Dataset card: illustrated walkthrough (organ coverage, example samples, images, sample size)

Five new figures drawn from the v1.0.0-20261025 catalog and two downloaded samples (numbers in assets/dataset-card/v3/facts.json). No data files changed.

README.md

@@ -19,8 +19,8 @@ configs:
 
 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), 1,850 fluorescence (mostly DAPI) and 227 other
-stains. Platforms include Visium, Xenium, legacy ST, CosMx, MERFISH/MERSCOPE, Slide-seq, Stereo-seq and Visium HD.
+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
+bright-field 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
@@ -37,8 +37,12 @@ per-sample JSON are in the [full dataset](https://huggingface.co/datasets/Biogod
 
 ## Is my tissue here?
 
-Samples whose GEO tissue text matches each organ. The counts are approximate, because tissue labels are free
-text; use the search for exact cohorts.
+![GEO samples per organ and platform](assets/dataset-card/v3/05-organ-platform.png)
+
+*Samples whose GEO tissue text matches each organ, by platform. The right column counts human samples across
+all platforms. Counts are approximate because tissue labels are free text; use the search for exact cohorts.*
+
+<details><summary>The same numbers as a table</summary>
 
 | Organ | Samples | Human | Studies | With H&E |
 |---|---:|---:|---:|---:|
@@ -55,6 +59,8 @@ text; use the search for exact cohorts.
 | Breast | 215 | 153 | 28 | 150 |
 | Prostate | 107 | 72 | 15 | 89 |
 
+</details>
+
 **No code needed.** Filter the `tissue`, `platform` or `organism` column in the Dataset Viewer on this page, or
 open `catalog/samples.csv` in Excel or R:
 
