stereo_gef_bins"}
 {"gsm": "GSM9004715", "disease": null, "condition": null, "age": null, "sex": null, "donor_id": null, "publication_pmid": null, "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.3.0", "audited_at": "2026-10-03T01:10:31.467911+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "stereo_gef_bins"}
-{"gsm": "GSM9008651", "disease": null, "condition": "WT", "age": null, "sex": "male", "donor_id": null, "publication_pmid": "41025096", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
-{"gsm": "GSM9008653", "disease": null, "condition": "Gcm2 variant p.Y392S", "age": null, "sex": "male", "donor_id": null, "publication_pmid": "41025096", "publication_doi": null, "counts_ready": "NOT_RECORDED", "audit": null}
 {"gsm": "GSM9008654", "disease": null, "condition": "WT", "age": null, "sex": null, "donor_id": null, "publication_pmid": "41025096", "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.6.3", "audited_at": "2026-10-08T16:27:50.198565+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "mtx_triplet"}
 {"gsm": "GSM9008655", "disease": null, "condition": "WT", "age": null, "sex": null, "donor_id": null, "publication_pmid": "41025096", "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.6.3", "audited_at": "2026-10-08T16:27:50.198565+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "mtx_triplet"}
 {"gsm": "GSM9008656", "disease": null, "condition": "Gcm2 variant p.Y392S", "age": null, "sex": null, "donor_id": null, "publication_pmid": "41025096", "publication_doi": null, "counts_ready": "VERIFIED", "audit": {"status": "PASS", "scorer_version": "sda-all-scorer-1.6.3", "audited_at": "2026-10-08T16:27:50.198565+00:00", "checks": {"IN1": true, "ID1": true, "EX3": true, "EX2": true, "EX1": true, "SP3": true}}, "counts_evidence": null, "expression_reader": "mtx_triplet"}

catalog/atlas-study-metadata.jsonl

@@ -295,7 +295,6 @@
 {"gse": "GSE244641", "title": "Recirculating regulatory T cells mediate thymic regeneration [visium]", "summary": "Recirculating regulatory T cells mediate thymic regeneration [visium]", "design": "Spatial transcriptomic profiles of thymic tissue from 2-month-old and 18-month-old mice after injury", "pubmed_ids": ["39892391"]}
 {"gse": "GSE244650", "title": "Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals", "summary": "Intrinsic molecular strategy at the organ level to injury stimuli remains elusive. Identifying and modulating such potential molecular strategy for systemic adaptations to injury is theoretically fascinating and therapeutically promising. Here, using integrative single-cell and spatial transcriptomic analysis, we reported that lysozyme 2 (Lyz2), a long-established myeloid marker, surprisingly indicated global injury status (across cell types and anatomic divisions) and influenced cardiac function after injury. We correlated the Lyz2 regulon of the lysosome-matrisome (particularly endocardial lysosomal-degrading Hspgs) with anatomical and functional relevance to cardiac injury and determined that such spatial model is consensus across various injury types, both mouse and human. Modulation of spatial model mediated by Lyz2 via genetic deletion or chemical inhibition in adult mice with myocardial infarction remarkably achieved immediate protective effects, a rare therapeutic benefit among current interventions for heart failure. These results provided the first molecular evidence for the unprecedented molecular strategy adopted by the heart with unparalleled therapeutic promising for organ repair.", "design": "We leveraged spatial transcriptomics to overview molecular organization with anatomical divisions during cardiac regeneration. We collected a total of 19 specimens from 10 hearts at 8 developmental points, including seven P1 hearts post-AR (P1+1dpr-7dpr) and four hearts as controls (WT: P1, P7; and SH: P1+4,6 dps). Sample sections were collected with the maximum 4-chamber view along the dorsal-ventral axis, and the sectioning depth of individual hearts increased with postnatal days, reflecting an increase in dorsal-ventral dimensions as the heart grew and ensuring comparable histological views across samples. After data trimming for quality control, the joint dataset yielded a pool of 16,654 individual spots (average 5,343 genes per spot) and identified 16 clusters by uniform manifold approximation and projection (UMAP) corresponding to cardiac anatomical divisions in high spatial and molecular resolution, allowing us to study molecular diversity in intact tissue in space without bias.", "pubmed_ids": ["40967223"]}
 {"gse": "GSE244659", "title": "A diverse network of pericoerulear neurons control arousal states", "summary": "As the primary source of norepinephrine (NE) in the brain, the locus coeruleus (LC) regulates both arousal and stress responses1,2. However, how local neuromodulatory inputs contribute to LC function remains unresolved. Here we identify a network of transcriptionally and functionally diverse GABAergic neurons in the LC dendritic field that integrate distant inputs and modulate modes of LC firing to control arousal. We define peri-LC anatomy using viral tracing and combine single-cell RNA sequencing and spatial transcriptomics to molecularly define both LC and peri-LC cell types. We identify several cell types which underlie peri-LC functional diversity using a series of complementary approaches in behaving mice. Our findings indicate that LC and peri-LC neurons comprise transcriptionally and functionally heterogenous neuronal populations, alongside anatomically segregated features which coordinate specific influences on behavioral arousal and avoidance states. Defining the molecular, cellular and functional diversity in the LC provides a road map for understanding the neurobiological basis of arousal alongside hyperarousal-related neuropsychiatric phenotypes.", "design": "six sections from female adult wild-type mouse and five sections from male adult mouse were used for spatial transcriptome analysis", "pubmed_ids": ["40335695"]}
-{"gse": "GSE244723", "title": "Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart", "summary": "Congenital heart defects are very common, with around 2% of the population having a valve anomaly. During development of the heart, and specifically the heart valves, cells change from distinct undifferentiated populations of progenitors into specialized cells organized with precise spatial locations within complex tissue structures. Knowledge of both the spatial location and the transcriptional profile of the progenitors and differentiated cells is necessary to understand the differentiation process and the formation of the complex 3-dimensional architecture of the valves. Disruption to these processes leads to congenital valve defects and these are associated with significant morbidity (valve disease is the most common cause of cardiac surgery in the over-50s), particularly during aging. Here we utilized a spatial transcriptomic approach (Stahl et al, 2016; DeLaughter et al, 2016; Vickovic et al, 2019) to derive data about gene expression in the arterial valves of the human embryo, during the sculpting phases of their development.  We identified a number of genes that have not been previously linked to valve development and are strongly expressed in the remodelling valve leaflets. Examination of the mouse model for one of these, RBP1, shows previously undescribed defects in the great arteries and valve anomalies in mutant animals, highlighting that these genes are good candidate genes for causing BAV. Thus, we have developed new methodologies for ST data analysis and show that they have the ability to identify previously unknown developmentally important genes. ST is thus an exciting tool for novel gene discovery in the developing human embryo.", "design": "Spatial transcriptomics of 2 embryonic human hearts. Consecutive tissue sections were taken from each sample CS19 (5 sections) and CS16 (4 sections)\nCS = Carnegie stage.", "pubmed_ids": ["38011284"]}
 {"gse": "GSE244803", "title": "Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2]", "summary": "Blood-stage malaria infection induces differentiation of several effector CD4 + T subsets including Tfh and Th1 cells. The cues and microarchitectural niches required in secondary lymphoid organs for their formation were previously uncharacterised. Here we used spatial transcriptomics to characterise the microarchitecture of mouse spleen before and during malaria infection, and mapping the spatial and molecular requirements of Tfh/Th1 differentiation.", "design": "Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasitised RBCs (pRBCs) or a saline control. At Day 7, whole spleens were recovered and fresh frozen to generate Slide-seqV2 datasets.", "pubmed_ids": ["38848213"]}
 {"gse": "GSE245097", "title": "Spatial transcriptomics of the achilles tendon harvested from the injury site with and without TrkA neuronal inhibition", "summary": "Peripheral afferent neurons terminate at the surfaces of tendons, yet their role after injury beyond nociceptive functions remain unclear.  Using transgenic animal models, sensory neurons were found to sprout after Achilles tendon injury in domains of Nerve growth factor (NGF) expression. Conditional deletion of Ngf in either myeloid or mesenchymal cell types led to tendon repair defects – findings phenocopied by inactivation of TrkA (Tropomyosin receptor kinase A) using a knockin mouse model. We sought to identify the signals modulated with neural TrkA inhibition. A combination of single cell and spatial transcriptomic analysis was performed on the Achilles injury site of TrkA^F592A animals and compared them to TrkA^WT.", "design": "The injury site was dissected from TrkAWT and TrkAF592A animals at 14 d post-operative for Spatial transcriptomics. Pooled N=4 mice per genotype", "pubmed_ids": ["38117901"]}
 {"gse": "GSE245111", "title": "Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen [Curio]", "summary": "The mechanisms that guide Th2 cell differentiation in barrier tissues are unclear but important for the development of allergic asthma. Using temporal, spatial and single cell transcriptomic tracking of house dust mite (HDM) specific T cells, we describe the molecular pathways driving allergen-specific Th2 cells. Early Blimp-1 expression occurs in a subset of CD4 T cells in the lymph node prior to lung migration driven by IL-10 from allergen-specific T cells, but was not required for GATA3 upregulation. Instead, IL-2 via STAT5 was required to directly repress Bcl6 and Bach2 to support GATA3 and Blimp-1 upregulation. Loss of Blimp-1 during priming in the lymph node ablated the formation of Th2 cells that migrate to the lung, indicating early Blimp-1 promotes the population of Th2 cells with migratory capability. Spatial microniches of IL-2 in the lymph node discriminate and support these earliest Blimp-1+ migratory Th2 cells, demonstrating that lymph node localization is a primary driver of differentiation. Our findings illuminate the molecular pathways for inhaled allergens to promote Th2 cells and identify an early requirement for IL-2 mediated spatial microniches and allergen-driven IL-10 from responding T cells that drive allergic asthma.", "design": "1DER CD45.1 Tg T cells were adoptively transferred to CD45.2 host, followed by intrasnasal immunization with 25ug of house dust mite daily for three days. Mediastinal lymph nodes (mLN) were isolated on day 4 and day 6, snap frozen and embedded in OCT for Curio Biosciences Slide Seeker Tile (3mm x 3mm).", "pubmed_ids": ["38374265"]}

catalog/feature-index-provenance.json

@@ -1,18 +1,18 @@
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   "source": "var tables (feature_name, source_feature_id, feature_type) of every released spatial.h5ad; expression matrices not read",
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+  "samples": 12157,
   "panels": 1954,
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+  "feature_rows": 35019675,
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   "checks": {
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@@ -21,5 +21,130 @@
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   "builder": "spatial-data-agent-db 0.3.0 tools/build_feature_index.py and tools/compact_feature_index.py",
-  "built": "2026-11-03"
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+}

