Correction 2026-11-11: image removed from 9 misaligned HESRT samples

The spots of these samples do not sit on the tissue in the image: GSE229175 (4), GSE302160 (2), GSM8925216, GSM8770960, GSM9317397. Expression and coordinates stay. Catalog, metadata v2 (2.2.4) and the dataset card are updated; no other sample changed.

README.md

@@ -21,14 +21,14 @@ configs:
 *Left to right: H&E and GFAP from the same Visium section (GSM9721856), Xenium DAPI (GSM9301054), and a CosMx composite (GSM9372712). The GFAP panel displays all 3,416 recorded spots using the existing log1p preview values.*
 
 Search 12,157 public spatial transcriptomics samples before you request any data. They come from 1,264 published
-GEO series and hold 635,244,564 spatial observations (spots, bins, cells or beads). 8,205 samples have a released
-tissue image: 5,256 H&E, 871 H&E-like (a pixel-based call that no reviewer confirmed), 1,424 DAPI, 427 other fluorescence and 227 other or
+GEO series and hold 635,244,564 spatial observations (spots, bins, cells or beads). 8,196 samples have a released
+tissue image: 5,247 H&E, 871 H&E-like (a pixel-based call that no reviewer confirmed), 1,424 DAPI, 427 other fluorescence and 227 other or
 undetermined stains. Platforms include Visium, Xenium, legacy ST, CosMx, MERFISH/MERSCOPE, Slide-seq, Stereo-seq and Visium HD.
 
 The samples were found and standardized from GEO by the [SpatialDataAgent](https://github.com/YSTLab/spatial-data-agent)
 workflow (7,789 samples, each checked by an independent scorer) and by the earlier HESRT H&E collection (4,368
 samples, each reviewed by eye). On 2026-11-11, 12 samples were replaced and 6 were withdrawn after a check
-against the GEO deposits; see [Corrections 2026-11-11](#corrections-2026-11-11). The atlas is described in the
+against the GEO deposits, and the image of 9 misaligned samples was removed; see [Corrections 2026-11-11](#corrections-2026-11-11). The atlas is described in the
 [bioRxiv preprint](https://doi.org/10.64898/2026.05.27.727615).
 
 This repository needs **no account**. It holds the catalog of all 12,157 samples and the complete files of 86
@@ -254,7 +254,7 @@ a selection).
 
 ## Corrections 2026-11-11
 
-On 2026-11-11 the samples that come from HESRT, the earlier H&E collection that is part of this dataset (`source_pipeline = hesrt`), were compared value by value with the files deposited in GEO. The check found problems in 18 samples. We replaced 12 of them and withdrew 6. No other sample file changed. The numbers at the top of this card describe the current data. The figures and composition tables further down still show the paper release (`v1.0.0-20261025`, 12,163 samples); they count the six withdrawn samples and describe the 12 replaced samples by their old files.
+On 2026-11-11 the samples that come from HESRT, the earlier H&E collection that is part of this dataset (`source_pipeline = hesrt`), were compared value by value with the files deposited in GEO. The check found problems in 18 samples. We replaced 12 of them and withdrew 6. No other expression or coordinate file changed. On the same day an image-registration screen led to the removal of the image of nine more samples (see the end of this section). The numbers at the top of this card describe the current data. The figures and composition tables further down still show the paper release (`v1.0.0-20261025`, 12,163 samples); they count the six withdrawn samples and describe the 12 replaced samples by their old files.
 
 **Replaced (12 samples).** Each sample was converted again from the deposited files. The new files were compared with the deposit value by value, and the author reviewed each sample by eye.
 
@@ -278,14 +278,15 @@ For these 12 samples the catalog (`catalog/samples.parquet`) now gives coordinat
 
 **If you used these samples.** Do not use results computed from the old files of the 12 replaced samples or of the two GSE298115 samples. For the 12 replaced samples, redo them with the new files. For the two GSE298115 samples, drop them. The four GSE244723 samples had correct values but placeholder gene names, so any result by gene from them has no meaning.
 
-**Samples whose spots do not sit on the tissue (8 samples, still in the data).** On the same day the image registration of the same HESRT samples was screened. Eight samples are still in the data although their spots do not match the image: `GSM7156292` to `GSM7156295` (GSE229175), `GSM9097318` and `GSM9097320` (GSE302160), `GSM8925216` (GSE294844) and `GSM8770960` (GSE288607). Their expression values and coordinates are equal to the deposit. Only the match between spots and image is wrong. Do not use them for analyses that pair image patches with expression until they are corrected or withdrawn. The samples that do not come from HESRT have not been screened in this way yet.
+**Samples whose spots do not sit on the tissue (9 samples, image removed).** On the same day the image registration of the same HESRT samples was screened, and the author looked at every flagged sample. In nine samples the spots do not match the image: `GSM7156292` to `GSM7156295` (GSE229175), `GSM9097318` and `GSM9097320` (GSE302160), `GSM8925216` (GSE294844), `GSM8770960` (GSE288607) and `GSM9317397` (GSE311123). Their image was removed from the data on 2026-11-11. Their expression values and coordinates are equal to the deposit and stay in the data. This differs from the HESRT dataset, where release `2026-09-17-v1.6` withdraws these nine samples completely. In the catalog these nine samples now have `has_image = False`, `image_registration = WITHHELD` and the flag `image_review_fail`. If you paired image patches with expression for these samples, drop those results. In 16 further HESRT samples the spots match the tissue, but the image covers only part of the spots (5% to 50% of the spots fall outside it). They carry the flag `image_partial_coverage`; filter spots by the image bounds before you extract patches. The samples that do not come from HESRT have not been screened in this way yet.
 
-**Versions.** The corrected data is tag `v1.2.0-20261111` of the main dataset. The paper tag `v1.0.0-20261025` is unchanged and still holds the old files, so earlier work can be traced. The gene search index was updated for the changed samples. The sample metadata is version 2.2.3: it drops the six withdrawn samples, and the curated annotations of all other samples did not change. The `sda-db` toolkit reads the paper tag by default, so it still returns the old files of these 18 samples until its next release; to get the corrected files now, download them with `huggingface_hub` and `revision="v1.2.0-20261111"`.
+**Versions.** The current data is tag `v1.3.0-20261111` of the main dataset. Tag `v1.2.0-20261111` holds the data after the 12 replacements and 6 withdrawals, but it still has the nine removed images. The paper tag `v1.0.0-20261025` is unchanged and still holds the old files, so earlier work can be traced. The gene search index was updated for the changed samples. The sample metadata is version 2.2.4: it drops the six withdrawn samples and marks the nine samples that lost their image; the curated annotations of all other samples did not change. The `sda-db` toolkit reads the paper tag by default, so it still returns the old files of these 27 samples (12 replaced, 6 withdrawn, 9 with the image removed) until its next release; to get the current files now, download them with `huggingface_hub` and `revision="v1.3.0-20261111"`.
 
-## Curated sample metadata v2 (version 2.2.3, 2026-11-11)
+## Curated sample metadata v2 (version 2.2.4, 2026-11-11)
 
 `metadata/v2/` adds a curated table on top of the current 12,157 samples. The paper release is still tag
-`v1.0.0-20261025`; the corrected data and the current metadata are tag `v1.2.0-20261111` of the main dataset. Version 2.2.3
+`v1.0.0-20261025`; the corrected data and the current metadata are tag `v1.3.0-20261111` of the main dataset. Version 2.2.4
+marks the nine samples whose image was removed on 2026-11-11 (`has_image`, `image_stain`, `image_registration`, `flags` and the review columns). Version 2.2.3
 drops the six samples withdrawn on 2026-11-11 and updates the file-derived columns (for example `n_obs`,
 `coordinate_units`, `image_registration`) of the 12 replaced samples; no curated annotation changed. Version 2.2.2
 (tag `metadata-v2.2.2-20261108`) only moved the most-used columns to the front.

