Reading seqFISH+ multi-omics data

In a ChromData the spots carry coordinates and per-spot signals (spot_tracks: the chromatin marks and nuclear bodies measured at each locus), the cells carry their type, position and expression (cells, cellm), and the transcript matrix can stay in its own AnnData, linked by cell.

Step

API

read the per-FOV spot tables with the locus map and the cell clustering

uchrom.io.read_seqfish_multiomics(csvs, locus_annotation=, cell_clustering=, out=)

a whole replicate, with the RNA matrix as a linked AnnData

uchrom.io.load_takei2025_cerebellum(), load_seqfish_multiomics_linked

the Takei 2021 tables as FOF-CT (DNA, RNA spots, cells)

ChromData.from_fofct(core, cell_table=, rna_table=) (chromatin tracing)

cell positions and outlines in the tissue

cd.cell_positions(), cd.set_cell_shapes()

the full Takei 2025 cerebellum without downloading it

uchrom.datasets.load("takei2025_cerebellum") (the atlas store)

Tutorial