@@ -64,7 +70,35 @@ kidney  <- subset(samples, grepl("kidney|renal", tissue, ignore.case = TRUE) & o
 nrow(kidney)   # 289
 ```
 
-The `sda-db` commands work from any terminal, also alongside an R workflow.
+The `sda-db` commands work from any terminal, also alongside an R workflow. For example, which kidney diseases
+are covered (no login):
+
+```bash
+sda-db values disease --tissue kidney --tissue renal --organism human
+```
+
+This lists 30 reported values in about 290 human kidney samples. Among them are ANCA-associated
+glomerulonephritis (20 samples), diabetic kidney disease (11), renal cell cancer (8) and acute kidney injury (6);
+178 samples report no disease.
+
+## What one sample contains
+
+Every sample folder in the full dataset has three files:
+
+- `spatial.h5ad`: expression for every spot, cell, bin or bead, with its coordinates;
+- `image.tif`: a registered pyramidal tissue image, when one was released;
+- `sample.json`: metadata, including the transform that places each observation on the image.
+
+![One Visium H&E sample: image, gene per spot and a patch](assets/dataset-card/v3/03-one-sample-visium.png)
+
+*a, the H&E image of GSM8714178 (human pancreatic cancer, Visium, 0.83 µm per pixel). b, KRT19 counts per spot,
+placed on the image by the transform in `sample.json`. c, a patch around the circled spot; patches like this,
+paired with the spot's expression, are the input of image-to-expression models.*
+
+![One Xenium sample: DAPI image and gene per cell](assets/dataset-card/v3/04-one-sample-xenium.png)
+
+*a, the DAPI image of GSM9448988 (human glioblastoma, Xenium, 0.50 µm per pixel). b, GFAP counts per cell from
+the 541-gene panel, on the same image.*
 
 ## Search in one minute
 
@@ -131,6 +165,24 @@ Source index SHA256: `909c4ec50e71c636eadc7bf01a9479fef1b4fd480ac348dfea6b785e56
 
 *Sample counts by platform, image availability, source collection and retained split (n = 12,163; source snapshot: sda-unified-20261010-v3).*
 
+## Images and resolution
+
+![Image stains and H&E resolution](assets/dataset-card/v3/06-images.png)
+
+*a, the 8,211 samples with an image, by stain. b, the micrometres per pixel of the 5,113 labelled H&E images
+whose scale is recorded.*
+
+Most H&E images are the processed images deposited in GEO, at about 4 µm per pixel, enough to see tissue
+architecture. 561 H&E images have 1 µm per pixel or finer, enough to see cells (as in the patch above).
+`image_um_per_px` in `samples.parquet` lets you choose by resolution.
+
+## Sample size
+
+![Observations per sample by platform](assets/dataset-card/v3/07-sample-size.png)
+
+*Observations per sample (log scale). A sample is one GEO sample (GSM), usually one tissue section. Spots, bins,
+beads and cells differ in size, so compare platforms by their own unit.*
+
 ## Splits for machine learning
 
 The `split` column assigns whole GEO series to train (9,249 samples), val (1,316) or test (1,598), so samples of

assets/dataset-card/v3/facts.json

@@ -0,0 +1,213 @@
+{
+ "visium": {
+  "gsm": "GSM8714178",
+  "spots": 660,
+  "genes": 36601,
+  "gene": "KRT19",
+  "detected_fraction": 0.42,
+  "um_per_px": 0.8308846776785371,
+  "split": "train"
+ },
+ "xenium": {
+  "gsm": "GSM9448988",
+  "cells": 1997,
+  "genes": 541,
+  "gfap_detected_fraction": 0.788
+ },
+ "coverage": {
+  "Brain": {
+   "Visium": 1394,
+   "Xenium": 259,
+   "ST (legacy)": 290,
+   "CosMx": 25,
+   "MERFISH/MERSCOPE": 305,
+   "Slide-seq": 61,
+   "Visium HD": 20,
+   "Stereo-seq": 71,
+   "Other platforms": 137,
+   "Human,\nall platforms": 999
+  },
+  "Intestine / colon": {
+   "Visium": 335,
+   "Xenium": 132,
+   "ST (legacy)": 395,
+   "CosMx": 445,
+   "MERFISH/MERSCOPE": 1,
+   "Slide-seq": 10,
+   "Visium HD": 29,
+   "Stereo-seq": 22,
+   "Other platforms": 47,
+   "Human,\nall platforms": 735
+  },
+  "Lung": {
+   "Visium": 458,
+   "Xenium": 190,
+   "ST (legacy)": 0,
+   "CosMx": 170,
+   "MERFISH/MERSCOPE": 11,
+   "Slide-seq": 5,
+   "Visium HD": 36,
+   "Stereo-seq": 15,
+   "Other platforms": 16,
+   "Human,\nall platforms": 649
+  },
+  "Liver": {
+   "Visium": 353,
+   "Xenium": 33,
+   "ST (legacy)": 50,
+   "CosMx": 264,
+   "MERFISH/MERSCOPE": 31,
+   "Slide-seq": 0,
+   "Visium HD": 13,
+   "Stereo-seq": 9,
+   "Other platforms": 7,
+   "Human,\nall platforms": 184
+  },
+  "Spinal cord": {
+   "Visium": 284,
+   "Xenium": 32,
+   "ST (legacy)": 317,
+   "CosMx": 0,
+   "MERFISH/MERSCOPE": 2,
+   "Slide-seq": 0,
+   "Visium HD": 2,
+   "Stereo-seq": 0,
+   "Other platforms": 0,
+   "Human,\nall platforms": 182
+  },
+  "Kidney": {
+   "Visium": 199,
+   "Xenium": 171,
+   "ST (legacy)": 0,
+   "CosMx": 13,
+   "MERFISH/MERSCOPE": 0,
+   "Slide-seq": 129,
+   "Visium HD": 19,
+   "Stereo-seq": 6,
+   "Other platforms": 26,
+   "Human,\nall platforms": 289
+  },
+  "Skin": {
+   "Visium": 201,
+   "Xenium": 125,
+   "ST (legacy)": 12,
+   "CosMx": 17,
+   "MERFISH/MERSCOPE": 0,
+   "Slide-seq": 0,
+   "Visium HD": 9,
+   "Stereo-seq": 9,
+   "Other platforms": 2,
+   "Human,\nall platforms": 238
+  },
+  "Heart": {
+   "Visium": 196,
+   "Xenium": 52,
+   "ST (legacy)": 8,
+   "CosMx": 3,
+   "MERFISH/MERSCOPE": 5,
+   "Slide-seq": 25,
+   "Visium HD": 4,
+   "Stereo-seq": 10,
+   "Other platforms": 6,
+   "Human,\nall platforms": 89
+  },
+  "Pancreas": {
+   "Visium": 205,
+   "Xenium": 74,
+   "ST (legacy)": 8,
+   "CosMx": 0,
+   "MERFISH/MERSCOPE": 13,
+   "Slide-seq": 0,
+   "Visium HD": 2,
+   "Stereo-seq": 0,
+   "Other platforms": 2,
+   "Human,\nall platforms": 200
+  },
+  "Lymph node / spleen": {
+   "Visium": 131,
+   "Xenium": 34,
+   "ST (legacy)": 0,
+   "CosMx": 1,
+   "MERFISH/MERSCOPE": 6,
+   "Slide-seq": 22,
+   "Visium HD": 12,
+   "Stereo-seq": 7,
+   "Other platforms": 41,
+   "Human,\nall platforms": 127
+  },
+  "Breast": {
+   "Visium": 162,
+   "Xenium": 38,
+   "ST (legacy)": 0,
+   "CosMx": 9,
+   "MERFISH/MERSCOPE": 0,
+   "Slide-seq": 0,
+   "Visium HD": 0,
+   "Stereo-seq": 0,
+   "Other platforms": 6,
+   "Human,\nall platforms": 153
+  },
+  "Prostate": {
+   "Visium": 100,
+   "Xenium": 6,
+   "ST (legacy)": 0,
+   "CosMx": 1,
+   "MERFISH/MERSCOPE": 0,
+   "Slide-seq": 0,
+   "Visium HD": 0,
+   "Stereo-seq": 0,
+   "Other platforms": 0,
+   "Human,\nall platforms": 72
+  }
+ },
+ "images": {
+  "classes": {
+   "H&E": 5263,
+   "Other or undetermined": 227,
+   "DAPI": 1423,
+   "H&E-like (pixel call)": 871,
+   "Other fluorescence": 427
+  },
+  "he_with_scale": 5113,
+  "he_median_um_per_px": 4.164,
+  "he_le_1um": 561
+ },
+ "sizes": {
+  "ST (legacy)": {
+   "n": 1098,
+   "median": 280.0
+  },
+  "CosMx": {
+   "n": 1092,
+   "median": 2161.5
+  },
+  "Visium": {
+   "n": 6512,
+   "median": 2683.5
+  },
+  "Other platforms": {
+   "n": 402,
+   "median": 4548.5
+  },
+  "MERFISH/MERSCOPE": {
+   "n": 463,
+   "median": 26829.0
+  },
+  "Slide-seq": {
+   "n": 380,
+   "median": 32647.5
+  },
+  "Stereo-seq": {
+   "n": 208,
+   "median": 43633.0
+  },
+  "Xenium": {
+   "n": 1785,
+   "median": 63041.0
+  },
+  "Visium HD": {
+   "n": 223,
+   "median": 269006.0
+  }
+ }
+}