catalog/samples.csv

@@ -2268,10 +2268,10 @@ GSM7146857,GSE228982,GSE228982,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo
 GSM7146858,GSE228982,GSE228982,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,synovial joint,spot,1368,36601,counts,human_visual_review,c25024316be736d8e32664f5adf8bb56adb1e94a95270b8e0ade9b4d48481263,pixel,platform_constant,3.9428570621074104,True,True,H&E,HESRT human review,3.9428570621074104,HESRT_HUMAN_REVIEW,e9fc1455fbfe2220ddcd23ce2bfa1eeb1223e17c78fbcc7de51ec41834c37f51,,,,,,,,,,GSM7146858,,,train,samples/GSE228982/GSM7146858
 GSM7146859,GSE228982,GSE228982,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,synovial joint,spot,927,36601,counts,human_visual_review,098107a189680c3103e4afbd84c4b56d04a881991a4e2a4e332904b4cd7eeda6,pixel,platform_constant,3.9428570621074104,True,True,H&E,HESRT human review,3.9428570621074104,HESRT_HUMAN_REVIEW,d32e43c78356d6181a91402df5e19e9825bb200fd8bb48ecefe23c49c2ad9db9,,,,,,,,,,GSM7146859,,,train,samples/GSE228982/GSM7146859
 GSM7146860,GSE228982,GSE228982,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,synovial joint,spot,899,36601,counts,human_visual_review,029e8e9aaf0f60891b2bb3424c38a77840e2f7e5686b71795afd296919347b86,pixel,platform_constant,3.9428570621074104,True,True,H&E,HESRT human review,3.9428570621074104,HESRT_HUMAN_REVIEW,6c35c94af46e38b7126bf98e2d4601b54551d9145171cb1abf4d7e5187101060,,,,,,,,,,GSM7146860,,,train,samples/GSE228982/GSM7146860
-GSM7156292,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,492,18788,counts,human_visual_review,d68c8c502c7c6562e3c842c7c142d981590a03b811060fbce6b3c19499c9983e,pixel,platform_constant,4.041316950226493,True,True,H&E,HESRT human review,4.041316950226493,HESRT_HUMAN_REVIEW,b3a2b93732f97466adc4339fc5fe4754c052a06e4a68dec58810425fada1062e,,,,,,,,,,GSM7156292,,,train,samples/GSE229175/GSM7156292
-GSM7156293,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,424,18788,counts,human_visual_review,fa1cb61faa78e4431d9dd23f89fa206f5024d674af0d0b4a525b6c65c5c1bc60,pixel,platform_constant,4.2855343622607105,True,True,H&E,HESRT human review,4.2855343622607105,HESRT_HUMAN_REVIEW,c359f29bd03c013946fb3324dfc4ccf70135bddd43ef6cc2d91599d62b9ab421,,,,,,,,,,GSM7156293,,,train,samples/GSE229175/GSM7156293
-GSM7156294,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,446,18788,counts,human_visual_review,dc3146ca2e16595c8ab99c4d5e70b4066bc056701ab01caa120bf5f183744e8a,pixel,platform_constant,4.318580697036812,True,True,H&E,HESRT human review,4.318580697036812,HESRT_HUMAN_REVIEW,09f5f0916dd1d8642e11bcadd9d04e42fdf337119fc711229c0dc414b685f661,,,,,,,,,,GSM7156294,,,train,samples/GSE229175/GSM7156294
-GSM7156295,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,648,18788,counts,human_visual_review,1d35a8800383c9ad0dd543adc176dcf1d4b359fdf61d9c8117cc99b2dab95098,pixel,platform_constant,4.252557856758691,True,True,H&E,HESRT human review,4.252557856758691,HESRT_HUMAN_REVIEW,7973d6489558ffdba7f179575f267384a4c73dd1777a4807d83f72fc088d5536,,,,,,,,,,GSM7156295,,,train,samples/GSE229175/GSM7156295
+GSM7156292,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,492,18788,counts,human_visual_review,d68c8c502c7c6562e3c842c7c142d981590a03b811060fbce6b3c19499c9983e,pixel,platform_constant,4.041316950226493,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM7156292,,,train,samples/GSE229175/GSM7156292
+GSM7156293,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,424,18788,counts,human_visual_review,fa1cb61faa78e4431d9dd23f89fa206f5024d674af0d0b4a525b6c65c5c1bc60,pixel,platform_constant,4.2855343622607105,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM7156293,,,train,samples/GSE229175/GSM7156293
+GSM7156294,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,446,18788,counts,human_visual_review,dc3146ca2e16595c8ab99c4d5e70b4066bc056701ab01caa120bf5f183744e8a,pixel,platform_constant,4.318580697036812,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM7156294,,,train,samples/GSE229175/GSM7156294
+GSM7156295,GSE229175,GSE229175,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Ciona intestinalis,neural complex,spot,648,18788,counts,human_visual_review,1d35a8800383c9ad0dd543adc176dcf1d4b359fdf61d9c8117cc99b2dab95098,pixel,platform_constant,4.252557856758691,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM7156295,,,train,samples/GSE229175/GSM7156295
 GSM7164655,GSE229508,GSE229508,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Mus musculus,forebrain,spot,979,32285,counts,human_visual_review,f33f5c75d4f936e51b845a435c92950953383e6fa761bc3066132e6b90d93462,pixel,platform_constant,4.339849705475763,True,True,H&E,HESRT human review,4.339849705475763,HESRT_HUMAN_REVIEW,c28dd2c4406a16979f8bdfe4e3883e9c156861da66f93ac591dc160cff455d26,,,,,,,,,,GSM7164655,,,train,samples/GSE229508/GSM7164655
 GSM7164656,GSE229508,GSE229508,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Forebrain,spot,1243,32285,counts,VERIFIED,5b609ffc7f700af4f5154928bb5b56bfc1eaf942b5d82effb2680b163c1baaae,um,verified,1.0,False,True,H&E-like (heuristic),pixels,4.3425740514866735,VERIFIED,9b22c72a583a14062994109f339f11e18c373f84f42bed5161b96c71143c8afd,ABSENT,ABSENT,,,,,PASS,,,GSM7164656,,,train,samples/GSE229508/GSM7164656
 GSM7169587,GSE229635,GSE229635,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Electrophorus voltai,the main electric organ,spot,2677,23221,counts,human_visual_review,f5a8e5b0e2219ad30732bd86a53c0bbc2411163c220a7bc01e1d596ab3049660,pixel,platform_constant,4.989781254820793,True,True,H&E,HESRT human review,4.989781254820793,HESRT_HUMAN_REVIEW,a492e06ab149a86cb8ffb6ca84952eb359717d304fef067b0b76e6fbcd77f8f8,,,,,,,,,,GSM7169587,,,train,samples/GSE229635/GSM7169587
@@ -6681,7 +6681,7 @@ GSM8770956,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo
 GSM8770957,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,3923,37082,counts,human_visual_review,0d9f046e0147b67c0bcf9a25180dbf6a5d842f1877af7a4f1f054b02f85a6af8,pixel,platform_constant,4.266666754047988,True,True,H&E,HESRT human review,4.266666754047988,HESRT_HUMAN_REVIEW,22167fab34503d805cb25a575f8f70de7d6b78b95bbc63faa906c207b7001fbc,,,,,,,,,,GSM8770957,,,val,samples/GSE288607/GSM8770957
 GSM8770958,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,3332,37082,counts,human_visual_review,1bbb10cae55d4df6cd05380247eaa7c6111e6eb51dcb922a5689257cb2c89b7c,pixel,platform_constant,4.117466871137884,True,True,H&E,HESRT human review,4.117466871137884,HESRT_HUMAN_REVIEW,f36bee2cc921bd33bd907645ed33cfca0cdefc96f3b35f6aeaa0d434a5997e73,,,,,,,,,,GSM8770958,,,val,samples/GSE288607/GSM8770958
 GSM8770959,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,2285,37082,counts,human_visual_review,02897abae2b5a52575cc145ee8d9f03e5fe6de1997a898af62a9d6613d70e46d,pixel,platform_constant,1.1903918403013953,True,True,H&E,HESRT human review,1.1903918403013953,HESRT_HUMAN_REVIEW,365f5a0d973538398e107e3ff1f8816ac6ba361ec1f740b37218f4aeda5d7ce5,,,,,,,,,,GSM8770959,,,val,samples/GSE288607/GSM8770959
-GSM8770960,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,4992,37082,counts,human_visual_review,ab224a7944345e5dade03a916ea9df27203e8a052c5339b2883d523b6a962239,pixel,platform_constant,0.5473313553908552,True,True,H&E,HESRT human review,0.5473313553908552,HESRT_HUMAN_REVIEW,2544b02d0da11be471cf595bf27f71416e034aa43e881ec126a2fbd897a9a277,,,,image_partial_coverage,,,,,,GSM8770960,,,val,samples/GSE288607/GSM8770960
+GSM8770960,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,4992,37082,counts,human_visual_review,ab224a7944345e5dade03a916ea9df27203e8a052c5339b2883d523b6a962239,pixel,platform_constant,0.5473313553908552,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: only 31% of the spots fall inside the image; the spot grid is about three times larger than the image. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM8770960,,,val,samples/GSE288607/GSM8770960
 GSM8770961,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,3043,37082,counts,human_visual_review,688028fad1431e8afe2d9ae353ed823fe481e2bbfa938e012efe38c039a691f3,pixel,platform_constant,0.502487185955009,True,True,H&E,HESRT human review,0.502487185955009,HESRT_HUMAN_REVIEW,cba3550ca5e4bb7be1175a7d4685d5b7d0a272e2a455b6ad3b74a6e81a4d9e32,,,,,,,,,,GSM8770961,,,val,samples/GSE288607/GSM8770961
 GSM8770962,GSE288607,GSE288607,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,lung,spot,4112,37082,counts,human_visual_review,c2c855d222cd4c8bb68b4d51fd13f149df99b134bfdd6dd13cd1cfb26e02b67f,pixel,platform_constant,0.5024554702869775,True,True,H&E,HESRT human review,0.5024554702869775,HESRT_HUMAN_REVIEW,46dc0bea5cee0c9c2144640a37709cf563a04cbca3b51eddbca8cb83e6663c0e,,,,,,,,,,GSM8770962,,,val,samples/GSE288607/GSM8770962
 GSM8772705,GSE288663,GSE288663,sda-all,sda-all-gap-20261009,Xenium,Xenium,Mus musculus,Lower abdominal muscle,cell,7797,5060,counts,VERIFIED,19176e4951ea6b1e63d40cea05dcef5195c4dafe380383999b0e6784edaa845e,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.499979353773098,VERIFIED,b627a58c4e8842cc56b2d88b6bedc469e30a19063461caf5c48db653104dc6c3,ABSENT,VERIFIED,,,,,PASS,,,GSM8772705,,,val,samples/GSE288663/GSM8772705
@@ -7216,7 +7216,7 @@ GSM8921749,GSE294814,GSE294814,sda-all,sda-all-v1.4.0,DBiT-seq,microDBiT,Mus mus
 GSM8921750,GSE294814,GSE294814,sda-all,sda-all-v1.4.0,DBiT-seq,microDBiT,Mus musculus,intestine,spot,2500,28198,unknown,VERIFIED,4bb2ac07a8caba9d71f164ee1e721beb36a42dd7bfe4fac28705220668f565a6,native_grid,unresolved,,False,False,,,,,,,,,,,,,,,GSM8921750,,,val,samples/GSE294814/GSM8921750
 GSM8921752,GSE294814,GSE294814,sda-all,sda-all-v1.4.0,DBiT-seq,microDBiT,Mus musculus,colon,spot,2498,35188,unknown,VERIFIED,404e95bc5da677de8012fa5214bf2ed6822f8556ce9f208cb4580885d4e3d452,native_grid,unresolved,,False,False,,,,,,,,,,,,,,,GSM8921752,,,val,samples/GSE294814/GSM8921752
 GSM8921753,GSE294814,GSE294814,sda-all,sda-all-v1.4.0,DBiT-seq,microDBiT,Mus musculus,colon,spot,2493,44662,unknown,VERIFIED,03a4945235c03122db8b2c520399a76b5893c8f4879b2eaa8a78958a54c42adc,native_grid,unresolved,,False,False,,,,,,,,,,,,,,,GSM8921753,,,val,samples/GSE294814/GSM8921753
