Card: corrections of 2026-11-11 (12 samples replaced, 6 withdrawn), current counts, metadata v2.2.3

README.md

@@ -20,17 +20,18 @@ 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 12,163 public spatial transcriptomics samples before you request any data. They come from 1,265 published
-GEO series and hold 635,240,170 spatial observations (spots, bins, cells or beads). 8,211 samples have a released
-tissue image: 5,263 H&E, 871 H&E-like (a pixel-based call that no reviewer confirmed), 1,423 DAPI, 427 other fluorescence and 227 other or
+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
 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 (7,777 samples, each checked by an independent scorer) and by the earlier HESRT H&E collection (4,386
-samples, each reviewed by eye). The atlas is described in the
+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 On 2026-11-11, 12 samples were replaced and 6 were withdrawn after a check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
 [bioRxiv preprint](https://doi.org/10.64898/2026.05.27.727615).
 
-This repository needs **no account**. It holds the catalog of all 12,163 samples and the complete files of 88
+This repository needs **no account**. It holds the catalog of all 12,157 samples and the complete files of 86
 starter samples (below). The files of every sample are in the
 [full dataset](https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB), about 1.8 TB, where access is
 approved manually.
@@ -39,13 +40,13 @@ approved manually.
 
 ![24 of the starter pack's samples with a tissue image](assets/dataset-card/v3/08-starter-gallery.png)
 
-88 samples of the release are in this repository and need **no login**. Each has the full three files:
-`spatial.h5ad`, `sample.json` and, for 60 of them, `image.tif`. The pack covers:
+86 samples of the release are in this repository and need **no login**. Each has the full three files:
+`spatial.h5ad`, `sample.json` and, for 58 of them, `image.tif`. The pack covers:
 
 - 12 platforms, 20 organ groups and 8 species;
-- 46 H&E images (8 at cell resolution, ≤ 1 µm per pixel) and 14 DAPI or CosMx images;
-- 41 samples with a reported disease and 79 from published studies;
-- 4.5 GB in total.
+- 43 H&E images (8 at cell resolution, ≤ 1 µm per pixel) and 15 DAPI or CosMx images;
+- 41 samples with a reported disease and 77 from published studies;
+- 5.1 GB in total.
 
 The files are byte-identical to the full dataset, and each is checked against its SHA256 when downloaded.
 `starter/starter.json` lists the samples.
@@ -68,7 +69,7 @@ From R, or any tool, download a starter sample's files directly, for example
 `https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB-Catalog/resolve/main/samples/GSE223559/GSM6963121/spatial.h5ad`
 (also `sample.json` and `image.tif`), and read the H5AD with `zellkonverter::readH5AD`.
 
-**All 12,163 samples.** Every file of the release has passed content verification. To download any sample:
+**All 12,157 samples.** Every file of the release has passed content verification. To download any sample:
 
 1. Request access on the [full dataset page](https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB) with
    your Hugging Face account and an institutional e-mail; requests are reviewed manually.
@@ -203,7 +204,7 @@ Source index SHA256: `909c4ec50e71c636eadc7bf01a9479fef1b4fd480ac348dfea6b785e56
 
 ![Sample counts by platform, image availability, source collection and split](assets/dataset-card/v2/02-composition.png)
 
-*Sample counts by platform, image availability, source collection and retained split (n = 12,163; source snapshot: sda-unified-20261010-v3).*
+*Sample counts by platform, image availability, source collection and retained split (n = 12,163, the paper release; source snapshot: sda-unified-20261010-v3).*
 
 ## Images and resolution
 
@@ -251,12 +252,43 @@ catalog has no per-sample license column. See the
 reuse terms and citation, and cite the original studies with the data you use (`sda-db cite` writes BibTeX for
 a selection).
 
