gefpy.cell_mask_annotation

Provides a way to generate gem gef tiff file based on contour information .

class cell_mask_annotation.MaskSegmentation(sampleid, infile, geneFile, outpath, binsize)

run_cellMask(self)

generate gem、gef、tiff file based on contour information.

Parameters

• sampleid – SampleID for input data

• infile – Segmentation mask or geojson

• geneFile – Path contains gene expression matrix

• outpath – saves the data to the outpath directory

• binsize – bin size