-GSM8925216,GSE294844,GSE294844,hesrt,hesrt-v1.3,Visium,10x Genomics Visium v2 CytAssist Spatial Gene Expression,human skin metagenome,skin,spot,1435,18085,counts,human_visual_review,77cd6b8608abb5cf300d1d5e6d7cd94a08fd90e26a3ac9b4501242ea045f1028,pixel,platform_constant,4.761904761904762,True,True,H&E,HESRT human review,4.761904761904762,HESRT_HUMAN_REVIEW,84fe7c55774bbefd4eee0dfe85e73a35f2e4e9fa86094f486daf7c5d7b257bd2,,,,,,,,,,GSM8925216,,,test,samples/GSE294844/GSM8925216
+GSM8925216,GSE294844,GSE294844,hesrt,hesrt-v1.3,Visium,10x Genomics Visium v2 CytAssist Spatial Gene Expression,human skin metagenome,skin,spot,1435,18085,counts,human_visual_review,77cd6b8608abb5cf300d1d5e6d7cd94a08fd90e26a3ac9b4501242ea045f1028,pixel,platform_constant,4.761904761904762,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,"Image registration screen 2026-11-11: the tissue forms two horizontal strips, but the spots form two vertical strips. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.",GSM8925216,,,test,samples/GSE294844/GSM8925216
 GSM8925217,GSE294844,GSE294844,sda-all,sda-all-gap-20261009,Visium,Visium,human skin metagenome,skin,spot,1505,18085,counts,VERIFIED,d43bcd2878dc9d8a954db381123cb7bf8602306033dd69c3fd255d860230e716,um,verified,1.0,False,False,,,,WITHHELD,,,,,hesrt_review_fail,,,,,,GSM8925217,,,test,samples/GSE294844/GSM8925217
 GSM8925218,GSE294844,GSE294844,hesrt,hesrt-v1.3,Visium,10x Genomics Visium v2 CytAssist Spatial Gene Expression,human skin metagenome,skin,spot,1706,18085,counts,human_visual_review,a91726f195fc3c763eb1ed5cce904d420706bf47bbd4e639021d1ace9b1dc66b,pixel,platform_constant,4.761904761904762,True,True,H&E,HESRT human review,4.761904761904762,HESRT_HUMAN_REVIEW,e21764fac660aa2f32703da8da41d326ca72105d49983be1ab74f9f776d22238,,,,,,,,,,GSM8925218,,,test,samples/GSE294844/GSM8925218
 GSM8925219,GSE294844,GSE294844,hesrt,hesrt-v1.3,Visium,10x Genomics Visium v2 CytAssist Spatial Gene Expression,human skin metagenome,skin,spot,921,18085,counts,human_visual_review,70ecbe6a358aa0bd66e4d90890e68284e8d163268ede8d960a0e73354f4a85df,pixel,platform_constant,4.761904761904762,True,True,H&E,HESRT human review,4.761904761904762,HESRT_HUMAN_REVIEW,cc5c0523ab947410a4b8411c11312df4ef2f9dfe0c214efc2caa7ba0058104f1,,,,,,,,,,GSM8925219,,,test,samples/GSE294844/GSM8925219
@@ -8025,9 +8025,9 @@ GSM9096730,GSE302128,GSE302128,sda-all,sda-all-v1.3.0,Xenium,Xenium,Mus musculus
 GSM9096731,GSE302128,GSE302128,sda-all,sda-all-v1.3.0,Xenium,Xenium,Mus musculus,tongue,cell,52889,9880,counts,VERIFIED,d9f2bb0303145c8df36c0e458f9274a63efaab2c3c46ba3a81e28953fe3828e1,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.4999873806901616,VERIFIED,f61e76134bb09ab5aaf03e745c314967ccac9731cae3bf3215f76624a8892906,VERIFIED,VERIFIED,,,,,PASS,,,GSM9096731,,,test,samples/GSE302128/GSM9096731
 GSM9096732,GSE302128,GSE302128,sda-all,sda-all-v1.3.0,Xenium,Xenium,Mus musculus,tongue,cell,50212,9880,counts,VERIFIED,517377736b5604428d3f1ea4cc10bbbd1e72a9d6c4461945dc42b13d0d0794d6,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.49998323878287776,VERIFIED,259ae4ae80cd9b44276bf48d4c5137c2948a88e548dbd666d830cbd7605df211,VERIFIED,VERIFIED,,,,,PASS,,,GSM9096732,,,test,samples/GSE302128/GSM9096732
 GSM9096733,GSE302128,GSE302128,sda-all,sda-all-v1.3.0,Xenium,Xenium,Mus musculus,tongue,cell,75178,9880,counts,VERIFIED,2ca1594138e5ac013edbd69c4ef0e843feddaa0fde62bc07ef0e93f8167beb45,um,verified,1.0,False,True,fluorescence: DAPI,platform,0.5000325922876355,VERIFIED,af88b73e62983041e0609ada9259a59fee5e4e63022bf17969dbe06259834589,VERIFIED,VERIFIED,,,,,PASS,,,GSM9096733,,,test,samples/GSE302128/GSM9096733
-GSM9097318,GSE302160,GSE302160,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,brain:primary motor cortex,spot,4763,18085,counts,human_visual_review,7d5b14aa9fb540b2af977778fbbca4481aeb7e35b0c0989b5abc37b0f28fa13d,pixel,platform_constant,3.037184984800885,True,True,H&E,HESRT human review,3.037184984800885,HESRT_HUMAN_REVIEW,4fe62dde6c4f9a6277c077201c229c0e430624356f6d29c5bc2e86d144832f5c,,,,,,,,,,GSM9097318,,,val,samples/GSE302160/GSM9097318
+GSM9097318,GSE302160,GSE302160,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,brain:primary motor cortex,spot,4763,18085,counts,human_visual_review,7d5b14aa9fb540b2af977778fbbca4481aeb7e35b0c0989b5abc37b0f28fa13d,pixel,platform_constant,3.037184984800885,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the spot grid is shifted and extends onto bare glass. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM9097318,,,val,samples/GSE302160/GSM9097318
 GSM9097319,GSE302160,GSE302160,sda-all,sda-all-gap-20261009,Visium,Visium,Homo sapiens,brain:primary motor cortex,spot,3837,18085,counts,VERIFIED,b79ed0a050a23d4d2a7a9ca9cbb978ca121d558bb70cb2abd96725505c902861,um,verified,1.0,False,True,fluorescence: blue (heuristic),pixels,4.545880211325501,VERIFIED,eb0345a1644d3df4d3ef386b29a180dd80d7578948bc4a5a4456296d787a52f9,ABSENT,ABSENT,,hesrt_review_fail;hesrt_fail_image_released,,,PASS,,,GSM9097319,,,val,samples/GSE302160/GSM9097319
-GSM9097320,GSE302160,GSE302160,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,brain:primary motor cortex,spot,4690,18085,counts,human_visual_review,707fd14cb25de0b7f1404fe2591f980c2c0f726815e60079bceab5298121135b,pixel,platform_constant,3.03578646514248,True,True,H&E,HESRT human review,3.03578646514248,HESRT_HUMAN_REVIEW,d3b81d43c02be68f27fcc96f10adc04a2ee0ee79aa589cf8788bf1c252e58e13,,,,,,,,,,GSM9097320,,,val,samples/GSE302160/GSM9097320
+GSM9097320,GSE302160,GSE302160,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,brain:primary motor cortex,spot,4690,18085,counts,human_visual_review,707fd14cb25de0b7f1404fe2591f980c2c0f726815e60079bceab5298121135b,pixel,platform_constant,3.03578646514248,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the spot grid is shifted and extends onto bare glass. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM9097320,,,val,samples/GSE302160/GSM9097320
 GSM9097321,GSE302160,GSE302160,sda-all,sda-all-gap-20261009,Visium,Visium,Homo sapiens,brain:primary motor cortex,spot,3508,18085,counts,VERIFIED,338aa52e0f62ec3e7fd2fc2e4b8ebd80c5c5fd14e0b4c877bda8ab588fc12ec3,um,verified,1.0,False,True,fluorescence: blue (heuristic),pixels,5.450765988787993,VERIFIED,2fe6544726bc0816e05dfd56b611e0e72ed6fb2b6e2b2c6e54de387fb9fc7f9f,ABSENT,ABSENT,,hesrt_review_fail;hesrt_fail_image_released,,,PASS,,,GSM9097321,,,val,samples/GSE302160/GSM9097321
 GSM9098123,GSE302187,GSE302187,sda-all,sda-all-gap-20261009,Visium,Visium,"Staphylococcus aureus
 Mus musculus",kidney,spot,5223,19812,counts,ATTESTED,a26e4a148d811e1e36bc7e229ca9fb2b011561fb018ee085c276a387bf7ad61e,um,declared_unverified,1.0,False,False,,,,,,,,,attested,,,,,,GSM9098123,,,train,samples/GSE302187/GSM9098123
@@ -9180,7 +9180,7 @@ GSM9312237,GSE310921,GSE310921,sda-all,sda-all-gap-20261009,Visium,Visium,Mus mu
 GSM9312238,GSE310921,GSE310921,sda-all,sda-all-gap-20261009,Visium,Visium,Mus musculus,Quadriceps Muscle,spot,2684,32285,counts,VERIFIED,a5c42f015079b562f455443178e494d0ce062499eaa9ee853ed29918975d9b2d,um,verified,1.0,False,True,H&E,sample text + pixels,3.971653797229367,VERIFIED,1837486234575c7410192706702afb350ca7594ce42e2254a107d9b38cc02f62,ABSENT,ABSENT,,,,,PASS,,,GSM9312238,,,train,samples/GSE310921/GSM9312238
 GSM9312239,GSE310921,GSE310921,sda-all,sda-all-gap-20261009,Visium,Visium,Homo sapiens,Pectoralis Major,spot,2168,36601,counts,VERIFIED,55274232053b7997593cb4d0b79bdcde2aff446113ea15e05f262a2c535c3be5,um,verified,1.0,False,True,H&E,sample text + pixels,4.179825593540337,UNRESOLVED,e93fed9189707b2058be86cf7579fcd566b85f3e73cf7842c1205f8bd2fd9c55,ABSENT,ABSENT,,,,,PASS,,,GSM9312239,,,train,samples/GSE310921/GSM9312239
 GSM9312240,GSE310921,GSE310921,sda-all,sda-all-gap-20261009,Visium,Visium,Homo sapiens,Pectoralis Major,spot,1939,36601,counts,VERIFIED,6f188cbd36c43d97e4e1eaddf95529be892712475451942de67ac0650ee5b6ff,um,verified,1.0,False,True,H&E,sample text + pixels,4.218754565904826,FAILED,67accf7bb12803fe32e2af6865ea519b04fe4712a617f3c559b8f2c9a217e481,ABSENT,ABSENT,,,,,PASS,,,GSM9312240,,,train,samples/GSE310921/GSM9312240
-GSM9317397,GSE311123,GSE311123,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,Distal femur,spot,4992,18085,counts,human_visual_review,3ba2ea4d6b196e4d3a676ee0fbbf03ce3607721c9183c7e8c5d6688b70e2dbc8,pixel,platform_constant,8.883456876836373,True,True,H&E,HESRT human review,8.883456876836373,HESRT_HUMAN_REVIEW,e5910a552b96b6916a88f46cbc661b93c086f0c1e519d80a14ac716c91cf843f,,,,,,,,,,GSM9317397,,,val,samples/GSE311123/GSM9317397
+GSM9317397,GSE311123,GSE311123,hesrt,hesrt-v1.3,Visium,10x Genomics Visium,Homo sapiens,Distal femur,spot,4992,18085,counts,human_visual_review,3ba2ea4d6b196e4d3a676ee0fbbf03ce3607721c9183c7e8c5d6688b70e2dbc8,pixel,platform_constant,8.883456876836373,True,False,,,,WITHHELD,,,,,image_review_fail,,,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the author judged on the review page that the spots do not match the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,GSM9317397,,,val,samples/GSE311123/GSM9317397
 GSM9320917,GSE311199,GSE311199,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain,spot,6275,48440,counts,VERIFIED,2f0a9e38b6c967b27e6be31f829e588fb417e7e420c14edc4488ca677977edd8,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM9320917,,,train,samples/GSE311199/GSM9320917
 GSM9320919,GSE311199,GSE311199,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse brain,spot,6199,48440,counts,VERIFIED,db48a7228fd0c7096bfff3ecf69c71f6f7c4bca849c0823f221186b607633453,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM9320919,,,train,samples/GSE311199/GSM9320919
 GSM9320921,GSE311199,GSE311199,sda-all,sda-all-v1.3.0,Other,other,Mus musculus,Mouse embryo,spot,32799,48440,counts,VERIFIED,bc84933fb4215ecbc3cc3f42785f5ab6c39f15e2f04dedfaf897c812678f1e6d,um,verified,1.0,False,False,,,,,,,,,,,,,,,GSM9320921,,,train,samples/GSE311199/GSM9320921