-## Curated sample metadata v2 (version 2.2.2, 2026-11-08)
+## Corrections 2026-11-11
 
-`metadata/v2/` adds a curated table on top of the same 12,163 samples. No data file changed: the paper release is
-still tag `v1.0.0-20261025`; the current metadata is tag `metadata-v2.2.2-20261108` (2.2.2 only moves the most-used columns
-to the front: organ, disease status and terms, tissue term, sample kind, organism, life stage, sex, platform; no value
-changed).
+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.
+
+**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.
+
+| Study | Samples | What was wrong | What changed |
+| --- | --- | --- | --- |
+| GSE205707 | `GSM6896311` to `GSM6896316` | The counts and gene names were generated by the conversion script. They were not read from the deposit. | New expression matrix from the deposited counts (32,285 genes for the two mouse samples and 32,704 for the four dog samples; more spots than before). Image unchanged. |
+| GSE275125 | `GSM8465980` to `GSM8465983` | The counts and gene names were generated by the conversion script. They were not read from the deposit. | New expression matrix from the deposited counts. Image unchanged. |
+| GSE294965 | `GSM8933093` | The cell positions were drawn at random. The image was a low-resolution copy that was labelled H&E. | Cell positions from the deposit, and the full-resolution DAPI image (0.5 µm per pixel). |
+| GSE186290 | `GSM5643203` | The expression rows were in a different order from the spots, so each spot carried the counts of another spot. The spot positions were right. | Each spot now has its own expression row. Image unchanged. |
+
+For these 12 samples the catalog (`catalog/samples.parquet`) now gives coordinates in micrometres (`coordinate_units = um`) and names the new conversion in `source_pipeline` and `source_release`. Two new values appear in `image_registration`: `DEPOSITED_ALIGNMENT_FIT` (the spot-to-image transform was fitted from the deposited alignment file) and `DEPOSITED_PIXEL_FRAME` (the deposited positions are already in image pixels).
+
+**Withdrawn (6 samples).** Their folders are removed from `main`. A note for each is in `review-revocations/` of the main dataset.
+
+| Study | Samples | Reason |
+| --- | --- | --- |
+| GSE298115 | `GSM9008651`, `GSM9008653` | The expression rows were in the wrong order. A corrected conversion has the right values, but the spots do not sit on the tissue in the image, because the deposit has no scale-factor file. It did not pass review. The other four samples of this study stay. |
+| GSE244723 | `GSM7825036` to `GSM7825039` | The deposited count tables have no gene names. The values were equal to the deposit, but the samples cannot be used for any analysis by gene. The whole study is withdrawn. |
+
+**Counts.** The paper release had 12,163 samples in 1,265 study folders. The current data has 12,157 samples in 1,264 study folders. The no-login starter pack has 86 samples (was 88): `GSM7825036` and `GSM7825037` are removed, and `GSM8933093` is replaced.
+
+**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.
+
+**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"`.
+
+## Curated sample metadata v2 (version 2.2.3, 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
+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.
 
 In the Dataset Viewer, `metadata_v2` (the default) shows this table and `samples` shows the catalog
 (`catalog/samples.parquet`).

metadata/v2/README.md

@@ -1,6 +1,7 @@
 # SpatialDataAgent-DB sample metadata v2
 
-Schema `sda-sample-metadata-2`, version 2.2.2 (2026-11-08), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
+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
+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.
 
 ## Files
@@ -9,7 +10,7 @@ No expression, coordinate or image file changes; v2 is a new metadata table that
 |---|---|
 | `samples_metadata_v2.parquet` | one row per sample, list columns kept as lists (recommended) |
 | `samples_metadata_v2.csv` | the same table; lists joined with `;`, confidence as JSON |
-| `studies_v2.csv` | one row per study (1,265): title, species, platforms, assays, organs, diseases, PubMed IDs, split |
+| `studies_v2.csv` | one row per study (1,264): title, species, platforms, assays, organs, diseases, PubMed IDs, split |
 | `schema_v2.json` | definition of every column |
 | `changes_v2.csv` | every value that differs from a v3 column, with its basis (204 platform changes, 32 manual corrections in 14 samples) |
 | `dropped_disease_terms.csv` | disease terms removed by the short-synonym filter (331) |
@@ -125,6 +126,9 @@ repository:
 
 ## Versions
 
+- **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).
 - **2.2.2** (tag `metadata-v2.2.2-20261108`): column order only. The columns users look for first lead the table
   (gsm, organ, disease_status, disease_ontology_names, tissue_ontology_name, sample_kind, organism,
   organism_common_name, life_stage, sex, platform, assay_name, has_image, image_stain, n_obs, study_title,