catalog/feature-index.sqlite.gz

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catalog/samples.csv

@@ -983,7 +983,7 @@ GSM5621977,GSE185715,GSE185715,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus m
 GSM5621978,GSE185715,GSE185715,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,hippocampus,spot,3047,31053,counts,human_visual_review,2477cd6a22734c80dc929c9cabb4e90a2546049ea3d51ad1154ec663138d68ba,pixel,platform_constant,0.1721170395869191,True,True,H&E,HESRT human review,0.5000015226020829,HESRT_HUMAN_REVIEW,121a9b990c5ad40cc6beebaae5eed76aa1a24d06bd9d358ef91de17d9c66e79b,,,,,,,,,,GSM5621978,,,train,samples/GSE185715/GSM5621978
 GSM5631821,GSE186097,GSE186097,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain Olfactory bulb,cell,20234,32711,counts,VERIFIED,256829b145b26b649f997ffb766f6ee7028bedee6d543286d788f8142904bc91,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM5631821,,,train,samples/GSE186097/GSM5631821
 GSM5631822,GSE186097,GSE186097,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain PBN region,cell,29911,30883,counts,VERIFIED,a9d736e6808aac408b01d8f5150f93733fc58a6e089b5026bf1d991c9b451ec6,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM5631822,,,train,samples/GSE186097/GSM5631822
-GSM5643203,GSE186290,GSE186290,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,GAN-KP tumor,spot,2429,31054,counts,human_visual_review,bfd7d2cc8ec6f3e0a5e7c8dc661ac85b42114c0dcb1657da218ff8b8ac8ed4ce,pixel,platform_constant,4.875407793576616,True,True,H&E,HESRT human review,4.875407793576616,HESRT_HUMAN_REVIEW,b8fe6ef947647282bd180034077858ae72afc60acd25adefba71fb7b1e88e77e,,,,,,,,,,GSM5643203,,,train,samples/GSE186290/GSM5643203
+GSM5643203,GSE186290,GSE186290,sda-all,sda-all-patch-20261111,Visium,Visium,Mus musculus,GAN-KP tumor,spot,2429,31054,counts,VERIFIED,5327b2dd75989fffa577e9d18dc531651200bcaf13ae5ba190b039607aebbf02,um,verified,1.0,False,True,H&E,HESRT human review,4.875407793576616,DEPOSITED_PIXEL_FRAME,b8fe6ef947647282bd180034077858ae72afc60acd25adefba71fb7b1e88e77e,,,,,,,,,,GSM5643203,,,train,samples/GSE186290/GSM5643203
 GSM5661565,GSE186818,GSE186818,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Takifugu alboplumbeus,brain,spot,3095,26886,counts,human_visual_review,7d1e0824b4aa2a3772b8f6d7718dfb01b397926c51c22e07e0ddecfe60dfe034,pixel,platform_constant,4.283860198380393,True,True,H&E,HESRT human review,4.283860198380393,HESRT_HUMAN_REVIEW,592cf3d5b88c9f61229488a2f385b509af51f542d872255fa0f0e1fdd5ea2d81,,,,,,,,,,GSM5661565,,,train,samples/GSE186818/GSM5661565
 GSM5673398,GSE188257,GSE188257,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Ovary,spot,841,32285,counts,human_visual_review,a9aae262e5b40f457bba5e9dea34c8403815d55f37c3fbb802b3cb382abeba9c,pixel,platform_constant,13.507416082123992,True,True,H&E,HESRT human review,13.507416082123992,HESRT_HUMAN_REVIEW,d20a8f05cba32ddbf33675a469f8a8e986bce011cd083bc4529e267356614d97,,,,,,,,,,GSM5673398,,,train,samples/GSE188257/GSM5673398
 GSM5673399,GSE188257,GSE188257,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Ovary,spot,1415,32285,counts,human_visual_review,0d21a541e5b130a37e215c97c4b7e0ce917f60bb82f9dd1bf9afcb33e90133f9,pixel,platform_constant,14.029939859788387,True,True,H&E,HESRT human review,14.029939859788387,HESRT_HUMAN_REVIEW,047d169a934560c338c7e0c1c69ae0d09539320bcae914ee06915b9be38bf273,,,,,,,,,,GSM5673399,,,train,samples/GSE188257/GSM5673399
@@ -1423,12 +1423,12 @@ GSM6219591,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus mu
 GSM6219592,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Skeletal Muscle,spot,654,32285,counts,VERIFIED,800c1be63f8dbe045e3eafadb5c52b1e531ce64d1e518fb67b826d4d2e2cf0d6,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM6219592,,,val,samples/GSE205707/GSM6219592
 GSM6219593,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Skeletal Muscle,spot,633,32285,counts,VERIFIED,7b25013fedeec7780acb59c2d8f85a7ebfadd3a1618dce447fc3865a40d49aaf,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM6219593,,,val,samples/GSE205707/GSM6219593
 GSM6219594,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Skeletal Muscle,spot,895,32285,counts,VERIFIED,783466d754bfe016a0bd20ed625e0d7722c4dfc2dabbfea126c315f966c2b09f,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM6219594,,,val,samples/GSE205707/GSM6219594
-GSM6896311,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Skeletal Muscle,spot,595,1000,counts,human_visual_review,c10c8f0048fe65305885c4dc9fa116d1723e0fd8cf08d79268d749a65e9a19c2,pixel,platform_constant,0.3071343144389113,True,True,H&E,HESRT human review,0.5000062390298768,HESRT_HUMAN_REVIEW,8a70b747714da76114802d81fa14bf18862e5a378960e2759e9d2f53598556cc,,,,,,,,,,GSM6896311,,,val,samples/GSE205707/GSM6896311
-GSM6896312,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Skeletal Muscle,spot,455,1000,counts,human_visual_review,2fcb70da668e7eb974753ab6c19254db98a3c2b5778f2ae10cb970f13eb60417,pixel,platform_constant,0.30806861461831603,True,True,H&E,HESRT human review,0.5000068389065571,HESRT_HUMAN_REVIEW,5576273a37a9fe969484c2184ade8b7d4c67178775de24768b4799bbefbbc2d6,,,,,,,,,,GSM6896312,,,val,samples/GSE205707/GSM6896312
-GSM6896313,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Canis lupus familiaris,Skeletal Muscle,spot,837,1000,counts,human_visual_review,beace7463a290f2343711c3f2c00742148715a9142c00ced22f6560b882a0406,pixel,platform_constant,0.30698353829866787,True,True,H&E,HESRT human review,0.4999913105374158,HESRT_HUMAN_REVIEW,91745c0424da16afa8a60f156e0ad0aae63def1fbc85b162c92c8cfcf042f070,,,,,,,,,,GSM6896313,,,val,samples/GSE205707/GSM6896313
-GSM6896314,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Canis lupus familiaris,Skeletal Muscle,spot,718,1000,counts,human_visual_review,a8f3eb73a380ef44feda38770d2f791f2969fa24b1717e18884769683b5bb5d1,pixel,platform_constant,0.30716517053229786,True,True,H&E,HESRT human review,0.4999971118002034,HESRT_HUMAN_REVIEW,4042d3efde6fa798392d25bc3a1db4640823f68e5e3e2a5aa38dc09895853675,,,,,,,,,,GSM6896314,,,val,samples/GSE205707/GSM6896314
-GSM6896315,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Canis lupus familiaris,Skeletal Muscle,spot,2005,1000,counts,human_visual_review,183c812b76ab0a0be1774f5657a96cb784356631ae8832592c745e1862b94fd5,pixel,platform_constant,0.3077052651812414,True,True,H&E,HESRT human review,0.4999895398119399,HESRT_HUMAN_REVIEW,7779131f29ba4f43b6948a159acb8c4ae02038d1970979fd2abefb67eebacfa0,,,,,,,,,,GSM6896315,,,val,samples/GSE205707/GSM6896315
-GSM6896316,GSE205707,GSE205707,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Canis lupus familiaris,Skeletal Muscle,spot,2402,1000,counts,human_visual_review,8adc7e630d58396cdd48a6684ca1b3e9cee1b3513762ecd22353117629c23c5e,pixel,platform_constant,0.3069243482901714,True,True,H&E,HESRT human review,0.49999654606770044,HESRT_HUMAN_REVIEW,b47dad41938e1a161d14a0433fa2f96d0597c6ab897b5ebd445ff67bbef4c971,,,,,,,,,,GSM6896316,,,val,samples/GSE205707/GSM6896316
+GSM6896311,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Skeletal Muscle,spot,708,32285,counts,VERIFIED,91255ff61da0e7918caafe4744b6a1182c2db4e361c843a70af739e505cc68b1,um,verified,1.0,False,True,H&E,HESRT human review,0.5000062390298768,DEPOSITED_ALIGNMENT_FIT,8a70b747714da76114802d81fa14bf18862e5a378960e2759e9d2f53598556cc,,,,,,,,,,GSM6896311,,,val,samples/GSE205707/GSM6896311
+GSM6896312,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Skeletal Muscle,spot,569,32285,counts,VERIFIED,e15bc8212090e5aa96c6307d13c2ec12d1598a192f4d3716fdb99cc963610a0e,um,verified,1.0,False,True,H&E,HESRT human review,0.5000068389065571,DEPOSITED_ALIGNMENT_FIT,5576273a37a9fe969484c2184ade8b7d4c67178775de24768b4799bbefbbc2d6,,,,,,,,,,GSM6896312,,,val,samples/GSE205707/GSM6896312
+GSM6896313,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Canis lupus familiaris,Skeletal Muscle,spot,2432,32704,counts,VERIFIED,d5274b1284439215fb2fa6c5cd3620efa8f5e73e44c680e2a7140882cca7c31d,um,verified,1.0,False,True,H&E,HESRT human review,0.4999913105374158,DEPOSITED_ALIGNMENT_FIT,91745c0424da16afa8a60f156e0ad0aae63def1fbc85b162c92c8cfcf042f070,,,,,,,,,,GSM6896313,,,val,samples/GSE205707/GSM6896313
+GSM6896314,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Canis lupus familiaris,Skeletal Muscle,spot,2600,32704,counts,VERIFIED,561b5bee2ac13d45c3c54bc247d9161e22100615434dc71b181dbdda02add4d8,um,verified,1.0,False,True,H&E,HESRT human review,0.4999971118002034,DEPOSITED_ALIGNMENT_FIT,4042d3efde6fa798392d25bc3a1db4640823f68e5e3e2a5aa38dc09895853675,,,,,,,,,,GSM6896314,,,val,samples/GSE205707/GSM6896314
+GSM6896315,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Canis lupus familiaris,Skeletal Muscle,spot,3122,32704,counts,VERIFIED,908369e3b848378823915f53db1f9eb6d9f1c0a90d5ec496c725f8f3ea9420e2,um,verified,1.0,False,True,H&E,HESRT human review,0.4999895398119399,DEPOSITED_ALIGNMENT_FIT,7779131f29ba4f43b6948a159acb8c4ae02038d1970979fd2abefb67eebacfa0,,,,,,,,,,GSM6896315,,,val,samples/GSE205707/GSM6896315
+GSM6896316,GSE205707,GSE205707,sda-all,sda-all-gap-20261009,Visium,Visium,Canis lupus familiaris,Skeletal Muscle,spot,3393,32704,counts,VERIFIED,7a29e3fcc4b45d24366b548cf2743d42dec352bbbcef15a829869fde541561e8,um,verified,1.0,False,True,H&E,HESRT human review,0.4999965460677004,DEPOSITED_ALIGNMENT_FIT,b47dad41938e1a161d14a0433fa2f96d0597c6ab897b5ebd445ff67bbef4c971,,,,,,,,,,GSM6896316,,,val,samples/GSE205707/GSM6896316
 GSM6248646,GSE206245,GSE206245,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,Nasopharynx,spot,2021,17943,counts,human_visual_review,d4b660c5f334cb38a6952e09968487b0211b2c581960434264c56bf47fc6965d,pixel,platform_constant,4.252777902405432,True,True,H&E,HESRT human review,4.252777902405432,HESRT_HUMAN_REVIEW,7aac4aab2df82287dc3025af9714e952924645c37bc63ec525b2b24404a7d855,,,,,,,,,,GSM6248646,,,train,samples/GSE206245/GSM6248646
 GSM6248647,GSE206245,GSE206245,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,Nasopharynx,spot,2614,17943,counts,human_visual_review,9c43918ede9cb37ae5fc71da74fdcba18016edccb38d7b8ebc7c487aff0edfe5,pixel,platform_constant,4.053282778974647,True,True,H&E,HESRT human review,4.053282778974647,HESRT_HUMAN_REVIEW,1728840c293f731aa736511cc6d680e50764e7008ea506e4f79358c9fae388ff,,,,,,,,,,GSM6248647,,,train,samples/GSE206245/GSM6248647
 GSM6248648,GSE206245,GSE206245,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,Nasopharynx,spot,1939,17943,counts,human_visual_review,619e7cd07f2a8bf105f4d1af45c30937cb1ddc86abc1900e26a50f4fd016edf5,pixel,platform_constant,4.103030398712962,True,True,H&E,HESRT human review,4.103030398712962,HESRT_HUMAN_REVIEW,16a8013de3b9b33745fc2145524e33df1e1fa3f5e78e12c83412d77de4218ae0,,,,,,,,,,GSM6248648,,,train,samples/GSE206245/GSM6248648
@@ -2936,10 +2936,6 @@ GSM7823259,GSE244650,GSE244650,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus m
 GSM7823260,GSE244650,GSE244650,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,heart,spot,1626,31053,counts,human_visual_review,ae86a0ea423439ccccc05924adffc1d20df98dc8f599517f6fe054d5e515f159,pixel,platform_constant,0.46794545208201044,True,True,H&E,HESRT human review,0.5000099095406314,HESRT_HUMAN_REVIEW,6bd21de793659fe47424a2bbd4d0c86aae974356c0b4f9d6b960f5bea39c2cd6,,,,,,,,,,GSM7823260,,,train,samples/GSE244650/GSM7823260
 GSM7823491,GSE244659,GSE244659,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain LC region,cell,59200,27561,counts,VERIFIED,fba2e14f619a5fc21177224c863adc09a0a189365519826b55846cce764194e7,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM7823491,,,train,samples/GSE244659/GSM7823491
 GSM7823492,GSE244659,GSE244659,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain LC region,cell,17963,27561,counts,VERIFIED,042a570b4cc10820595d84723f944777dc7d6dad02bfb59d1f44ea0d7b416da9,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM7823492,,,train,samples/GSE244659/GSM7823492
-GSM7825036,GSE244723,GSE244723,hesrt,hesrt-v1.3,ST (legacy),Spatial Transcriptomics,Homo sapiens,embryonic heart,spot,37,57486,counts,human_visual_review,6696e53908e1b77097bb6886753f1f8d8a1ebb3c182af90ba457c68407814d66,pixel,platform_constant,3.637241489832318,True,True,H&E,HESRT human review,3.637241489832318,HESRT_HUMAN_REVIEW,bc868dd62027415de8b77fe9ac9f9d4bc6974ea38c149d7ba2a04984908d7712,,,,,,,,,,GSM7825036,,,train,samples/GSE244723/GSM7825036
-GSM7825037,GSE244723,GSE244723,hesrt,hesrt-v1.3,ST (legacy),Spatial Transcriptomics,Homo sapiens,embryonic heart,spot,61,57486,counts,human_visual_review,f4ecdd3862087c30e2b3f7d12a51c1881feccfb11877c56e5e38fdcfce29833a,pixel,platform_constant,3.5858299684584076,True,True,H&E,HESRT human review,3.5858299684584076,HESRT_HUMAN_REVIEW,fccb624e617ce44ee73d7ce7a15682b3d7bbfd68c11e5357fa344e61e2545a2c,,,,,,,,,,GSM7825037,,,train,samples/GSE244723/GSM7825037
-GSM7825038,GSE244723,GSE244723,hesrt,hesrt-v1.3,ST (legacy),Spatial Transcriptomics,Homo sapiens,embryonic heart,spot,59,57486,counts,human_visual_review,fbfe455942040c0a92c6755e4933ece9a23458fde97832752b3a97a43d806c43,pixel,platform_constant,3.534890945650585,True,True,H&E,HESRT human review,3.534890945650585,HESRT_HUMAN_REVIEW,f2ee828b9ecd9bfd3a40b7b1a44d828198b25526bc8c45cc06766e4573ad376c,,,,,,,,,,GSM7825038,,,train,samples/GSE244723/GSM7825038