catalog/samples.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:91f6f2c965c977332ec38f1dd37f16780507021319525fd5d852739e9831b470
-size 1882036
+oid sha256:891b850e99f1eeb681ed5fe94941655491f89074836bd8b3ac7504568e67c9db
+size 1897080

catalog/schema.json

@@ -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; 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_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); WITHHELD is also used for 9 HESRT samples whose image was removed on 2026-11-11 because the spots do not sit on the tissue (flag image_review_fail)",
   "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

@@ -211,7 +211,7 @@ GSE228516,1,2116,1,Visium,Mus musculus,hesrt,train
 GSE228534,4,4532,4,Visium,Mus musculus,sda-all,test
 GSE228685,1,3584,1,Visium,Homo sapiens,hesrt,train
 GSE228982,4,4583,4,Visium,Homo sapiens,hesrt,train
-GSE229175,4,2010,4,Visium,Ciona intestinalis,hesrt,train
+GSE229175,4,2010,0,Visium,Ciona intestinalis,hesrt,train
 GSE229508,2,2222,2,Visium,Mus musculus,hesrt;sda-all,train
 GSE229635,3,8317,3,Visium,Electrophorus voltai,hesrt,train
 GSE229699,5,6156,5,Visium,Mus musculus,hesrt,train
@@ -688,7 +688,7 @@ GSE288235,3,12882,0,Other,Homo sapiens,sda-all,test
 GSE288365,18,137375,0,Visium,Homo sapiens,sda-all,train
 GSE288483,8,15322,8,Visium,Homo sapiens,hesrt,train
 GSE288576,1,40583,0,Slide-seq,Mus musculus,sda-all,train
-GSE288607,9,36114,9,Visium,Homo sapiens,hesrt,val
+GSE288607,9,36114,8,Visium,Homo sapiens,hesrt,val
 GSE288663,6,38965,6,Xenium,Mus musculus,sda-all,val
 GSE288758,2,107163,2,Visium HD,Homo sapiens,hesrt,train
 GSE288888,2,4228,2,Visium,Homo sapiens,hesrt,train
@@ -760,7 +760,7 @@ GSE294669,13,32083,13,Visium,Homo sapiens,hesrt,test
 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
+GSE294844,5,7856,3,Visium,human skin metagenome,hesrt;sda-all,test
 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
@@ -877,7 +877,7 @@ GSE301696,4,523080,0,MERFISH/MERSCOPE,Mus musculus,sda-all,train
 GSE301720,8,19047,8,Visium,Homo sapiens,hesrt,train
 GSE301973,2,211291,2,Visium HD,Homo sapiens,hesrt,train
 GSE302128,8,542669,8,Xenium,Mus musculus,sda-all,test
-GSE302160,4,16798,4,Visium,Homo sapiens,hesrt;sda-all,val
+GSE302160,4,16798,2,Visium,Homo sapiens,hesrt;sda-all,val
 GSE302187,2,10561,0,Visium,"Staphylococcus aureus
 Mus musculus",sda-all,train
 GSE302264,4,375444,4,Xenium,Homo sapiens,sda-all,train
@@ -982,7 +982,7 @@ GSE310610,12,43435,12,Visium,Homo sapiens,hesrt,train
 GSE310658,2,62005,2,Xenium,Mus musculus,sda-all,train
 GSE310797,3,5499,0,Visium,Homo sapiens,sda-all,train
 GSE310921,8,20256,8,Visium,Homo sapiens;Mus musculus,sda-all,train
-GSE311123,1,4992,1,Visium,Homo sapiens,hesrt,val
+GSE311123,1,4992,0,Visium,Homo sapiens,hesrt,val
 GSE311199,7,89984,0,Other,Homo sapiens;Mus musculus,sda-all,train
 GSE311294,5,21073,5,Visium,Homo sapiens,hesrt,train
 GSE311369,1,14886,1,Xenium,Mus musculus,sda-all,train

