fishtank.scripts.decode_spots

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fishtank.scripts.decode_spots#

fishtank.scripts.decode_spots(input, strategy, output='decoded_spots', file_pattern='spots_{fov}.csv', fovs=None, color_usage='{input}/color_usage.csv', max_dist=1.7, min_snr=4, normalize_colors=True, filter_output=True, save_intensities=False, **kwargs)#

Decode spots using specified strategy.

fishtank decode-spots -i input -s strategy -o output

Parameters:

  • input (str | Path) – Input file path or directory.

  • strategy (str | Path) – Decoding strategy file.

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

  • file_pattern (str (default: 'spots_{fov}.csv')) – Naming pattern for files if input is a directory.

  • fovs (Union[list[int], slice, None] (default: None)) – Set of fields of view to process.

  • color_usage (str (default: '{input}/color_usage.csv')) – Path to color usage file.

  • max_dist (float (default: 1.7)) – Maximum distance between intensity and codebook vectors.

  • min_snr (float (default: 4)) – Minimum signal-to-noise for bits in the codebook.

  • normalize_colors (bool (default: True)) – Normalize intensities by color.

  • filter_output (bool (default: True)) – Exclude spots with distance > max_dist from output.

  • save_intensities (bool (default: False)) – Include spot intensities in output.

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