-GSM7825039,GSE244723,GSE244723,hesrt,hesrt-v1.3,ST (legacy),Spatial Transcriptomics,Homo sapiens,embryonic heart,spot,60,57486,counts,human_visual_review,edbde19a0a12fb8e9f617ca108d0dd2b8ffb73be35c7886424cb76f516b46e3d,pixel,platform_constant,3.649330911960079,True,True,H&E,HESRT human review,3.649330911960079,HESRT_HUMAN_REVIEW,aec5a51e3ef1fa8c5df2b0ab65ab2217ed372eca0598d64636fe69d8bd28cc71,,,,,,,,,,GSM7825039,,,train,samples/GSE244723/GSM7825039
 GSM7829909,GSE244803,GSE244803,sda-all,sda-all-v1.3.0,Slide-seq,Slide-seqV2,Mus musculus,Spleen,bead,42666,22019,unknown,VERIFIED,a87f200cd88e92cdb243f4819ac1c9472fe1c8ac3262af06cbc7d1964e4eb7a6,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM7829909,,,train,samples/GSE244803/GSM7829909
 GSM7829910,GSE244803,GSE244803,sda-all,sda-all-v1.3.0,Slide-seq,Slide-seqV2,Mus musculus,Spleen,bead,45840,22555,unknown,VERIFIED,986bb7afb236aa5249c29a08a25c986f348dd555d3d93acb3697261f97ea1886,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM7829910,,,train,samples/GSE244803/GSM7829910
 GSM7829911,GSE244803,GSE244803,sda-all,sda-all-v1.3.0,Slide-seq,Slide-seqV2,Mus musculus,Spleen,bead,50181,22455,unknown,VERIFIED,4d5518aa80c1add071150759c6e3273c221650c2cdc235be686113a103c53c22,pixel,unresolved,,False,False,,,,,,,,,,,,,,,GSM7829911,,,train,samples/GSE244803/GSM7829911
@@ -4916,10 +4912,10 @@ GSM8464548,GSE275026,GSE275026,sda-all,sda-all-v1.4.0,MERFISH/MERSCOPE,MERSCOPE,
 GSM8970742,GSE275026,GSE275026,sda-all,sda-all-v1.4.0,MERFISH/MERSCOPE,MERSCOPE,Mus musculus,brain,cell,126024,462,counts,VERIFIED,4ff2db5168026207ca1b6dc6411cd3353f4c4d484f1a457f3d3ac3c2d73f9729,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM8970742,,,val,samples/GSE275026/GSM8970742
 GSM8970743,GSE275026,GSE275026,sda-all,sda-all-v1.4.0,MERFISH/MERSCOPE,MERSCOPE,Mus musculus,brain,cell,131251,462,counts,VERIFIED,3cb39a86028e8e617506dd409ad447f07977c28c78bf19cf65decc818c3463dd,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM8970743,,,val,samples/GSE275026/GSM8970743
 GSM8970744,GSE275026,GSE275026,sda-all,sda-all-v1.4.0,MERFISH/MERSCOPE,MERSCOPE,Mus musculus,brain,cell,120318,462,counts,VERIFIED,dd0b69008e17de1e900704b09f4d92027397d2074c132aecafea58d52ee87149,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM8970744,,,val,samples/GSE275026/GSM8970744
-GSM8465980,GSE275125,GSE275125,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Lymph node,spot,1650,32378,counts,human_visual_review,c0deb74236d9d029b9bc6561167214a0e07e48890f620f6ba528929d16867826,pixel,platform_constant,0.6578947368421053,True,True,H&E,HESRT human review,0.6578947368421053,HESRT_HUMAN_REVIEW,364d7eea0642b5752a455142bda7074ad7b38b90dbbd5d927a625ea97b54c222,,,,,,,,,,GSM8465980,,,train,samples/GSE275125/GSM8465980
-GSM8465981,GSE275125,GSE275125,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Lymph node,spot,1876,32378,counts,human_visual_review,654121e33ec7fa9673d4fdd70dfa5110c5e2521f34450fc6a39047f15d925390,pixel,platform_constant,0.6578947368421053,True,True,H&E,HESRT human review,0.6578947368421053,HESRT_HUMAN_REVIEW,28bcfb143f512e2f14af53d27f19a72870f8d85ce51240be37e34814544a0a72,,,,,,,,,,GSM8465981,,,train,samples/GSE275125/GSM8465981
-GSM8465982,GSE275125,GSE275125,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Lymph node,spot,1858,32378,counts,human_visual_review,d8c380625e8230599fa18a2d5e14bc1abdcd7dbef420d9f90da7cd848c4f6da4,pixel,platform_constant,0.7352941176470589,True,True,H&E,HESRT human review,0.7352941176470589,HESRT_HUMAN_REVIEW,3645bce316439716b211c9df58dcfa9615a9dc97c87786fd9b879591cb7eba03,,,,,,,,,,GSM8465982,,,train,samples/GSE275125/GSM8465982
-GSM8465983,GSE275125,GSE275125,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,Lymph node,spot,1887,32378,counts,human_visual_review,2d7efef4f5112847acb1754fb7e3163d69ff3248c47edbe2115477a5d562ca47,pixel,platform_constant,0.6711409395973155,True,True,H&E,HESRT human review,0.6711409395973155,HESRT_HUMAN_REVIEW,6d700f11df6d8dc0565fd11bca4e6d0a7f853e22eeedb9da86c310764cf7de4a,,,,,,,,,,GSM8465983,,,train,samples/GSE275125/GSM8465983
+GSM8465980,GSE275125,GSE275125,sda-all,sda-all-patch-20261111,Visium,Visium,Mus musculus,Lymph node,spot,1650,32378,counts,VERIFIED,7326eb0faf6cc6dd601f2802ae48f1eaa74b80a3ef32c47a8e18d68ecfb5ab0a,um,verified,1.0,False,True,H&E,HESRT human review,0.6578947368421053,DEPOSITED_ALIGNMENT_FIT,364d7eea0642b5752a455142bda7074ad7b38b90dbbd5d927a625ea97b54c222,,,,,,,,,,GSM8465980,,,train,samples/GSE275125/GSM8465980
+GSM8465981,GSE275125,GSE275125,sda-all,sda-all-patch-20261111,Visium,Visium,Mus musculus,Lymph node,spot,1876,32378,counts,VERIFIED,b6b24f72884fd0452dcc37148093fa34c9f1f851e003a364c7b62034a58e0b6d,um,verified,1.0,False,True,H&E,HESRT human review,0.6578947368421053,DEPOSITED_ALIGNMENT_FIT,28bcfb143f512e2f14af53d27f19a72870f8d85ce51240be37e34814544a0a72,,,,,,,,,,GSM8465981,,,train,samples/GSE275125/GSM8465981
+GSM8465982,GSE275125,GSE275125,sda-all,sda-all-patch-20261111,Visium,Visium,Mus musculus,Lymph node,spot,1858,32378,counts,VERIFIED,a0f3f3c0fc711f83ae94d82c58af1d48f44b9cbe34e28e934cc6da6c806e061b,um,verified,1.0,False,True,H&E,HESRT human review,0.7352941176470589,DEPOSITED_ALIGNMENT_FIT,3645bce316439716b211c9df58dcfa9615a9dc97c87786fd9b879591cb7eba03,,,,,,,,,,GSM8465982,,,train,samples/GSE275125/GSM8465982
+GSM8465983,GSE275125,GSE275125,sda-all,sda-all-patch-20261111,Visium,Visium,Mus musculus,Lymph node,spot,1887,32378,counts,VERIFIED,fbe5ed7ee46f1ba79c619f36bc0902434f39380656777cc085f76e8ae70eacff,um,verified,1.0,False,True,H&E,HESRT human review,0.6711409395973155,DEPOSITED_ALIGNMENT_FIT,6d700f11df6d8dc0565fd11bca4e6d0a7f853e22eeedb9da86c310764cf7de4a,,,,,,,,,,GSM8465983,,,train,samples/GSE275125/GSM8465983
 GSM8471249,GSE275131,GSE275131,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,brain,spot,2934,32285,counts,human_visual_review,b72d51c7b601353d3ea66147e4daf8818a937c8376d52ec8506c9c0a192785fa,pixel,platform_constant,4.355401436942718,True,True,H&E,HESRT human review,4.355401436942718,HESRT_HUMAN_REVIEW,817afa05e088baac1b708f543716b4ac3498002963a3d005b63c22486cb6f53e,,,,,,,,,,GSM8471249,,,test,samples/GSE275131/GSM8471249
 GSM8471250,GSE275131,GSE275131,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,brain,spot,3080,32285,counts,human_visual_review,97f014b6918a7c3e8cb3e8c8d80bce0e127bc0b41d784d260cf0877a1f25cb98,pixel,platform_constant,4.761410998503646,True,True,H&E,HESRT human review,4.761410998503646,HESRT_HUMAN_REVIEW,20159ad686897533f68584ae71adfd86cb60c9cb6f7fc9dfec230701a39bb7b2,,,,,,,,,,GSM8471250,,,test,samples/GSE275131/GSM8471250
 GSM8471251,GSE275131,GSE275131,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,brain,spot,2789,32285,counts,human_visual_review,85cb748005d62d080fabfec4622a180dc503cd35940ccb3c1b09f4d73db2dacd,pixel,platform_constant,4.53387806511062,True,True,H&E,HESRT human review,4.53387806511062,HESRT_HUMAN_REVIEW,de74fed894b84b2a68eb2a3952949598fc47c76c2ff1ccf6e9313248217fb93b,,,,,,,,,,GSM8471251,,,test,samples/GSE275131/GSM8471251
@@ -7231,7 +7227,7 @@ GSM8933089,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo s
 GSM8933090,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,441503,541,counts,VERIFIED,911ad7bcb2cba055a1d390e44569d365b1d7f8d5ec7612b34f5a9a2976c48039,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.49999106062273085,VERIFIED,dceccb885fac981f338ba28c55970bb541971f08bbb8c9e4916c4ab132feb9ee,VERIFIED,VERIFIED,,,,,PASS,,,GSM8933090,,,train,samples/GSE294965/GSM8933090
 GSM8933091,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,339498,541,counts,VERIFIED,c3086ee4f8e80b99ebc40963256ef40bb866626fbe6fc29267afe52a89337580,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.5000012167226359,VERIFIED,db430140677a1f109a54e3a651e5edffdcb6b326596a04eaacc8401a14335d34,VERIFIED,VERIFIED,,,,,PASS,,,GSM8933091,,,train,samples/GSE294965/GSM8933091
 GSM8933092,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,334451,541,counts,VERIFIED,709d106444f7498b02d3ee0e436007aa96ac2e661956bd9f9e863f3b43da800f,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.49999032208113964,VERIFIED,f99a07192955ebd9db19c92f76d41486aea65cb3f8f7592798f1a670feaed215,VERIFIED,VERIFIED,,,,,PASS,,,GSM8933092,,,train,samples/GSE294965/GSM8933092
-GSM8933093,GSE294965,GSE294965,hesrt,hesrt-v1.3,Xenium,10x Genomics Xenium In Situ,Homo sapiens,kidney,cell,317414,541,counts,human_visual_review,49731c5977d2c6fe5fffea88906cb9db24c1c0b47405d9d15871c7ae58130c90,pixel,unresolved,,False,True,H&E,HESRT human review,,HESRT_HUMAN_REVIEW,01ef1cd43a0695094645e4d298f18bc26bef173f2a5192809450ad32cc156c26,,,,,,,,,,GSM8933093,,,train,samples/GSE294965/GSM8933093
+GSM8933093,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,317414,541,counts,VERIFIED,2ed265ff4ca61397f5967c5a67ec598ad67cf4952c5f28593d9d961534d42f01,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.5000097690170198,VERIFIED,93f170f7d2fb6d2e66e30487acea741b1810b00934c98f800a88aac7fb3c1326,VERIFIED,VERIFIED,,,,,,,,GSM8933093,,,train,samples/GSE294965/GSM8933093
 GSM8933094,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,481717,541,counts,VERIFIED,a7a64d015a5e6e52a04b72884ce03fd285efd787396bc06a72b7730d3a3a88fa,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.5000032303080423,VERIFIED,edbb9f3c6277d56acfb42c87d1f1cb7867ce2eff1d6bccf0d412dbd66fe382e4,VERIFIED,VERIFIED,,,,,PASS,,,GSM8933094,,,train,samples/GSE294965/GSM8933094
 GSM8933095,GSE294965,GSE294965,sda-all,sda-all-gap-20261009,Xenium,Xenium,Homo sapiens,kidney,cell,307653,541,counts,VERIFIED,4f533f3750a5ec7abc9baa3351c999eb0e184ed61fe1bfb49892bd9d2815dde0,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.5000115027146407,VERIFIED,3953f934f5746313bc748cd739302f85df779a04c95f3f7bb72ae0f3ec45fd27,VERIFIED,VERIFIED,,,,,PASS,,,GSM8933095,,,train,samples/GSE294965/GSM8933095
 GSM8941069,GSE295043,GSE295043,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,prostate,spot,1980,19465,counts,human_visual_review,156c23e2739f2dd9283610b4967deac5f5957f8607ef6b01ec319658072ca747,pixel,platform_constant,4.847669641121826,True,True,H&E,HESRT human review,4.847669641121826,HESRT_HUMAN_REVIEW,ddf1322f63bada07137159f1a8186964e9325c5c17fbaf5089c1c3cabfe6f441,,,,,,,,,,GSM8941069,,,train,samples/GSE295043/GSM8941069
@@ -7597,8 +7593,6 @@ GSM9002336,GSE297947,GSE297947,sda-all,sda-all-v1.3.0,Visium,Visium,Mus musculus
 GSM9004713,GSE298021,GSE298021,sda-all,sda-all-v1.3.0,Stereo-seq,STOmics,Triticum aestivum,seed,bin,151711,70766,counts,VERIFIED,ae692014006cc5242b7cc2fb5eda0bf306fd8e42bd7c155f0b14a902cb25bc85,um,verified,1.0,False,False,,,,,,,,,,,,PASS,,,GSM9004713,,,train,samples/GSE298021/GSM9004713
 GSM9004714,GSE298021,GSE298021,sda-all,sda-all-v1.3.0,Stereo-seq,STOmics,Triticum aestivum,seed,bin,156493,63481,counts,VERIFIED,739a9c8a8878576839db55daf75271b5a9685fcbdb8ae83af4acc87d0dccb382,um,verified,1.0,False,False,,,,,,,,,,,,PASS,,,GSM9004714,,,train,samples/GSE298021/GSM9004714
 GSM9004715,GSE298021,GSE298021,sda-all,sda-all-v1.3.0,Stereo-seq,STOmics,Triticum aestivum,seed,bin,136491,62432,counts,VERIFIED,76e41ae2377611b9881a5159101762b188200c66fabddf9b059068989c67bfba,um,verified,1.0,False,False,,,,,,,,,,,,PASS,,,GSM9004715,,,train,samples/GSE298021/GSM9004715
-GSM9008651,GSE298115,GSE298115,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,parathyroid,spot,230,19465,counts,human_visual_review,7ff58bf904fefa1da7a4d4b5af35f8c5c2b15fbecc44ce87fadf280327ad0b6b,pixel,platform_constant,4.761904761904762,True,True,H&E,HESRT human review,4.761904761904762,HESRT_HUMAN_REVIEW,fbc215721904d4f470c88a13e636a492e6721422e148c094006e0142994f7a2c,,,,,,,,,,GSM9008651,,,test,samples/GSE298115/GSM9008651
-GSM9008653,GSE298115,GSE298115,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,parathyroid,spot,971,19465,counts,human_visual_review,58ed0b5a50b689ee1279b5b3533c0475997265f7224fb5893af6e65f401ffbf7,pixel,platform_constant,4.761904761904762,True,True,H&E,HESRT human review,4.761904761904762,HESRT_HUMAN_REVIEW,bd63ad31695cb45aab40fb57a139f288ee4b978c6937125797544dff60a88903,,,,,,,,,,GSM9008653,,,test,samples/GSE298115/GSM9008653
 GSM9008654,GSE298115,GSE298115,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Parathyroid,spot,1544,19465,counts,VERIFIED,496a01f638a9c3f2948728e88b592c140ab502796c281ee3e00d44ec311bec46,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM9008654,,,test,samples/GSE298115/GSM9008654
 GSM9008655,GSE298115,GSE298115,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Parathyroid,spot,737,19465,counts,VERIFIED,1676f1e9c7c81a7a70c49cae7ad3d691b308162220532b14f588f0e9d16c426c,um,verified,1.0,False,False,,,,WITHHELD,,,,,hesrt_review_fail,,,,,,GSM9008655,,,test,samples/GSE298115/GSM9008655
 GSM9008656,GSE298115,GSE298115,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Parathyroid,spot,1531,19465,counts,VERIFIED,5d3de2061a3ee88cd6b67e1d9c73cc518fbf48e3492ea99137e971304f04b869,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM9008656,,,test,samples/GSE298115/GSM9008656