catalog/summary.json

@@ -28,9 +28,9 @@
   "test": 1596,
   "val": 1316
  },
- "with_image": 8205,
+ "with_image": 8196,
  "image_stain": {
-  "H&E": 5256,
+  "H&E": 5247,
   "fluorescence: DAPI": 1424,
   "H&E-like (heuristic)": 871,
   "fluorescence: CosMx multichannel composite": 256,
@@ -50,13 +50,13 @@
   "fluorescence: yellow (heuristic)": 1
  },
  "image_registration": {
-  "HESRT_HUMAN_REVIEW": 4368,
+  "HESRT_HUMAN_REVIEW": 4359,
   "VERIFIED": 3473,
   "(none)": 3237,
   "ABSENT": 570,
   "UNRESOLVED": 190,
   "FAILED": 135,
-  "WITHHELD": 98,
+  "WITHHELD": 107,
   "PARTIAL": 75,
   "DEPOSITED_ALIGNMENT_FIT": 10,
   "DEPOSITED_PIXEL_FRAME": 1
@@ -79,6 +79,6 @@
   "unknown": 417,
   "non-integer": 8
  },
- "reviewed": 4084,
+ "reviewed": 4093,
  "qc_flagged": 405
 }

metadata/v2/README.md

@@ -1,6 +1,6 @@
 # SpatialDataAgent-DB sample metadata v2
 
-Schema `sda-sample-metadata-2`, version 2.2.3 (2026-11-11), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples) and reduced to the
+Schema `sda-sample-metadata-2`, version 2.2.4 (2026-11-11), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples) and reduced to the
 12,157 samples that remain after the corrections of 2026-11-11.
 No expression, coordinate or image file changes; v2 is a new metadata table that sits next to the release.
 
@@ -126,6 +126,10 @@ repository:
 
 ## Versions
 
+- **2.2.4** (tag `v1.3.0-20261111` of the main dataset): the image of nine misaligned HESRT samples was removed (GSE229175, four
+  samples; GSE302160, two samples; `GSM8925216`; `GSM8770960`; `GSM9317397`). For these samples `has_image` is False,
+  `image_stain` and `image_um_per_px` are empty, `image_registration` is `WITHHELD`, and `flags` holds
+  `image_review_fail`. No curated annotation changed.
 - **2.2.3** (tag `v1.2.0-20261111` of the main dataset): six withdrawn samples removed (GSE244723, four samples; GSE298115,
   `GSM9008651` and `GSM9008653`); for 12 samples whose files were replaced, the file-derived columns were
   updated. No curated annotation changed. Counts elsewhere in this file describe version 2.2.2 (12,163 samples).

metadata/v2/provenance.json

@@ -57,12 +57,12 @@
   "changes_v2.csv": "9f096e905effabc808c1b5ac142ff8cab3d9a367774ae82757b7406d23e631dc",
   "dropped_disease_terms.csv": "28412ef3f7f7660ea7a85ed46ebcfecec08728dadc549e03510d31a2cce11b80",
   "qa_v2.json": "a8120c035389e56aeb8667358d8df555501e864acb2656d9d9cdba6c63f14775",
-  "samples_metadata_v2.csv": "33ddaf57ea789c7ad9d5d49415978832331d2d7cfd0d80ead747713ed66e596b",
-  "samples_metadata_v2.parquet": "60156a0eede0114ca5160140eb99d02265ea53bc74de2f9a9a3b54b4639761ac",
+  "samples_metadata_v2.csv": "14abf0323606e0246ce6d2cdb63ff4d3b25c7e2daa55b664e79fe9a8ace575f6",
+  "samples_metadata_v2.parquet": "c41e8e9fc5ed172729d08fb881142bdd8f06f70646f6da45132ff870f6aeb598",
   "schema_v2.json": "1c1569b29f9563b84c4c7a22d7acbcc1304476b0d71466e4450a41c212e084cf",
-  "studies_v2.csv": "a333386cf38b83dc974324ca5737de6dc8563d6deffd61e8ad341152f283169d"
+  "studies_v2.csv": "1369bee55ef19aad2bf5d9819fec955331d6c31144174fa19a991e0ee52947aa"
  },
- "version": "2.2.3",
+ "version": "2.2.4",
  "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": {
@@ -84,6 +84,7 @@
  },
  "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": "2.2.3 (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."
+ "version_note": "2.2.4 (2026-11-11): the image of 9 misaligned HESRT samples was removed; no annotation changed (other values = 2.2.3)",
+ "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.",
+ "changes_from_2.2.3": "9 samples (GSE229175 x4, GSE302160 x2, GSM8925216, GSM8770960, GSM9317397): has_image False, image_stain and image_um_per_px empty, image_registration WITHHELD, flag image_review_fail, review_decision FAIL. 12,157 samples and 1,264 studies as before. No other row changed."
 }

