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MIMYR benchmark data
The preprocessed tissue sections used to train and evaluate
MIMYR, a generative model of missing tissue in
spatial transcriptomics. Each section is an AnnData .h5ad file whose cells have
CCF coordinates (x_ccf, y_ccf, z_ccf), Allen Brain Cell Atlas cell-type labels
(class, subclass, supertype, cluster), and a gene expression matrix.
MIMYR downloads only the archives a run needs, and extracts them into its
--data_dir:
| Archive | Contents | MIMYR data modes |
|---|---|---|
rq1-merscope.zip |
53 coronal sections of one mouse brain (donor C57BL6J-638850), 550 genes | rq1 |
Zhuang-ABCA-1.zip |
Zhuang-ABCA-1 (147 coronal sections), 1,122 genes, plus ccf-ABCA-1.csv |
base_zhuang1, rq4_noref |
Zhuang-ABCA-2.zip |
Zhuang-ABCA-2 (66 coronal sections), plus ccf-ABCA-2.csv |
rq3, rq3_v2*, rq4_rq3 |
Zhuang-ABCA-3.zip |
Zhuang-ABCA-3 (23 sagittal sections), plus ccf-ABCA-3.csv |
rq4* |
Zhuang-ABCA-4.zip |
Zhuang-ABCA-4 (3 sections), plus ccf-ABCA-4.csv |
— |
The files are identical to the ones used for the paper.
Sources and attribution
All sections are derived from data released through the Allen Brain Cell Atlas under CC BY 4.0. If you use them, please cite the original datasets as well as MIMYR:
- MERSCOPE whole-brain atlas (
rq1-merscope.zip): Yao Z, et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). - Zhuang-ABCA-1 to 4: Zhang M, et al. Molecularly defined and spatially resolved cell atlas of the whole mouse brain. Nature 624, 343–354 (2023).
Citation
Deshpande A, Bei Z, Ma J, Krieger S. MIMYR: Generative modeling of missing tissue in spatial transcriptomics. bioRxiv [Preprint]. 2025 Nov 27:2025.11.24.690239. doi: 10.1101/2025.11.24.690239. PMID: 41394599; PMCID: PMC12697367.
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