catalog/samples.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a5deedecd5e0fbe0d2598947e4bead93e7f5c757037bf3cb25fc71b4fdf02cf7
-size 1900742
+oid sha256:91f6f2c965c977332ec38f1dd37f16780507021319525fd5d852739e9831b470
+size 1882036

catalog/schema.json

@@ -4,7 +4,7 @@
   "gse": "all GEO series listing the GSM, joined with '+'; the split is computed on this string",
   "published_gse": "series folder of the sample: samples/<published_gse>/<gsm>",
   "source_pipeline": "sda-all (agent standardization, independent scorer) or hesrt (H&E Visium/ST, human review)",
-  "source_release": "SDA-All scorer version of the batch, sda-all-gap-20261009, or hesrt-v1.3",
+  "source_release": "SDA-All scorer version of the batch, sda-all-gap-20261009, or hesrt-v1.3; sda-all-patch-20261111 (samples re-converted for the 2026-11-11 correction)",
   "platform": "harmonized platform",
   "technology": "technology as written by the authors",
   "organism": "as written in GEO",
@@ -23,7 +23,7 @@
   "image_stain": "stain of image.tif ('(heuristic)' = pixel-only call)",
   "image_stain_basis": "basis of the stain label",
   "image_um_per_px": "micrometres per image.tif pixel when known",
-  "image_registration": "VERIFIED / PARTIAL / UNRESOLVED / FAILED / ABSENT (modality acceptance), WITHHELD (HESRT review FAIL: no image delivered), HESRT_HUMAN_REVIEW, empty = no registrable image",
+  "image_registration": "VERIFIED / PARTIAL / UNRESOLVED / FAILED / ABSENT (modality acceptance), WITHHELD (HESRT review FAIL: no image delivered), HESRT_HUMAN_REVIEW, empty = no registrable image; DEPOSITED_ALIGNMENT_FIT / DEPOSITED_PIXEL_FRAME (samples corrected on 2026-11-11: spot-to-image transform fitted from the deposited Loupe alignment / taken from the deposited pixel frame, checked by the author)",
   "image_sha256": "SHA256 of image.tif",
   "segmentation": "cell / nucleus boundary acceptance (sources in sample.json)",
   "molecules": "molecule table acceptance (sources in sample.json)",