metadata/v2/samples_metadata_v2.csv

@@ -2268,10 +2268,10 @@ GSM7146857,other,disease,psoriatic arthritis,synovial joint,primary tissue,Homo
 GSM7146858,other,disease,psoriatic arthritis,synovial joint,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,1368,Molecular reframing of fibroblasts during resolution of arthritis,GSE228982,GSE228982,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002217,synovial joint,MONDO:0011849,luna,psoriatic arthritis,psoriatic arthritis,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,36601,counts,pixel,3.9428570621074104,platform_constant,3.9428570621074104,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38396288,,GSM7146858,,,train,hesrt,samples/GSE228982/GSM7146858,sda-tissue-disease-2.5,"{""organ"": 0.87, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.97, ""life_stage"": 1.0}",,
 GSM7146859,other,normal,,synovial joint,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,927,Molecular reframing of fibroblasts during resolution of arthritis,GSE228982,GSE228982,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002217,synovial joint,,luna,healthy,healthy,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,36601,counts,pixel,3.9428570621074104,platform_constant,3.9428570621074104,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38396288,,GSM7146859,,,train,hesrt,samples/GSE228982/GSM7146859,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.96, ""life_stage"": 1.0}",,
 GSM7146860,other,normal,,synovial joint,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,899,Molecular reframing of fibroblasts during resolution of arthritis,GSE228982,GSE228982,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002217,synovial joint,,luna,healthy,healthy,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,36601,counts,pixel,3.9428570621074104,platform_constant,3.9428570621074104,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,38396288,,GSM7146860,,,train,hesrt,samples/GSE228982/GSM7146860,sda-tissue-disease-2.3,"{""organ"": 0.9, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.97, ""life_stage"": 1.0}",,
-GSM7156292,brain,normal,,,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,True,H&E,492,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.041316950226493,platform_constant,4.041316950226493,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40970208,,GSM7156292,,,train,hesrt,samples/GSE229175/GSM7156292,sda-tissue-disease-2.4,"{""organ"": 0.56, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.22, ""life_stage"": 1.0}",organ;uberon,low_confidence_annotation
-GSM7156293,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,True,H&E,424,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.2855343622607105,platform_constant,4.2855343622607105,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40970208,,GSM7156293,,,train,hesrt,samples/GSE229175/GSM7156293,sda-tissue-disease-2.4,"{""organ"": 0.61, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.37, ""life_stage"": 1.0}",uberon,low_confidence_annotation
-GSM7156294,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,True,H&E,446,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.318580697036812,platform_constant,4.318580697036812,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40970208,,GSM7156294,,,train,hesrt,samples/GSE229175/GSM7156294,sda-tissue-disease-2.4,"{""organ"": 0.62, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.45, ""life_stage"": 1.0}",uberon,low_confidence_annotation
-GSM7156295,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,True,H&E,648,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.252557856758691,platform_constant,4.252557856758691,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40970208,,GSM7156295,,,train,hesrt,samples/GSE229175/GSM7156295,sda-tissue-disease-2.4,"{""organ"": 0.52, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.35000000000000003, ""life_stage"": 1.0}",organ;uberon,low_confidence_annotation
+GSM7156292,brain,normal,,,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,False,,492,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.041316950226493,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,40970208,,GSM7156292,,,train,hesrt,samples/GSE229175/GSM7156292,sda-tissue-disease-2.4,"{""organ"": 0.56, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.22, ""life_stage"": 1.0}",organ;uberon,low_confidence_annotation
+GSM7156293,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,False,,424,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.2855343622607105,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,40970208,,GSM7156293,,,train,hesrt,samples/GSE229175/GSM7156293,sda-tissue-disease-2.4,"{""organ"": 0.61, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.37, ""life_stage"": 1.0}",uberon,low_confidence_annotation
+GSM7156294,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,False,,446,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.318580697036812,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,40970208,,GSM7156294,,,train,hesrt,samples/GSE229175/GSM7156294,sda-tissue-disease-2.4,"{""organ"": 0.62, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.45, ""life_stage"": 1.0}",uberon,low_confidence_annotation
+GSM7156295,brain,normal,,central nervous system,primary tissue,Ciona intestinalis,vase tunicate,adult,unknown,Visium,Visium,False,,648,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,GSE229175,GSE229175,7719,Ciona intestinalis,7719,,False,False,GEO organism field,Ciona intestinalis,,luna,UBERON:0001017,neural complex,,luna,,WT,luna,adult,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18788,counts,pixel,4.252557856758691,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the whole block of spots is shifted down and to the right of the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,40970208,,GSM7156295,,,train,hesrt,samples/GSE229175/GSM7156295,sda-tissue-disease-2.4,"{""organ"": 0.52, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.35000000000000003, ""life_stage"": 1.0}",organ;uberon,low_confidence_annotation
 GSM7164655,brain,normal,,forebrain,primary tissue,Mus musculus,house mouse,embryonic,unknown,Visium,Visium,True,H&E,979,Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum,GSE229508,GSE229508,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001890,forebrain,,luna,,,luna,embryonic,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,32285,counts,pixel,4.339849705475763,platform_constant,4.339849705475763,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40210990,,GSM7164655,,,train,hesrt,samples/GSE229508/GSM7164655,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM7164656,brain,normal,,forebrain,primary tissue,Mus musculus,house mouse,neonatal or infant,unknown,Visium,Visium,True,H&E-like (heuristic),1243,Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum,GSE229508,GSE229508,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001890,Forebrain,,luna,,WT,luna,neonatal or infant,,not stated,,,,,,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,4.3425740514866735,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,40210990,,GSM7164656,,,train,sda-all,samples/GSE229508/GSM7164656,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM7169587,skeletal muscle,normal,,electric organ,primary tissue,Electrophorus voltai,,not stated,unknown,Visium,Visium,True,H&E,2677,Spatial transcriptome of muscle sample from the main electric organ of electric eel,GSE229635,GSE229635,2609070,Electrophorus voltai,2609070,,False,False,GEO organism field,Electrophorus voltai,,luna,UBERON:0006869,the main electric organ,,luna,,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,23221,counts,pixel,4.989781254820793,platform_constant,4.989781254820793,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM7169587,,,train,hesrt,samples/GSE229635/GSM7169587,sda-tissue-disease-2.4,"{""organ"": 0.55, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.98, ""life_stage"": 1.0}",organ,low_confidence_annotation
@@ -6681,7 +6681,7 @@ GSM8770956,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,h
 GSM8770957,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,3923,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,4.266666754047988,platform_constant,4.266666754047988,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8770957,,,val,hesrt,samples/GSE288607/GSM8770957,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8770958,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,3332,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,4.117466871137884,platform_constant,4.117466871137884,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8770958,,,val,hesrt,samples/GSE288607/GSM8770958,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8770959,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,2285,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,1.1903918403013953,platform_constant,1.1903918403013953,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8770959,,,val,hesrt,samples/GSE288607/GSM8770959,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM8770960,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,4992,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,0.5473313553908552,platform_constant,0.5473313553908552,HESRT_HUMAN_REVIEW,,,image_partial_coverage,,human_visual_review,,,,,,GSM8770960,,,val,hesrt,samples/GSE288607/GSM8770960,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 1.0}",,
+GSM8770960,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,False,,4992,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,0.5473313553908552,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: only 31% of the spots fall inside the image; the spot grid is about three times larger than the image. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,,,GSM8770960,,,val,hesrt,samples/GSE288607/GSM8770960,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8770961,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,3043,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,0.502487185955009,platform_constant,0.502487185955009,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8770961,,,val,hesrt,samples/GSE288607/GSM8770961,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8770962,lung,disease,pulmonary sarcoidosis,lung,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,4112,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,GSE288607,GSE288607,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002048,lung,MONDO:0001708,luna,sarcoidosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,37082,counts,pixel,0.5024554702869775,platform_constant,0.5024554702869775,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8770962,,,val,hesrt,samples/GSE288607/GSM8770962,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8772705,skeletal muscle,normal,,muscle of abdomen,primary tissue,Mus musculus,house mouse,not stated,unknown,Xenium,Xenium,True,fluorescence: DAPI,7797,Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis [Hernia_Xenium],GSE288663,GSE288663,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0002378,Lower abdominal muscle,,luna,,Vehicle,luna,not stated,,not stated,,,,,,release v3,imaging-based,Xenium,,,cell,5060,counts,um,1.0,verified,0.499979353773098,VERIFIED,ABSENT,VERIFIED,,,VERIFIED,PASS,,,40504614,,GSM8772705,,,val,sda-all,samples/GSE288663/GSM8772705,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.41000000000000003, ""uberon"": 0.78, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
@@ -7216,7 +7216,7 @@ GSM8921749,colon,normal,,colon,primary tissue,Mus musculus,house mouse,not state
 GSM8921750,small intestine,normal,,intestine,primary tissue,Mus musculus,house mouse,not stated,unknown,DBiT-seq,microDBiT,False,,2500,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,GSE294814,GSE294814,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0000160,intestine,,luna,,No treatment,luna,not stated,,not stated,,,,,,release v3,sequencing-based,microDBiT,,,spot,28198,unknown,native_grid,,unresolved,,,,,,,VERIFIED,,,,,,GSM8921750,,,val,sda-all,samples/GSE294814/GSM8921750,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 1.0, ""disease_status"": 0.92, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM8921752,colon,normal,,colon,primary tissue,Mus musculus,house mouse,not stated,unknown,DBiT-seq,microDBiT,False,,2498,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,GSE294814,GSE294814,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001155,colon,,luna,,No treatment,luna,not stated,,not stated,,,,,,release v3,sequencing-based,microDBiT,,,spot,35188,unknown,native_grid,,unresolved,,,,,,,VERIFIED,,,,,,GSM8921752,,,val,sda-all,samples/GSE294814/GSM8921752,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.85, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8921753,colon,normal,,colon,primary tissue,Mus musculus,house mouse,not stated,unknown,DBiT-seq,microDBiT,False,,2493,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,GSE294814,GSE294814,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,luna,UBERON:0001155,colon,,luna,,No treatment,luna,not stated,,not stated,,,,,,release v3,sequencing-based,microDBiT,,,spot,44662,unknown,native_grid,,unresolved,,,,,,,VERIFIED,,,,,,GSM8921753,,,val,sda-all,samples/GSE294814/GSM8921753,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.61, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM8925216,skin,disease,actinic keratosis,zone of skin,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium CytAssist,True,H&E,1435,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,GSE294844,GSE294844,9606,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,luna,UBERON:0000014,skin,MONDO:0005173,manual,actinic keratosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,18085,counts,pixel,4.761904761904762,platform_constant,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925216,,,test,hesrt,samples/GSE294844/GSM8925216,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.67, ""life_stage"": 1.0}",,
+GSM8925216,skin,disease,actinic keratosis,zone of skin,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium CytAssist,False,,1435,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,GSE294844,GSE294844,9606,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,luna,UBERON:0000014,skin,MONDO:0005173,manual,actinic keratosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,18085,counts,pixel,4.761904761904762,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,"Image registration screen 2026-11-11: the tissue forms two horizontal strips, but the spots form two vertical strips. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.",,,GSM8925216,,,test,hesrt,samples/GSE294844/GSM8925216,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.67, ""life_stage"": 1.0}",,
