fishtank.scripts.assign_proseg

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fishtank.scripts.assign_proseg#

fishtank.scripts.assign_proseg(transcripts, proseg_transcripts, output='proseg_counts.csv', min_jaccard=0.4, min_prob=0.5, cell_column='cell', cell_missing=0, barcode_column='barcode_id', x_column='global_x', y_column='global_y', z_column='global_z', codebook=None, **kwargs)#

Assign additional transcripts to cells using ProSeg.

fishtank assign-proseg -t transcripts -p proseg_transcripts -o output

Parameters:

  • transcripts (str | Path) – Transcripts input file path.

  • proseg_transcripts (str | Path) – ProSeg transcripts input file path.

  • output (str | Path (default: 'proseg_counts.csv')) – Output file path.

  • min_jaccard (float (default: 0.4)) – Minimum transcript overlap for matching cells.

  • min_prob (float (default: 0.5)) – Minimum ProSeg probability for a transcript to be assigned.

  • cell_column (str (default: 'cell')) – Column containing cell ID in transcripts.

  • cell_missing (int (default: 0)) – Cell ID for unassigned transcripts.

  • barcode_column (str (default: 'barcode_id')) – Column containing barcdoe ID in transcripts.

  • x_column (str (default: 'global_x')) – Column containing x-coordinate in transcripts.

  • y_column (str (default: 'global_y')) – Column containing y-coordinate in transcripts.

  • z_column (str (default: 'global_z')) – Column containing z-slice in transcripts.

  • codebook (Union[str, Path, None] (default: None)) – Codebook for assigning barcodes IDs to genes.

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