catalog/studies.csv

@@ -55,7 +55,7 @@ GSE185386,15,430191,0,Slide-seq,Homo sapiens,sda-all,train
 GSE185477,1,2265,1,Visium,Homo sapiens,sda-all,train
 GSE185715,14,21548,14,Visium,Homo sapiens;Mus musculus,hesrt,train
 GSE186097,2,50145,0,Other,Mus musculus,sda-all,train
-GSE186290,1,2429,1,Visium,Mus musculus,hesrt,train
+GSE186290,1,2429,1,Visium,Mus musculus,sda-all,train
 GSE186818,1,3095,1,Visium,Takifugu alboplumbeus,hesrt,train
 GSE188257,4,4263,4,Visium,Mus musculus,hesrt,train
 GSE188888,4,6150,4,Visium,Mus musculus,hesrt,val
@@ -100,7 +100,7 @@ GSE203612,12,25529,12,Visium,Homo sapiens,hesrt,train
 GSE205054,4,15833,0,Other,Mus musculus,sda-all,train
 GSE205055,7,45382,0,Other,Homo sapiens;Mus musculus,sda-all,train
 GSE205307,2,4172,2,Visium,Mus musculus,hesrt,test
-GSE205707,14,12999,6,Visium,Canis lupus familiaris;Mus musculus,hesrt;sda-all,val
+GSE205707,14,18811,6,Visium,Canis lupus familiaris;Mus musculus,sda-all,val
 GSE206245,17,40768,14,ST (legacy);Visium,Homo sapiens,hesrt;sda-all,train
 GSE206306,7,9789,7,Visium,Homo sapiens,hesrt,train
 GSE206552,4,10059,4,Visium,Homo sapiens,hesrt,train
@@ -298,7 +298,6 @@ GSE244536,4,16690,3,Visium,Mus musculus,sda-all,test
 GSE244641,6,8949,6,Visium,Mus musculus,hesrt;sda-all,train
 GSE244650,13,17541,13,Visium,Mus musculus,hesrt,train
 GSE244659,2,77163,0,Other,Mus musculus,sda-all,train
-GSE244723,4,217,4,ST (legacy),Homo sapiens,hesrt,train
 GSE244803,8,366345,0,Slide-seq,Mus musculus,sda-all,train
 GSE245097,4,10662,4,Visium,Mus musculus,hesrt,train
 GSE245111,4,176854,0,Slide-seq,Mus musculus,sda-all,train
@@ -530,7 +529,7 @@ GSE274767,2,6200,2,Visium,Mus musculus,hesrt,val
 GSE274782,12,24438,12,Visium,Mus musculus,hesrt,train
 GSE274970,1,315012,0,Stereo-seq,Gallus gallus,sda-all,train
 GSE275026,8,952393,0,MERFISH/MERSCOPE,Mus musculus,sda-all,val
-GSE275125,4,7271,4,Visium,Mus musculus,hesrt,train
+GSE275125,4,7271,4,Visium,Mus musculus,sda-all,train
 GSE275131,4,11929,4,Visium,Mus musculus,hesrt,test
 GSE275144,2,4052,2,Visium,Homo sapiens,hesrt,train
 GSE275201,2,5555,2,Visium,Mus musculus,hesrt,val
@@ -762,7 +761,7 @@ GSE294759,9,562096,0,Stereo-seq,Homo sapiens;Mus musculus,sda-all,train
 GSE294765,6,6926,6,Visium,Mus musculus,sda-all,train
 GSE294814,7,17460,0,DBiT-seq,Mus musculus,sda-all,val
 GSE294844,5,7856,4,Visium,human skin metagenome,hesrt;sda-all,test
-GSE294965,9,3421800,9,Xenium,Homo sapiens,hesrt;sda-all,train
+GSE294965,9,3421800,9,Xenium,Homo sapiens,sda-all,train
 GSE295043,8,15439,8,Visium,Mus musculus,hesrt,train
 GSE295060,2,5688,2,Visium,Mus musculus,hesrt,train
 GSE295061,2,92679,2,Xenium,Mus musculus,sda-all,train
@@ -814,7 +813,7 @@ GSE297745,4,10744,4,Visium,Mus musculus,sda-all,train
 GSE297945,34,1170328,8,Xenium,Homo sapiens,sda-all,train
 GSE297947,1,2444,1,Visium,Mus musculus,sda-all,train
 GSE298021,3,444695,0,Stereo-seq,Triticum aestivum,sda-all,train
-GSE298115,6,6479,2,Visium,Mus musculus,hesrt;sda-all,test
+GSE298115,4,5278,0,Visium,Mus musculus,sda-all,test
 GSE298286,14,39545,14,Visium,Homo sapiens,hesrt,train
 GSE298314,4,863580,0,MERFISH/MERSCOPE,Mus musculus,sda-all,val
 GSE298545,4,3282,4,Visium,Mus musculus,sda-all,test

catalog/summary.json

@@ -1,18 +1,18 @@
 {
  "release_id": "sda-unified-20261010-v3",
  "contract": "sda-release-sample-1",
- "samples": 12163,
- "series_published": 1265,
- "series_all": 1333,
- "observations": 635240170,
+ "samples": 12157,
+ "series_published": 1264,
+ "series_all": 1332,
+ "observations": 635244564,
  "by_pipeline": {
-  "sda-all": 7777,
-  "hesrt": 4386
+  "sda-all": 7789,
+  "hesrt": 4368
  },
  "by_platform": {
-  "Visium": 6512,
+  "Visium": 6510,
   "Xenium": 1785,
-  "ST (legacy)": 1098,
+  "ST (legacy)": 1094,
   "CosMx": 1092,
   "MERFISH/MERSCOPE": 463,
   "Slide-seq": 380,
@@ -24,14 +24,14 @@
   "BMK S1000": 24
  },
  "by_split": {
-  "train": 9249,
-  "test": 1598,
+  "train": 9245,
+  "test": 1596,
   "val": 1316
  },
- "with_image": 8211,
+ "with_image": 8205,
  "image_stain": {
-  "H&E": 5263,
-  "fluorescence: DAPI": 1423,
+  "H&E": 5256,
+  "fluorescence: DAPI": 1424,
   "H&E-like (heuristic)": 871,
   "fluorescence: CosMx multichannel composite": 256,
   "blue bright-field stain (heuristic)": 125,
@@ -50,30 +50,32 @@
   "fluorescence: yellow (heuristic)": 1
  },
  "image_registration": {
-  "HESRT_HUMAN_REVIEW": 4386,
-  "VERIFIED": 3472,
+  "HESRT_HUMAN_REVIEW": 4368,
+  "VERIFIED": 3473,
   "(none)": 3237,
   "ABSENT": 570,
   "UNRESOLVED": 190,
   "FAILED": 135,
   "WITHHELD": 98,
-  "PARTIAL": 75
+  "PARTIAL": 75,
+  "DEPOSITED_ALIGNMENT_FIT": 10,
+  "DEPOSITED_PIXEL_FRAME": 1
  },
  "coordinate_units": {
-  "pixel": 5795,
-  "um": 5175,
+  "pixel": 5777,
+  "um": 5187,
   "native_grid": 830,
   "unstated": 363
  },
  "um_basis": {
-  "verified": 5151,
-  "platform_constant": 4236,
-  "unresolved": 2752,
+  "verified": 5163,
+  "platform_constant": 4219,
+  "unresolved": 2751,
   "declared_unverified": 24
  },
- "with_spatial_um": 4236,
+ "with_spatial_um": 4219,
  "expression_state": {
-  "counts": 11738,
+  "counts": 11732,
   "unknown": 417,
   "non-integer": 8
  },

metadata/v2/provenance.json

@@ -56,13 +56,13 @@
   "README.md": "633883366b4f0829b07579ca8cbdadb8f776a8efe04a32f0ef14e6096971e62e",
   "changes_v2.csv": "9f096e905effabc808c1b5ac142ff8cab3d9a367774ae82757b7406d23e631dc",
   "dropped_disease_terms.csv": "28412ef3f7f7660ea7a85ed46ebcfecec08728dadc549e03510d31a2cce11b80",
-  "qa_v2.json": "43002bf2ee515e39c60b81bbd51fc5f313f2ec84a99d1a69a7a1061cf02c8466",
-  "samples_metadata_v2.csv": "9352ad65c498c862b596c2197ac8ac184df760d9fbcfad7283206c7af2fc8549",
-  "samples_metadata_v2.parquet": "c69c25eed912f837122fec75c123ee6f93948f2ce06408d26431ea84b3fb7191",
+  "qa_v2.json": "a8120c035389e56aeb8667358d8df555501e864acb2656d9d9cdba6c63f14775",
+  "samples_metadata_v2.csv": "33ddaf57ea789c7ad9d5d49415978832331d2d7cfd0d80ead747713ed66e596b",
+  "samples_metadata_v2.parquet": "60156a0eede0114ca5160140eb99d02265ea53bc74de2f9a9a3b54b4639761ac",
   "schema_v2.json": "1c1569b29f9563b84c4c7a22d7acbcc1304476b0d71466e4450a41c212e084cf",
-  "studies_v2.csv": "47ae0513a19ebaea9282d8362164b5b898cd143ad7132310cba4d78ee5bb8150"
+  "studies_v2.csv": "a333386cf38b83dc974324ca5737de6dc8563d6deffd61e8ad341152f283169d"
  },
- "version": "2.2.2",
+ "version": "2.2.3",
  "changes_from_2.0": "one name per assay (ASSAY_CANON, 261 rows); assay_type of 6 ISS (Cartana) samples (GSE227046) now imaging-based; um_per_unit and image_um_per_px copied exactly from the release parquet; organ, tissue, disease, life stage and other annotations unchanged",
  "sensitivity_balanced_r2_series_units": {
   "human": {
@@ -84,5 +84,6 @@
  },
  "changes_from_2.1": "rules: non-human-animal MONDO terms removed from human samples (16); culture/organoid/engineered life stage = not stated; sex from male/female words in sample text (77); rodent day ages in age series; manual corrections in 10 samples (overrides_v2.csv); new column sex_source",
  "changes_from_2.2": "manually corrected fields: model confidence set to null and removed from annotation_low_confidence; schema text for life_stage_source; no label changed",
- "version_note": "2.2.2 (2026-11-08): column order only, no value changed (values = 2.2.1, built 2026-11-06)"
+ "version_note": "2.2.3 (2026-11-11): 12 samples re-converted, 6 withdrawn; no annotation changed (other values = 2.2.2)",
+ "changes_from_2.2.2": "12 samples re-converted (catalog-derived columns updated; curated annotations unchanged) and 6 samples withdrawn (rows removed): 12,163 -> 12,157 samples, 1,265 -> 1,264 studies. No other row changed."
 }