 GSM8925217,skin,disease,actinic keratosis,zone of skin,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,False,,1505,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,GSE294844,GSE294844,9606,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,luna,UBERON:0000014,skin,MONDO:0005173,manual,,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,Visium,,,spot,18085,counts,um,1.0,verified,,WITHHELD,,,hesrt_review_fail,,VERIFIED,,,,,,GSM8925217,,,test,sda-all,samples/GSE294844/GSM8925217,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.49, ""life_stage"": 1.0}",uberon,low_confidence_annotation
 GSM8925218,skin,disease,actinic keratosis,zone of skin,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium CytAssist,True,H&E,1706,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,GSE294844,GSE294844,9606,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,luna,UBERON:0000014,skin,MONDO:0005173,manual,actinic keratosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,18085,counts,pixel,4.761904761904762,platform_constant,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925218,,,test,hesrt,samples/GSE294844/GSM8925218,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.5700000000000001, ""life_stage"": 0.99}",uberon,low_confidence_annotation
 GSM8925219,skin,disease,actinic keratosis,zone of skin,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium CytAssist,True,H&E,921,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,GSE294844,GSE294844,9606,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,luna,UBERON:0000014,skin,MONDO:0005173,manual,actinic keratosis,,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,18085,counts,pixel,4.761904761904762,platform_constant,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925219,,,test,hesrt,samples/GSE294844/GSM8925219,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.54, ""life_stage"": 1.0}",uberon,low_confidence_annotation
@@ -8025,9 +8025,9 @@ GSM9096730,oral cavity,disease,neoplasm of neck,tongue,tumour tissue,Mus musculu
 GSM9096731,oral cavity,disease,neoplasm of neck,tongue,tumour tissue,Mus musculus,house mouse,not stated,female,Xenium,Xenium,True,fluorescence: DAPI,52889,Xenium Spatial Transcriptomics of Cisplatin-Resistant Head and Neck Tumors in Humanized Mice Treated with PI3K Inhibitor Gedatolisib,GSE302128,GSE302128,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Homo sapiens,luna,UBERON:0001723,tongue,MONDO:0021351,luna,,Gedatolisib,luna,not stated,,extracted field,Female,GSE302128:734,734,,,release v3,imaging-based,Xenium,,,cell,9880,counts,um,1.0,verified,0.4999873806901616,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,41053162,,GSM9096731,,,test,sda-all,samples/GSE302128/GSM9096731,sda-tissue-disease-2.3,"{""organ"": 0.9500000000000001, ""sample_kind"": 0.63, ""disease_status"": 0.99, ""uberon"": 0.6900000000000001, ""life_stage"": 1.0}",,feature_species_differs
 GSM9096732,oral cavity,disease,neoplasm of neck,tongue,tumour tissue,Mus musculus,house mouse,not stated,female,Xenium,Xenium,True,fluorescence: DAPI,50212,Xenium Spatial Transcriptomics of Cisplatin-Resistant Head and Neck Tumors in Humanized Mice Treated with PI3K Inhibitor Gedatolisib,GSE302128,GSE302128,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Homo sapiens,luna,UBERON:0001723,tongue,MONDO:0021351,luna,,Gedatolisib,luna,not stated,,extracted field,Female,GSE302128:735,735,,,release v3,imaging-based,Xenium,,,cell,9880,counts,um,1.0,verified,0.49998323878287776,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,41053162,,GSM9096732,,,test,sda-all,samples/GSE302128/GSM9096732,sda-tissue-disease-2.3,"{""organ"": 0.88, ""sample_kind"": 0.61, ""disease_status"": 0.99, ""uberon"": 0.9400000000000001, ""life_stage"": 1.0}",,feature_species_differs
 GSM9096733,oral cavity,disease,neoplasm of neck,tongue,tumour tissue,Mus musculus,house mouse,not stated,female,Xenium,Xenium,True,fluorescence: DAPI,75178,Xenium Spatial Transcriptomics of Cisplatin-Resistant Head and Neck Tumors in Humanized Mice Treated with PI3K Inhibitor Gedatolisib,GSE302128,GSE302128,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Homo sapiens,luna,UBERON:0001723,tongue,MONDO:0021351,luna,,Gedatolisib,luna,not stated,,extracted field,Female,GSE302128:737,737,,,release v3,imaging-based,Xenium,,,cell,9880,counts,um,1.0,verified,0.5000325922876355,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,41053162,,GSM9096733,,,test,sda-all,samples/GSE302128/GSM9096733,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 0.8200000000000001, ""disease_status"": 0.96, ""uberon"": 0.9500000000000001, ""life_stage"": 1.0}",,feature_species_differs
-GSM9097318,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,4763,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (low seeder),low seeder,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,3.037184984800885,platform_constant,3.037184984800885,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41476155,,GSM9097318,,,val,hesrt,samples/GSE302160/GSM9097318,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.99, ""life_stage"": 1.0}",,
+GSM9097318,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,False,,4763,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (low seeder),low seeder,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,3.037184984800885,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the spot grid is shifted and extends onto bare glass. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,41476155,,GSM9097318,,,val,hesrt,samples/GSE302160/GSM9097318,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9097319,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,fluorescence: blue (heuristic),3837,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (low seeder),,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,18085,counts,um,1.0,verified,4.545880211325501,VERIFIED,ABSENT,ABSENT,hesrt_review_fail;hesrt_fail_image_released,,VERIFIED,PASS,,,41476155,,GSM9097319,,,val,sda-all,samples/GSE302160/GSM9097319,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.99, ""life_stage"": 1.0}",,
-GSM9097320,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,4690,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (high seeder),high seeder,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,3.03578646514248,platform_constant,3.03578646514248,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41476155,,GSM9097320,,,val,hesrt,samples/GSE302160/GSM9097320,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 0.99}",,
+GSM9097320,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,False,,4690,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (high seeder),high seeder,luna,not stated,,not stated,,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,3.03578646514248,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the spot grid is shifted and extends onto bare glass. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,41476155,,GSM9097320,,,val,hesrt,samples/GSE302160/GSM9097320,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 0.99}",,
 GSM9097321,brain,disease,"supranuclear palsy, progressive, 1;palsy",primary motor cortex,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,fluorescence: blue (heuristic),3508,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,GSE302160,GSE302160,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0001384,brain:primary motor cortex,MONDO:0010997;MONDO:0006496,luna,PSP (high seeder),,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,18085,counts,um,1.0,verified,5.450765988787993,VERIFIED,ABSENT,ABSENT,hesrt_review_fail;hesrt_fail_image_released,,VERIFIED,PASS,,,41476155,,GSM9097321,,,val,sda-all,samples/GSE302160/GSM9097321,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9098123,kidney,disease,pyelonephritis,kidney,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,False,,5223,Murine model of MRSA-induced kidney injury (spatial transcriptomics),GSE302187,GSE302187,10090,Mus musculus,10090,Staphylococcus aureus,False,False,GEO organism field,"Staphylococcus aureus
 Mus musculus",,luna,UBERON:0002113,kidney,MONDO:0006939,luna,,MRSA_day2_and_day4,luna,not stated,,not stated,,,,FFPE,FFPE,release v3,sequencing-based,Visium,,,spot,19812,counts,um,1.0,declared_unverified,,,,,attested,,ATTESTED,,,,,,GSM9098123,,,train,sda-all,samples/GSE302187/GSM9098123,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 0.99, ""life_stage"": 0.9400000000000001}",,
@@ -9180,7 +9180,7 @@ GSM9312237,skeletal muscle,perturbation,,quadriceps femoris,primary tissue,Mus m
 GSM9312238,skeletal muscle,perturbation,,quadriceps femoris,primary tissue,Mus musculus,house mouse,not stated,unknown,Visium,Visium,True,H&E,2684,Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses,GSE310921,GSE310921,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0001377,Quadriceps Muscle,,luna,,Postmortem 48hr,luna,not stated,,not stated,,,,fresh frozen,Fresh Frozen,release v3,sequencing-based,Visium,,,spot,32285,counts,um,1.0,verified,3.971653797229367,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9312238,,,train,sda-all,samples/GSE310921/GSM9312238,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.35000000000000003, ""uberon"": 0.8300000000000001, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
 GSM9312239,skeletal muscle,perturbation,,pectoralis major,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,2168,Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses,GSE310921,GSE310921,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002381,Pectoralis Major,,luna,,Transplant Solution 24hr,luna,not stated,,not stated,,,,fresh frozen,Fresh Frozen,release v3,sequencing-based,Visium,,,spot,36601,counts,um,1.0,verified,4.179825593540337,UNRESOLVED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9312239,,,train,sda-all,samples/GSE310921/GSM9312239,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.44, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM9312240,skeletal muscle,perturbation,,pectoralis major,primary tissue,Homo sapiens,human,not stated,unknown,Visium,Visium,True,H&E,1939,Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses,GSE310921,GSE310921,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0002381,Pectoralis Major,,luna,,Transplant Solution 24hr,luna,not stated,,not stated,,,,fresh frozen,Fresh Frozen,release v3,sequencing-based,Visium,,,spot,36601,counts,um,1.0,verified,4.218754565904826,FAILED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9312240,,,train,sda-all,samples/GSE310921/GSM9312240,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.75, ""uberon"": 0.99, ""life_stage"": 1.0}",,
-GSM9317397,bone,disease,bone giant cell tumor;giant cell tumor,femur,tumour tissue,Homo sapiens,human,not stated,male,Visium,Visium,True,H&E,4992,Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone,GSE311123,GSE311123,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0000981,Distal femur,MONDO:0005674;MONDO:0002171,luna,Giant Cell Tumor of Bone,surgical curettage,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,8.883456876836373,platform_constant,8.883456876836373,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41872383,,GSM9317397,,,val,hesrt,samples/GSE311123/GSM9317397,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.9400000000000001, ""disease_status"": 1.0, ""uberon"": 0.72, ""life_stage"": 1.0}",,
+GSM9317397,bone,disease,bone giant cell tumor;giant cell tumor,femur,tumour tissue,Homo sapiens,human,not stated,male,Visium,Visium,False,,4992,Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone,GSE311123,GSE311123,9606,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,luna,UBERON:0000981,Distal femur,MONDO:0005674;MONDO:0002171,luna,Giant Cell Tumor of Bone,surgical curettage,luna,not stated,,extracted field,male,,,,,release v3,sequencing-based,10x Genomics Visium,,,spot,18085,counts,pixel,8.883456876836373,platform_constant,,WITHHELD,,,image_review_fail,,human_visual_review,FAIL,图像与细胞/spot 错位,Image registration screen 2026-11-11: the author judged on the review page that the spots do not match the tissue. The image was removed on 2026-11-11. Expression values and coordinates equal the GEO deposit.,41872383,,GSM9317397,,,val,hesrt,samples/GSE311123/GSM9317397,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.9400000000000001, ""disease_status"": 1.0, ""uberon"": 0.72, ""life_stage"": 1.0}",,
 GSM9320917,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,unknown,DBiT-seq,DBiT-seq,False,,6275,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,GSE311199,GSE311199,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000955,Mouse brain,,luna,,,luna,not stated,,not stated,,,,,,GEO series text (assay_final.csv),sequencing-based,other,,,spot,48440,counts,um,1.0,verified,,,,,,,VERIFIED,,,,42641604,,GSM9320917,,,train,sda-all,samples/GSE311199/GSM9320917,sda-tissue-disease-2.3,"{""organ"": 0.99, ""sample_kind"": 1.0, ""disease_status"": 0.52, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM9320919,brain,normal,,brain,primary tissue,Mus musculus,house mouse,not stated,unknown,DBiT-seq,DBiT-seq,False,,6199,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,GSE311199,GSE311199,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000955,Mouse brain,,luna,,,luna,not stated,,not stated,,,,,,GEO series text (assay_final.csv),sequencing-based,other,,,spot,48440,counts,um,1.0,verified,,,,,,,VERIFIED,,,,42641604,,GSM9320919,,,train,sda-all,samples/GSE311199/GSM9320919,sda-tissue-disease-2.3,"{""organ"": 0.98, ""sample_kind"": 1.0, ""disease_status"": 0.87, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9320921,embryo (whole),normal,,embryo,primary tissue,Mus musculus,house mouse,embryonic,unknown,DBiT-seq,DBiT-seq,False,,32799,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,GSE311199,GSE311199,10090,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,luna,UBERON:0000922,Mouse embryo,,luna,,,luna,embryonic,,not stated,,,,,,GEO series text (assay_final.csv),sequencing-based,other,,,spot,48440,counts,um,1.0,verified,,,,,,,VERIFIED,,,,42641604,,GSM9320921,,,train,sda-all,samples/GSE311199/GSM9320921,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.56, ""disease_status"": 0.99, ""uberon"": 1.0, ""life_stage"": 1.0}",sample_kind,low_confidence_annotation

