| --- |
| license: cc-by-4.0 |
| tags: |
| - spatial-transcriptomics |
| - merfish |
| - mouse-brain |
| - single-cell |
| pretty_name: MIMYR benchmark data |
| --- |
| |
| # MIMYR benchmark data |
|
|
| The preprocessed tissue sections used to train and evaluate |
| [MIMYR](https://github.com/gkrieg/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](https://portal.brain-map.org/atlases-and-data/bkp/abc-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](https://doi.org/10.1101/2025.11.24.690239). |
| > PMID: 41394599; PMCID: PMC12697367. |
|
|