metadata/v2/qa_v2.json

@@ -1,6 +1,6 @@
 {
- "samples": 12163,
- "annotated": 12163,
+ "samples": 12157,
+ "annotated": 12157,
  "flags": {
   "low_confidence_annotation": 3113,
   "feature_species_differs": 47,
@@ -9,7 +9,7 @@
  "changes_vs_v3": 236,
  "dropped_short_synonym_disease_terms": 347,
  "life_stage_source": {
-  "luna": 8172,
+  "luna": 8170,
   "age rule: age with unit": 1630,
   "age rule: bare number read as years": 1351,
   "age rule: postnatal day": 404,
@@ -18,7 +18,6 @@
   "age rule: age in years": 113,
   "age rule: post-conception / gestational weeks": 64,
   "age rule: days in an age series": 28,
-  "age rule: Carnegie stage": 4,
   "age rule: age range midpoint": 4
  },
  "life_stage_rule_vs_luna_disagree": 624,
@@ -31,8 +30,8 @@
   "kidney": 590,
   "skin": 489,
   "pancreas": 488,
-  "other": 400,
-  "heart": 292,
+  "other": 398,
+  "heart": 288,
   "breast": 267,
   "small intestine": 251,
   "unknown": 185,
@@ -68,7 +67,7 @@
   "cartilage": 1
  },
  "sample_kind": {
-  "primary tissue": 8574,
+  "primary tissue": 8568,
   "tumour tissue": 2754,
   "metastasis": 352,
   "organoid": 212,
@@ -80,33 +79,33 @@
  },
  "disease_status": {
   "disease": 7023,
-  "normal": 3948,
-  "perturbation": 1125,
+  "normal": 3943,
+  "perturbation": 1124,
   "not stated": 67
  },
  "life_stage": {
-  "not stated": 7060,
+  "not stated": 7058,
   "adult": 2838,
   "aged": 1182,
   "juvenile": 330,
   "neonatal or infant": 324,
-  "embryonic": 282,
+  "embryonic": 278,
   "fetal": 147
  },
  "sex": {
-  "unknown": 7441,
-  "male": 2689,
+  "unknown": 7437,
+  "male": 2687,
   "female": 2012,
   "mixed": 21
  },
  "preservation": {
-  "null": 6957,
+  "null": 6951,
   "FFPE": 2839,
   "fresh frozen": 2327,
   "fixed frozen": 40
  },
- "with_tissue_term": 11605,
+ "with_tissue_term": 11599,
  "with_disease_term": 6479,
- "with_pubmed": 8479,
+ "with_pubmed": 8473,
  "with_donor_key": 3391
 }

