---
pretty_name: SubcellPert
language: [en]
tags: [biology, spatial-transcriptomics, perturbation, subcellular]
configs:
- config_name: catalog
  default: true
  data_files:
  - split: inventory
    path: catalog/datasets.parquet
---

<h1 align="center">SubcellPert: Benchmarking Subcellular Perturbation Prediction</h1>

<p align="center">SubcellPert benchmarks perturbation-response prediction across 14 imaging datasets and eight baselines, extending virtual cell evaluation from gene counts to intracellular RNA organization.</p>

<p align="center">
  <a href="https://personal-page.wjh.app/SubcellPert/">Project page</a> ·
  <a href="https://www.biorxiv.org/content/10.64898/2026.10.11.758305v1">Paper</a> ·
  <a href="https://github.com/king159/SubcellPert">Code</a>
</p>

## Dataset overview

This snapshot contains **14 datasets, 13,880,723 cells, and
3,653,986,724 retained RNA events**, with frozen benchmark splits and
intervention descriptors. Each physical dataset is counted once. Seeds,
baselines, and oracle/joint settings reuse the observations.

| Dataset | Cells | RNA events | Genes |
| --- | ---: | ---: | ---: |
| DSS-Colitis | 1,439,542 | 119,553,365 | 940 |
| ATM-RT | 790,166 | 147,722,071 | 298 |
| Kidney-IRI | 1,374,915 | 168,519,194 | 300 |
| Cardiac-MI | 225,023 | 61,134,068 | 475 |
| Ddx54-PD1 | 1,155,233 | 494,265,984 | 5,006 |
| Spinal-KO | 122,645 | 36,073,815 | 347 |
| Adipose | 13,972 | 1,907,755 | 477 |
| Breast-FUS | 880,565 | 102,102,171 | 1,000 |
| GBM-oHSV | 2,401,940 | 520,974,197 | 480 |
| Lung-Drug | 1,561,700 | 681,015,170 | 5,006 |
| Gut-Microbiota | 2,057,563 | 189,197,264 | 1,815 |
| Sickness | 1,765,443 | 1,101,298,121 | 941 |
| PF-Astro | 11,454 | 10,670,839 | 485 |
| UC-VDZ | 80,562 | 19,552,710 | 1,000 |