Input / Output

Imaging

io.adata_to_qupath(adata, geodataframe[, ...])	Export a GeoDataFrame with QuPath-compatible annotations, using AnnData for classification and color mapping.
io.import_thresholds(gates_csv_path[, ...])	Read gate thresholds from a CSV file, filter, and optionally log1p-transform for scimap compatibility.
io.quant_to_adata(path[, ...])	Convert cell quantification CSV data to an AnnData object for downstream analysis.
io.segmask_to_qupath(path_to_mask[, ...])	Convert a segmentation mask (TIFF) to QuPath-compatible detections as a GeoDataFrame or GeoJSON file.

Proteomics

io.DIANN_to_adata(DIANN_path[, DIANN_sep, ...])	Converts DIANN output file and metadata file into an AnnData object.
io.import_perseus(path_to_perseus_txt[, ...])	Convert a Perseus text file to an AnnData object.

Utils

io.export_adata(adata, path_to_dir, ...[, ...])	Save an AnnData object as both .h5ad and optionally .parquet, .csv, or Perseus files in a checkpoint directory.
io.export_figure(fig, path_to_dir, suffix[, dpi])	Save a matplotlib figure as both PDF and SVG files with a timestamped filename.