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CCF Gene Atlas · per-cell MERFISH expression
Per-cell log2 expression of every panel gene for five whole-brain MERFISH datasets from the Allen Brain Cell Atlas, packaged for the browser viewer of the CCF Gene Atlas (ISH x MERFISH). Each brain is kept separate.
| brain | dataset | cells | genes |
|---|---|---|---|
| yao638850 | MERFISH-C57BL6J-638850 | 3,739,961 | 550 |
| zhuang1 | Zhuang-ABCA-1 | 2,616,328 | 1122 |
| zhuang2 | Zhuang-ABCA-2 | 1,056,520 | 1122 |
| zhuang3 | Zhuang-ABCA-3 | 1,566,842 | 1122 |
| zhuang4 | Zhuang-ABCA-4 | 162,361 | 1122 |
Layout: merfish/<brain>/expr/<gene>.u8.gz, gzip-compressed uint8 arrays, one value per cell. Cell order and
per-gene vmax are in the site's docs/data/merfish/<brain>/manifest.json. Decoding: log2 value = q / 255 * vmax,
and 0 means not detected.
Sources and citation:
- Yao Z. et al., Nature 624, 317-332 (2023): MERFISH C57BL6J-638850.
- Zhang M. et al., Nature 624, 343-354 (2023): Zhuang-ABCA-1 to -4.
- Allen Brain Cell Atlas (Allen Institute for Brain Science).
This is a re-packaging for visualisation; the original data and their terms are at the Allen Brain Cell Atlas.
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