metadata/v2/samples_metadata_v2.csv

@@ -983,7 +983,7 @@ GSM5621977,brain,normal,,hippocampal formation,primary tissue,Mus musculus,house
 GSM5621978,brain,normal,,hippocampal formation,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,3047,Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues,GSE185715,GSE185715,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0002421,hippocampus,,luna,,FFPE,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,31053,counts,pixel,0.1721170395869191,platform_constant,0.5000015226020829,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,36776149,,GSM5621978,,,train,hesrt,samples/GSE185715/GSM5621978,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.53, ""uberon"": 0.88, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM5631821,brain,normal,,olfactory bulb,primary tissue,Mus musculus,house mouse,not stated,male,Other,Pixel-seq,False,,20234,Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain,GSE186097,GSE186097,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0002264,Mouse brain Olfactory bulb,,luna,,Wild-type,luna,not stated,,sample text,,,,,,release v3,sequencing-based,other,,,cell,32711,counts,pixel,,unresolved,,,,,,,VERIFIED,,,,36368323,,GSM5631821,,,train,sda-all,samples/GSE186097/GSM5631821,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM5631822,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,male,Other,Pixel-seq,False,,29911,Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain,GSE186097,GSE186097,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,Mouse brain PBN region,,luna,,Wild-type,luna,not stated,,sample text,,,,,,release v3,sequencing-based,other,,,cell,30883,counts,pixel,,unresolved,,,,,,,VERIFIED,,,,36368323,,GSM5631822,,,train,sda-all,samples/GSE186097/GSM5631822,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.9500000000000001, ""life_stage"": 1.0}",,
-GSM5643203,stomach,disease,gastric cancer,stomach,xenograft,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,2429,Spatial transcriptome analysis of gastric cancer which GAN-KP transplanted C57BL/6J mouse,GSE186290,GSE186290,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000945,GAN-KP tumor,MONDO:0001056,luna,gastric cancer,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,31054,counts,pixel,4.875407793576616,platform_constant,4.875407793576616,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,34931404,,GSM5643203,,,train,hesrt,samples/GSE186290/GSM5643203,sda-tissue-disease-2.3,"{""organ"": 0.9500000000000001, ""sample_kind"": 0.8300000000000001, ""disease_status"": 0.99, ""uberon"": 0.9400000000000001, ""life_stage"": 1.0}",,
+GSM5643203,stomach,disease,gastric cancer,stomach,xenograft,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,2429,Spatial transcriptome analysis of gastric cancer which GAN-KP transplanted C57BL/6J mouse,GSE186290,GSE186290,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000945,GAN-KP tumor,MONDO:0001056,luna,gastric cancer,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,Visium,,,spot,31054,counts,um,1.0,verified,4.875407793576616,DEPOSITED_PIXEL_FRAME,,,,,VERIFIED,,,,34931404,,GSM5643203,,,train,sda-all,samples/GSE186290/GSM5643203,sda-tissue-disease-2.3,"{""organ"": 0.9500000000000001, ""sample_kind"": 0.8300000000000001, ""disease_status"": 0.99, ""uberon"": 0.9400000000000001, ""life_stage"": 1.0}",,
 GSM5661565,brain,normal,,brain,primary tissue,Takifugu alboplumbeus,komon-damashi,not stated,male,Visium,Visium,True,H&E,3095,Spatial transcriptome analysis of brain region in grass puffer (Takifugu alboplumbeus),GSE186818,GSE186818,433688,Takifugu alboplumbeus,433688,,False,False,GEO organism field,Takifugu alboplumbeus,,luna,UBERON:0000955,brain,,luna,,,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,26886,counts,pixel,4.283860198380393,platform_constant,4.283860198380393,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,36306789,,GSM5661565,,,train,hesrt,samples/GSE186818/GSM5661565,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM5673398,ovary,normal,,ovary,primary tissue,Mus musculus,house mouse,adult,female,Visium,Visium,True,H&E,841,Spatial transcriptomics of the ageing ovary,GSE188257,GSE188257,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000992,Ovary,,luna,,young and aged,luna,adult,3-4 months and 15-16 months,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,13.507416082123992,platform_constant,13.507416082123992,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,35996587,,GSM5673398,,,train,hesrt,samples/GSE188257/GSM5673398,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 1.0, ""life_stage"": 0.87}",,
 GSM5673399,ovary,normal,,ovary,primary tissue,Mus musculus,house mouse,adult,female,Visium,Visium,True,H&E,1415,Spatial transcriptomics of the ageing ovary,GSE188257,GSE188257,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000992,Ovary,,luna,,young and aged,luna,adult,3-4 months and 15-16 months,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,14.029939859788387,platform_constant,14.029939859788387,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,35996587,,GSM5673399,,,train,hesrt,samples/GSE188257/GSM5673399,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.9500000000000001, ""uberon"": 1.0, ""life_stage"": 0.89}",,
@@ -1423,12 +1423,12 @@ GSM6219591,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,M
 GSM6219592,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,False,,654,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,ITD1,luna,not stated,,extracted field,Female,,,fresh frozen,OCT embedded,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,,,,,,,VERIFIED,,,,,,GSM6219592,,,val,sda-all,samples/GSE205707/GSM6219592,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.6900000000000001, ""uberon"": 0.93, ""life_stage"": 1.0}",,
 GSM6219593,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,male,Visium,Visium,False,,633,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,ITD1,luna,not stated,,extracted field,Male,,,fresh frozen,OCT embedded,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,,,,,,,VERIFIED,,,,,,GSM6219593,,,val,sda-all,samples/GSE205707/GSM6219593,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.88, ""uberon"": 0.9400000000000001, ""life_stage"": 1.0}",,
 GSM6219594,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,male,Visium,Visium,False,,895,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,ITD1,luna,not stated,,extracted field,Male,,,fresh frozen,OCT embedded,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,,,,,,,VERIFIED,,,,,,GSM6219594,,,val,sda-all,samples/GSE205707/GSM6219594,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.88, ""uberon"": 0.91, ""life_stage"": 1.0}",,
-GSM6896311,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,595,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.3071343144389113,platform_constant,0.5000062390298768,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896311,,,val,hesrt,samples/GSE205707/GSM6896311,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.81, ""uberon"": 0.93, ""life_stage"": 1.0}",,
-GSM6896312,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,455,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.30806861461831603,platform_constant,0.5000068389065571,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896312,,,val,hesrt,samples/GSE205707/GSM6896312,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.72, ""uberon"": 0.92, ""life_stage"": 1.0}",,
-GSM6896313,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,837,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.30698353829866787,platform_constant,0.4999913105374158,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896313,,,val,hesrt,samples/GSE205707/GSM6896313,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.67, ""uberon"": 0.9400000000000001, ""life_stage"": 0.97}",,
-GSM6896314,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,718,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.30716517053229786,platform_constant,0.4999971118002034,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896314,,,val,hesrt,samples/GSE205707/GSM6896314,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.6900000000000001, ""uberon"": 0.96, ""life_stage"": 0.97}",,
-GSM6896315,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,2005,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.3077052651812414,platform_constant,0.4999895398119399,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896315,,,val,hesrt,samples/GSE205707/GSM6896315,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 0.98, ""life_stage"": 0.98}",disease_status,low_confidence_annotation
-GSM6896316,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,2402,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,1000,counts,pixel,0.3069243482901714,platform_constant,0.49999654606770044,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,10.1172/jci.insight.162835,GSM6896316,,,val,hesrt,samples/GSE205707/GSM6896316,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.27, ""uberon"": 0.97, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
+GSM6896311,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,708,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,0.5000062390298768,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896311,,,val,sda-all,samples/GSE205707/GSM6896311,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.81, ""uberon"": 0.93, ""life_stage"": 1.0}",,
+GSM6896312,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,569,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,0.5000068389065571,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896312,,,val,sda-all,samples/GSE205707/GSM6896312,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.72, ""uberon"": 0.92, ""life_stage"": 1.0}",,
+GSM6896313,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,2432,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32704,counts,um,1.0,verified,0.4999913105374158,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896313,,,val,sda-all,samples/GSE205707/GSM6896313,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.67, ""uberon"": 0.9400000000000001, ""life_stage"": 0.97}",,
+GSM6896314,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,2600,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32704,counts,um,1.0,verified,0.4999971118002034,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896314,,,val,sda-all,samples/GSE205707/GSM6896314,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.6900000000000001, ""uberon"": 0.96, ""life_stage"": 0.97}",,
+GSM6896315,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,3122,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32704,counts,um,1.0,verified,0.4999895398119399,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896315,,,val,sda-all,samples/GSE205707/GSM6896315,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 0.98, ""life_stage"": 0.98}",disease_status,low_confidence_annotation
+GSM6896316,skeletal muscle,perturbation,,skeletal muscle tissue,primary tissue,Canis lupus familiaris,dog,not stated,female,Visium,Visium,True,H&E,3393,Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss,GSE205707,GSE205707,9615,Canis lupus familiaris,9615,,False,False,GEO organism field,Canis lupus familiaris,,luna,UBERON:0001134,Skeletal Muscle,,luna,,,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,Visium,,,spot,32704,counts,um,1.0,verified,0.4999965460677004,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,10.1172/jci.insight.162835,GSM6896316,,,val,sda-all,samples/GSE205707/GSM6896316,sda-tissue-disease-2.5,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.27, ""uberon"": 0.97, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
 GSM6248646,airway,disease,nasopharyngeal carcinoma,nasopharynx,tumour tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,2021,Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma,GSE206245,GSE206245,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,uberon_chain,UBERON:0001728,Nasopharynx,MONDO:0015459,luna,Nasopharyngeal carcinoma,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,17943,counts,pixel,4.252777902405432,platform_constant,4.252777902405432,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,39231979,,GSM6248646,,,train,hesrt,samples/GSE206245/GSM6248646,sda-tissue-disease-2.3,"{""organ"": 0.71, ""sample_kind"": 0.99, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM6248647,airway,disease,nasopharyngeal carcinoma,nasopharynx,tumour tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,2614,Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma,GSE206245,GSE206245,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,uberon_chain,UBERON:0001728,Nasopharynx,MONDO:0015459,luna,Nasopharyngeal carcinoma,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,17943,counts,pixel,4.053282778974647,platform_constant,4.053282778974647,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,39231979,,GSM6248647,,,train,hesrt,samples/GSE206245/GSM6248647,sda-tissue-disease-2.3,"{""organ"": 0.87, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM6248648,airway,disease,nasopharyngeal carcinoma,nasopharynx,tumour tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,1939,Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma,GSE206245,GSE206245,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,uberon_chain,UBERON:0001728,Nasopharynx,MONDO:0015459,luna,Nasopharyngeal carcinoma,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,17943,counts,pixel,4.103030398712962,platform_constant,4.103030398712962,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,39231979,,GSM6248648,,,train,hesrt,samples/GSE206245/GSM6248648,sda-tissue-disease-2.3,"{""organ"": 0.7000000000000001, ""sample_kind"": 0.99, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
@@ -2936,10 +2936,6 @@ GSM7823259,heart,perturbation,,heart,primary tissue,Mus musculus,house mouse,not
 GSM7823260,heart,perturbation,,heart,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1626,Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals,GSE244650,GSE244650,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000948,heart,,luna,,Apex resection,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,31053,counts,pixel,0.46794545208201044,platform_constant,0.5000099095406314,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40967223,,GSM7823260,,,train,hesrt,samples/GSE244650/GSM7823260,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 1.0, ""life_stage"": 0.92}",,
 GSM7823491,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,female,Other,Pixel-seq,False,,59200,A diverse network of pericoerulear neurons control arousal states,GSE244659,GSE244659,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,Mouse brain LC region,,luna,,wildtype,luna,not stated,,extracted field,female,,,fresh frozen,Fresh Frozen,release v3,sequencing-based,other,,,cell,27561,counts,pixel,,unresolved,,,,,,,VERIFIED,,,,40335695,,GSM7823491,,,train,sda-all,samples/GSE244659/GSM7823491,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.84, ""life_stage"": 1.0}",,
 GSM7823492,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,male,Other,Pixel-seq,False,,17963,A diverse network of pericoerulear neurons control arousal states,GSE244659,GSE244659,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,Mouse brain LC region,,luna,,wildtype,luna,not stated,,extracted field,male,,,fresh frozen,Fresh Frozen,release v3,sequencing-based,other,,,cell,27561,counts,pixel,,unresolved,,,,,,,VERIFIED,,,,40335695,,GSM7823492,,,train,sda-all,samples/GSE244659/GSM7823492,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.85, ""life_stage"": 1.0}",,
-GSM7825036,heart,normal,,heart,primary tissue,Homo sapiens,human,embryonic,unknown,ST (legacy),ST (legacy),True,H&E,37,Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart,GSE244723,GSE244723,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,,luna,UBERON:0000948,embryonic heart,,luna,,control,age rule: Carnegie stage,embryonic,CS16,not stated,,,,,,release v3,sequencing-based,Spatial Transcriptomics,,,spot,57486,counts,pixel,3.637241489832318,platform_constant,3.637241489832318,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38011284,,GSM7825036,,,train,hesrt,samples/GSE244723/GSM7825036,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM7825037,heart,normal,,heart,primary tissue,Homo sapiens,human,embryonic,unknown,ST (legacy),ST (legacy),True,H&E,61,Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart,GSE244723,GSE244723,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,,luna,UBERON:0000948,embryonic heart,,luna,,control,age rule: Carnegie stage,embryonic,CS16,not stated,,,,,,release v3,sequencing-based,Spatial Transcriptomics,,,spot,57486,counts,pixel,3.5858299684584076,platform_constant,3.5858299684584076,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38011284,,GSM7825037,,,train,hesrt,samples/GSE244723/GSM7825037,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 0.93}",,
-GSM7825038,heart,normal,,heart,primary tissue,Homo sapiens,human,embryonic,unknown,ST (legacy),ST (legacy),True,H&E,59,Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart,GSE244723,GSE244723,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,,luna,UBERON:0000948,embryonic heart,,luna,,control,age rule: Carnegie stage,embryonic,CS16,not stated,,,,,,release v3,sequencing-based,Spatial Transcriptomics,,,spot,57486,counts,pixel,3.534890945650585,platform_constant,3.534890945650585,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38011284,,GSM7825038,,,train,hesrt,samples/GSE244723/GSM7825038,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.96, ""life_stage"": 0.98}",,
-GSM7825039,heart,normal,,heart,primary tissue,Homo sapiens,human,embryonic,unknown,ST (legacy),ST (legacy),True,H&E,60,Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart,GSE244723,GSE244723,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,,luna,UBERON:0000948,embryonic heart,,luna,,control,age rule: Carnegie stage,embryonic,CS16,not stated,,,,,,release v3,sequencing-based,Spatial Transcriptomics,,,spot,57486,counts,pixel,3.649330911960079,platform_constant,3.649330911960079,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38011284,,GSM7825039,,,train,hesrt,samples/GSE244723/GSM7825039,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.98, ""life_stage"": 1.0}",,
 GSM7829909,spleen,normal,,spleen,primary tissue,Mus musculus,house mouse,adult,unknown,Slide-seq,Slide-seqV2,False,,42666,Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2],GSE244803,GSE244803,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0002106,Spleen,,luna,,saline control,age rule: age with unit,juvenile,6-12 weeks,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,Slide-seqV2,,,bead,22019,unknown,pixel,,unresolved,,,,,,,VERIFIED,,,,38848213,,GSM7829909,,,train,sda-all,samples/GSE244803/GSM7829909,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.9500000000000001, ""uberon"": 1.0, ""life_stage"": 0.87}",,
 GSM7829910,spleen,normal,,spleen,primary tissue,Mus musculus,house mouse,adult,unknown,Slide-seq,Slide-seqV2,False,,45840,Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2],GSE244803,GSE244803,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0002106,Spleen,,luna,,saline control,age rule: age with unit,juvenile,6-12 weeks,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,Slide-seqV2,,,bead,22555,unknown,pixel,,unresolved,,,,,,,VERIFIED,,,,38848213,,GSM7829910,,,train,sda-all,samples/GSE244803/GSM7829910,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.89, ""uberon"": 1.0, ""life_stage"": 0.7000000000000001}",,
 GSM7829911,spleen,normal,,spleen,primary tissue,Mus musculus,house mouse,adult,unknown,Slide-seq,Slide-seqV2,False,,50181,Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2],GSE244803,GSE244803,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0002106,Spleen,,luna,,saline control,age rule: age with unit,juvenile,6-12 weeks,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,Slide-seqV2,,,bead,22455,unknown,pixel,,unresolved,,,,,,,VERIFIED,,,,38848213,,GSM7829911,,,train,sda-all,samples/GSE244803/GSM7829911,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.84, ""uberon"": 1.0, ""life_stage"": 0.88}",,
@@ -4916,10 +4912,10 @@ GSM8464548,brain,disease,Alzheimer disease,brain,primary tissue,Mus musculus,hou
 GSM8970742,brain,normal,,brain,primary tissue,Mus musculus,house mouse,adult,male,MERFISH/MERSCOPE,MERSCOPE,False,,126024,Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer’s disease.,GSE275026,GSE275026,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,brain,,luna,,Cx3cr1CreErt2/+(Litt),age rule: age with unit,adult,12 months,extracted field,M,,,,,release v3,imaging-based,MERSCOPE,,,cell,462,counts,um,1.0,verified,,,,,,,VERIFIED,,,,41193812,,GSM8970742,,,val,sda-all,samples/GSE275026/GSM8970742,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.44, ""uberon"": 0.98, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8970743,brain,disease,Alzheimer disease,brain,primary tissue,Mus musculus,house mouse,adult,male,MERFISH/MERSCOPE,MERSCOPE,False,,131251,Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer’s disease.,GSE275026,GSE275026,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,brain,MONDO:0004975,luna,,Cx3cr1CreErt2/+(Litt); 5xFAD,age rule: age with unit,adult,11 months,extracted field,M,,,,,release v3,imaging-based,MERSCOPE,,,cell,462,counts,um,1.0,verified,,,,,,,VERIFIED,,,,41193812,,GSM8970743,,,val,sda-all,samples/GSE275026/GSM8970743,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.98, ""life_stage"": 1.0}",,
 GSM8970744,brain,disease,Alzheimer disease,brain,primary tissue,Mus musculus,house mouse,adult,male,MERFISH/MERSCOPE,MERSCOPE,False,,120318,Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer’s disease.,GSE275026,GSE275026,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000955,brain,MONDO:0004975,luna,,5xFAD; Cx3cr1CreErt2/+(Litt);Spi1fl/+,age rule: age with unit,adult,13 months,extracted field,M,,,,,release v3,imaging-based,MERSCOPE,,,cell,462,counts,um,1.0,verified,,,,,,,VERIFIED,,,,41193812,,GSM8970744,,,val,sda-all,samples/GSE275026/GSM8970744,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.97, ""life_stage"": 1.0}",,
-GSM8465980,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1650,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32378,counts,pixel,0.6578947368421053,platform_constant,0.6578947368421053,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8465980,,,train,hesrt,samples/GSE275125/GSM8465980,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.6900000000000001, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM8465981,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1876,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32378,counts,pixel,0.6578947368421053,platform_constant,0.6578947368421053,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8465981,,,train,hesrt,samples/GSE275125/GSM8465981,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.64, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM8465982,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1858,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32378,counts,pixel,0.7352941176470589,platform_constant,0.7352941176470589,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8465982,,,train,hesrt,samples/GSE275125/GSM8465982,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.79, ""uberon"": 0.99, ""life_stage"": 0.99}",,
-GSM8465983,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1887,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32378,counts,pixel,0.6711409395973155,platform_constant,0.6711409395973155,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8465983,,,train,hesrt,samples/GSE275125/GSM8465983,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.52, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM8465980,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1650,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,Visium,,,spot,32378,counts,um,1.0,verified,0.6578947368421053,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,,GSM8465980,,,train,sda-all,samples/GSE275125/GSM8465980,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.6900000000000001, ""uberon"": 1.0, ""life_stage"": 1.0}",,
+GSM8465981,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1876,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,Visium,,,spot,32378,counts,um,1.0,verified,0.6578947368421053,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,,GSM8465981,,,train,sda-all,samples/GSE275125/GSM8465981,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.64, ""uberon"": 1.0, ""life_stage"": 1.0}",,
+GSM8465982,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1858,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,Visium,,,spot,32378,counts,um,1.0,verified,0.7352941176470589,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,,GSM8465982,,,train,sda-all,samples/GSE275125/GSM8465982,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.79, ""uberon"": 0.99, ""life_stage"": 0.99}",,
+GSM8465983,lymph node,normal,,lymph node,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,1887,Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 6),GSE275125,GSE275125,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000029,Lymph node,,luna,,,luna,not stated,,not stated,,GSE275125:JLB6J8116,JLB6J8116,,,release v3,sequencing-based,Visium,,,spot,32378,counts,um,1.0,verified,0.6711409395973155,DEPOSITED_ALIGNMENT_FIT,,,,,VERIFIED,,,,,,GSM8465983,,,train,sda-all,samples/GSE275125/GSM8465983,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.52, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8471249,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,2934,Effects of inhibiting stearoyl-CoA desaturase (SCD) on the spatial transcriptome in a mouse model of Alzheimer's disease (AD),GSE275131,GSE275131,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000955,brain,,luna,,Control (DMSO; 0.11 ul/hour infusion rate) - WT,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,4.355401436942718,platform_constant,4.355401436942718,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41539386,10.1016/j.neuropharm.2026.110835,GSM8471249,,,test,hesrt,samples/GSE275131/GSM8471249,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.77, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8471250,brain,disease,Alzheimer disease,brain,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,3080,Effects of inhibiting stearoyl-CoA desaturase (SCD) on the spatial transcriptome in a mouse model of Alzheimer's disease (AD),GSE275131,GSE275131,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000955,brain,MONDO:0004975,luna,Alzheimer's disease,Control (DMSO; 0.11 ul/hour infusion rate) - 3xTg,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,4.761410998503646,platform_constant,4.761410998503646,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41539386,10.1016/j.neuropharm.2026.110835,GSM8471250,,,test,hesrt,samples/GSE275131/GSM8471250,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8471251,brain,perturbation,,brain,primary tissue,Mus musculus,house mouse,not stated,female,Visium,Visium,True,H&E,2789,Effects of inhibiting stearoyl-CoA desaturase (SCD) on the spatial transcriptome in a mouse model of Alzheimer's disease (AD),GSE275131,GSE275131,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000955,brain,,luna,,Stearoyl-CoA desaturase inhibitor (SCDi; 80 uM) - WT,luna,not stated,,extracted field,female,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,4.53387806511062,platform_constant,4.53387806511062,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41539386,10.1016/j.neuropharm.2026.110835,GSM8471251,,,test,hesrt,samples/GSE275131/GSM8471251,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.6900000000000001, ""uberon"": 1.0, ""life_stage"": 1.0}",,
@@ -7231,7 +7227,7 @@ GSM8933089,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,hum
 GSM8933090,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,441503,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,luna,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,541,counts,um,1.0,verified,0.49999106062273085,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933090,,,train,sda-all,samples/GSE294965/GSM8933090,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.63, ""uberon"": 1.0, ""life_stage"": 0.99}",,
 GSM8933091,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,339498,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,luna,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,541,counts,um,1.0,verified,0.5000012167226359,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933091,,,train,sda-all,samples/GSE294965/GSM8933091,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.59, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8933092,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,334451,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,luna,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,541,counts,um,1.0,verified,0.49999032208113964,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933092,,,train,sda-all,samples/GSE294965/GSM8933092,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.35000000000000003, ""uberon"": 1.0, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
-GSM8933093,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,H&E,317414,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,mondo_predicate,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,10x Genomics Xenium In Situ,,,cell,541,counts,pixel,,unresolved,,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40393992,10.1101/2024.12.18.629206,GSM8933093,,,train,hesrt,samples/GSE294965/GSM8933093,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM8933093,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,317414,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,mondo_predicate,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,,,cell,541,counts,um,1.0,verified,0.5000097690170198,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,,,,40393992,10.1101/2024.12.18.629206,GSM8933093,,,train,sda-all,samples/GSE294965/GSM8933093,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8933094,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,481717,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,mondo_predicate,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,541,counts,um,1.0,verified,0.5000032303080423,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933094,,,train,sda-all,samples/GSE294965/GSM8933094,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.33, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8933095,kidney,disease,kidney disorder,kidney,primary tissue,Homo sapiens,human,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,307653,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,GSE294965,GSE294965,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002113,kidney,MONDO:0005240,mondo_predicate,,,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,541,counts,um,1.0,verified,0.5000115027146407,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933095,,,train,sda-all,samples/GSE294965/GSM8933095,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.31, ""uberon"": 1.0, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
 GSM8941069,prostate,perturbation,,prostate gland,primary tissue,Mus musculus,house mouse,not stated,male,Visium,Visium,True,H&E,1980,A spatiotemporal atlas of orchiectomy-induced modulation of cellular composition and gene expression in the mouse prostate,GSE295043,GSE295043,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0002367,prostate,,luna,,Castracted D10,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,19465,counts,pixel,4.847669641121826,platform_constant,4.847669641121826,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40974890,,GSM8941069,,,train,hesrt,samples/GSE295043/GSM8941069,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.93, ""uberon"": 1.0, ""life_stage"": 0.99}",,
@@ -7597,8 +7593,6 @@ GSM9002336,skin,normal,,skin of external ear,primary tissue,Mus musculus,house m
 GSM9004713,plant,normal,,,primary tissue,Triticum aestivum,bread wheat,not stated,unknown,Stereo-seq,Stereo-seq,False,,151711,Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes,GSE298021,GSE298021,4565,Triticum aestivum,4565,,False,False,GEO organism field,Triticum aestivum,,luna,,seed,,luna,,,luna,not stated,,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,STOmics,,,bin,70766,counts,um,1.0,verified,,,,,,,VERIFIED,PASS,,,40904198;42192524,,GSM9004713,,,train,sda-all,samples/GSE298021/GSM9004713,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 1.0, ""uberon"": NaN, ""life_stage"": 0.92}",,
 GSM9004714,plant,normal,,,primary tissue,Triticum aestivum,bread wheat,not stated,unknown,Stereo-seq,Stereo-seq,False,,156493,Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes,GSE298021,GSE298021,4565,Triticum aestivum,4565,,False,False,GEO organism field,Triticum aestivum,,luna,,seed,,luna,,,luna,not stated,,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,STOmics,,,bin,63481,counts,um,1.0,verified,,,,,,,VERIFIED,PASS,,,40904198;42192524,,GSM9004714,,,train,sda-all,samples/GSE298021/GSM9004714,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": NaN, ""life_stage"": 0.84}",,
 GSM9004715,plant,normal,,,primary tissue,Triticum aestivum,bread wheat,not stated,unknown,Stereo-seq,Stereo-seq,False,,136491,Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes,GSE298021,GSE298021,4565,Triticum aestivum,4565,,False,False,GEO organism field,Triticum aestivum,,luna,,seed,,luna,,,luna,not stated,,not stated,,,,fresh frozen,Fresh frozen,release v3,sequencing-based,STOmics,,,bin,62432,counts,um,1.0,verified,,,,,,,VERIFIED,PASS,,,40904198;42192524,,GSM9004715,,,train,sda-all,samples/GSE298021/GSM9004715,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": NaN, ""life_stage"": 0.85}",,
-GSM9008651,other,normal,,parathyroid gland,primary tissue,Mus musculus,house mouse,not stated,male,Visium,Visium,True,H&E,230,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,GSE298115,GSE298115,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001132,parathyroid,,luna,,WT,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,19465,counts,pixel,4.761904761904762,platform_constant,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41025096,,GSM9008651,,,test,hesrt,samples/GSE298115/GSM9008651,sda-tissue-disease-2.3,"{""organ"": 0.97, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.97, ""life_stage"": 1.0}",,
-GSM9008653,other,perturbation,,parathyroid gland,primary tissue,Mus musculus,house mouse,not stated,male,Visium,Visium,True,H&E,971,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,GSE298115,GSE298115,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001132,parathyroid,,luna,,Gcm2 variant p.Y392S,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,19465,counts,pixel,4.761904761904762,platform_constant,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41025096,,GSM9008653,,,test,hesrt,samples/GSE298115/GSM9008653,sda-tissue-disease-2.3,"{""organ"": 0.9400000000000001, ""sample_kind"": 1.0, ""disease_status"": 0.9500000000000001, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9008654,other,normal,,parathyroid gland,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,False,,1544,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,GSE298115,GSE298115,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001132,Parathyroid,,luna,,WT,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,19465,counts,um,1.0,verified,,,,,,,VERIFIED,,,,41025096,,GSM9008654,,,test,sda-all,samples/GSE298115/GSM9008654,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 1.0, ""disease_status"": 0.93, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9008655,other,normal,,parathyroid gland,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,False,,737,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,GSE298115,GSE298115,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001132,Parathyroid,,luna,,WT,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,19465,counts,um,1.0,verified,,WITHHELD,,,hesrt_review_fail,,VERIFIED,,,,41025096,,GSM9008655,,,test,sda-all,samples/GSE298115/GSM9008655,sda-tissue-disease-2.3,"{""organ"": 0.97, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9008656,other,perturbation,,parathyroid gland,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,False,,1531,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,GSE298115,GSE298115,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001132,Parathyroid,,luna,,Gcm2 variant p.Y392S,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,19465,counts,um,1.0,verified,,,,,,,VERIFIED,,,,41025096,,GSM9008656,,,test,sda-all,samples/GSE298115/GSM9008656,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 0.99, ""life_stage"": 1.0}",,

