Why a file format

An AnnData lives in memory, so peak memory scales with the number of cells. A cytome file lives on disk, and PIASO reads it in chunks — peak memory is set by the batch size instead.

The calls are nearly identical:

import cytome, piaso

cytome.from_10x_h5("filtered_feature_bc_matrix.h5", "sample.cytome")
ds = cytome.open("sample.cytome")

piaso.pp.calculateCellMetrics(ds, modality="RNA")
piaso.tl.infog(ds, modality="RNA", n_top_genes=3000, save_layer=True)
piaso.tl.runSVD(ds, modality="RNA", layer="infog", n_components=50, key_added="X_svd")

Results are written back onto the file, so reopening gives them all back with no recomputation and no export step.

	AnnData	cytome
Matrix location	memory	disk, read in chunks
Peak memory	scales with cells	set by batch size
Good for	up to ~10⁵ cells	10⁶+ cells, repeated analyses
Results	in the object	persisted on the file

For a 10k-cell dataset either is fine and AnnData is simpler. The cytome path is what lets the same code run when the dataset is a hundred times larger.