metadata/v2/samples_metadata_v2.parquet

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metadata/v2/studies_v2.csv

@@ -210,7 +210,7 @@ GSE228516,Aristolochic Acid Nephropathy 2 week time point of CD45+ cells,1,Mus m
 GSE228534,Spatial transcriptomic profiling reveals local and domain-establishing regulatory signaling networks within the bone marrow,4,Mus musculus,Visium,Visium,bone,,normal,4,37926705,test
 GSE228685,Spatial transcriptomics of adenoid cystic carcinoma of the lacrimal gland,1,Homo sapiens,Visium,Visium,eye,lacrimal gland carcinoma;adenoid cystic carcinoma,disease,1,37370820,train
 GSE228982,Molecular reframing of fibroblasts during resolution of arthritis,4,Homo sapiens,Visium,Visium,other,psoriatic arthritis,disease;normal,4,38396288,train
-GSE229175,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,4,Ciona intestinalis,Visium,Visium,brain,,normal,4,40970208,train
+GSE229175,Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A,4,Ciona intestinalis,Visium,Visium,brain,,normal,0,40970208,train
 GSE229508,Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum,2,Mus musculus,Visium,Visium,brain,,normal,2,40210990,train
 GSE229635,Spatial transcriptome of muscle sample from the main electric organ of electric eel,3,Electrophorus voltai,Visium,Visium,skeletal muscle,,normal,3,,train
 GSE229699,"Bacterial TLR2/6 Ligands Block Ciliogenesis, Derepress Hedgehog Signaling, and Expand the Neocortex",5,Mus musculus,Visium,Visium,brain,pneumonia,normal;disease,5,37052506,train
@@ -680,7 +680,7 @@ GSE288235,"Clonal cell states link gastroesophageal junction tissues, metaplasia
 GSE288365,Molecular Drivers of Neuroinflammation in Amyotrophic Lateral Sclerosis,18,Homo sapiens,Visium,Visium,spinal cord,amyotrophic lateral sclerosis;lateral sclerosis;hereditary motor neuron disease,disease,0,42135512,train
 GSE288483,Spatial transcriptomics for high-grade serous ovarian carcinoma who were treated with Olaparib maintenance therapy,8,Homo sapiens,Visium,Visium,peritoneum;other;ovary,ovarian carcinoma,disease,8,41219363,train
 GSE288576,Effect of Pdk4 smooth muscle cell-specific knockout on atherosclerosis,1,Mus musculus,Slide-seq,Slide-seq,blood vessel,atherosclerosis,disease,0,,train
-GSE288607,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,9,Homo sapiens,Visium,Visium,lung,pulmonary sarcoidosis,disease,9,,val
+GSE288607,Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients,9,Homo sapiens,Visium,Visium,lung,pulmonary sarcoidosis,disease,8,,val
 GSE288663,Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis [Hernia_Xenium],6,Mus musculus,Xenium,Xenium,skeletal muscle,,normal;perturbation,6,40504614,val
 GSE288758,Spatial dynamics of the tumor microenvironment associated with emerging resistance to targeted therapy in EGFR-mutated non–small cell lung cancer,2,Homo sapiens,Visium HD,Visium HD,lung,non-small cell lung carcinoma,disease,2,41152910,train
 GSE288888,"Spatial Transcriptomics, Histopathology, and Magnetic Resonance Subfield Segmentation of Hippocampal Sclerosis Compared to Normal Hippocampus: A Proof-of-Concept Study",2,Homo sapiens,Visium,Visium,brain,temporal lobe epilepsy,normal;disease,2,,train
@@ -752,7 +752,7 @@ GSE294669,Spatial Proteomics and Transcriptomics Reveal Early Immune Cell Organi
 GSE294759,Application of spatial transcriptomics across organoids for a high-resolution spatial whole-transcriptome benchmarking dataset,9,Mus musculus;Homo sapiens,Stereo-seq,Stereo-seq,head and neck;heart;brain;cartilage;lung;other;kidney,,normal,0,42164865,train
 GSE294765,A skeletal muscle atlas shows neuromuscular junction adaptations to growth and atrophy,6,Mus musculus,Visium,Visium,skeletal muscle,,perturbation;normal,6,42019489,train
 GSE294814,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,7,Mus musculus,DBiT-seq,microDBiT,colon;small intestine,,normal,0,,val
-GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,5,Homo sapiens,Visium,Visium CytAssist;Visium,skin,actinic keratosis,disease,4,,test
+GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,5,Homo sapiens,Visium,Visium CytAssist;Visium,skin,actinic keratosis,disease,3,,test
 GSE294965,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,9,Homo sapiens,Xenium,Xenium,kidney,kidney disorder,disease,9,40393992,train
 GSE295043,A spatiotemporal atlas of orchiectomy-induced modulation of cellular composition and gene expression in the mouse prostate,8,Mus musculus,Visium,Visium,prostate,,perturbation,8,40974890,train
 GSE295060,Gain-of-function PPM1D mutations attenuate ischemic stroke,2,Mus musculus,Visium,Visium,brain,cerebral artery occlusion;ischemic stroke,disease,2,,train
@@ -869,7 +869,7 @@ GSE301696,Single-cell spatial transcriptomic profiling defines a pathogenic infl
 GSE301720,Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response,8,Homo sapiens,Visium,Visium,head and neck;airway;oral cavity,malignant tumor of neck,disease,8,41837744,train
 GSE301973,The spatial transcriptomics of EGFR-mutant non-small cell lung cancer before osimertinib treatment,2,Homo sapiens,Visium HD,Visium HD,lung,non-small cell lung carcinoma,disease,2,41152910,train
 GSE302128,Xenium Spatial Transcriptomics of Cisplatin-Resistant Head and Neck Tumors in Humanized Mice Treated with PI3K Inhibitor Gedatolisib,8,Mus musculus,Xenium,Xenium,oral cavity,neoplasm of neck,disease,8,41053162,test
-GSE302160,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,4,Homo sapiens,Visium,Visium,brain,"supranuclear palsy, progressive, 1;palsy",disease,4,41476155,val
+GSE302160,4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy,4,Homo sapiens,Visium,Visium,brain,"supranuclear palsy, progressive, 1;palsy",disease,2,41476155,val
 GSE302187,Murine model of MRSA-induced kidney injury (spatial transcriptomics),2,Mus musculus,Visium,Visium,kidney,pyelonephritis,disease,0,,train
 GSE302264,PHLOWER - Single cell trajectory analysis using Decomposition of the Hodge Laplacian [Xenium],4,Homo sapiens,Xenium,Xenium,kidney,,normal;perturbation,4,,train
 GSE302356,Decoding Lymphangioleiomyomatosis (LAM) Niche Environment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics,3,Homo sapiens,Visium HD;Xenium;Visium,Visium HD;Xenium;Visium,lung,lymphangioleiomyomatosis,disease,3,,test
@@ -973,7 +973,7 @@ GSE310610,Spatial Transcriptomics of Human Fetal Lungs,12,Homo sapiens,Visium,Vi
 GSE310658,Xenium In Situ analysis of mouse skin mock-treated or treated with SspA and HDM,2,Mus musculus,Xenium,Xenium,skin,,normal;perturbation,2,,train
 GSE310797,Single cell and Spatial RNA-seq in Oral Squamous Cell Carcinoma with Different Stage,3,Homo sapiens,Visium,Visium,oral cavity,oral cavity squamous cell carcinoma,disease,0,41851114,train
 GSE310921,Use of Organ Transplant Solution to Preserve Skeletal Muscle for Cellular and Spatial Transcriptomic Analyses,8,Mus musculus;Homo sapiens,Visium,Visium,skeletal muscle,,normal;perturbation,8,,train
-GSE311123,Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone,1,Homo sapiens,Visium,Visium,bone,bone giant cell tumor;giant cell tumor,disease,1,41872383,val
+GSE311123,Spatial analysis revealed localization of osteblastogenesis-inhibitory factors in Giant Cell Tumor of Bone,1,Homo sapiens,Visium,Visium,bone,bone giant cell tumor;giant cell tumor,disease,0,41872383,val
 GSE311199,Integrative spatial profiling of 3D genome organization and gene expression in complex tissue,7,Mus musculus;Homo sapiens,DBiT-seq,DBiT-seq,brain;embryo (whole);skin,melanoma,normal;disease,0,42641604,train
 GSE311294,Collagen Alignment and Spatial Transcriptomics Analysis (CASTA) reveals gene programs associated with collagen alignmet in colorectal cancer,5,Homo sapiens,Visium,Visium,colon,colorectal cancer,disease,5,,train
 GSE311369,A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [RGC_CrossSection],1,Mus musculus,Xenium,Xenium,eye,,normal,1,41452983,train