metadata/v2/samples_metadata_v2.parquet

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metadata/v2/studies_v2.csv

@@ -296,7 +296,6 @@ GSE244536,Deterministic reprogramming of neutrophils in tumors,4,Mus musculus,Vi
 GSE244641,Recirculating regulatory T cells mediate thymic regeneration [visium],6,Mus musculus,Visium,Visium,thymus,,normal,6,39892391,train
 GSE244650,Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals,13,Mus musculus,Visium,Visium,heart,,perturbation;normal,13,40967223,train
 GSE244659,A diverse network of pericoerulear neurons control arousal states,2,Mus musculus,Other,Pixel-seq,brain,,normal,0,40335695,train
-GSE244723,Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart,4,Homo sapiens,ST (legacy),ST (legacy),heart,,normal,4,38011284,train
 GSE244803,Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2],8,Mus musculus,Slide-seq,Slide-seqV2,spleen,malaria,normal;disease,0,38848213,train
 GSE245097,Spatial transcriptomics of the achilles tendon harvested from the injury site with and without TrkA neuronal inhibition,4,Mus musculus,Visium,Visium,other,,perturbation;disease,4,38117901,train
 GSE245111,Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen [Curio],4,Mus musculus,Slide-seq,Slide-seq,lymph node,,perturbation;disease,0,38374265,train
@@ -806,7 +805,7 @@ GSE297745,IL-17A Neutralization Prevents Immune Checkpoint Inhibitor-Associated
 GSE297945,A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity,34,Homo sapiens,Xenium,Xenium,lung,pulmonary hypoplasia;bronchopulmonary dysplasia;congenital heart disease;perinatal asphyxia;necrotizing enterocolitis;meningitis,normal;disease,8,40502191,train
 GSE297947,IL-33/IL1RL1 (ST2) signalling drives immune suppression in HPV-mediated epithelial hyperplasia,1,Mus musculus,Visium,Visium,skin,,normal,1,42679897,train
 GSE298021,Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes,3,Triticum aestivum,Stereo-seq,Stereo-seq,plant,,normal,0,40904198;42192524,train
-GSE298115,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,6,Mus musculus,Visium,Visium,other,,normal;perturbation,2,41025096,test
+GSE298115,Spatial Transcriptomic Analysis of Mouse Parathyroid Gland Cells Expressing an Activating Variant of Gcm2,4,Mus musculus,Visium,Visium,other,,normal;perturbation,0,41025096,test
 GSE298286,In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics,14,Homo sapiens,Visium,Visium,bone;breast,breast neoplasm;metastatic neoplasm,disease,14,41734374,train
 GSE298314,Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling,4,Mus musculus,MERFISH/MERSCOPE,MERSCOPE,brain,,perturbation,0,40934914,val
 GSE298545,Molecular pathology of acute spinal cord injury in middle-aged mice,4,Mus musculus,Visium,Visium,spinal cord,spinal cord injury,disease,4,40653490,test