fishtank.scripts.cellpose

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fishtank.scripts.cellpose#

fishtank.scripts.cellpose(input, fov, channels, output='./cellpose_polygons', file_pattern='{series}/Conv_zscan_{fov}.dax', corrections=None, color_usage='{input}/color_usage.csv', z_slices=None, model='cpsam', diameter=None, cellprob_threshold=0.0, downsample=None, do_3D=False, model_args=None, clear_border=False, min_size=1000, filter=None, filter_args=None, gpu=False, **kwargs)#

Segment cells using Cellpose.

fishtank cellpose -i input -f 1 –channels DAPI -o cellpose_polygons

Parameters:

  • input (str | Path) – Image file directory.

  • fov (int) – Field of view to process.

  • channels (list[str]) – Channel for segmentation (e.g., DAPI or PolyT,DAPI).

  • output (str | Path (default: './cellpose_polygons')) – Output directory.

  • file_pattern (str (default: '{series}/Conv_zscan_{fov}.dax')) – Naming pattern for image files.

  • corrections (Union[str, Path, None] (default: None)) – Path to image corrections directory.

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

  • z_slices (Union[list[int], slice, None] (default: None)) – Z-slices to use for segmentation (e.g., 1 or 1,2,3 or 1:20:5).

  • model (str (default: 'cpsam')) – Cellpose model (e.g., cyto or nuclei).

  • diameter (Optional[int] (default: None)) – Cellpose diameter.

  • cellprob_threshold (float (default: 0.0)) – Cell probability threshold.

  • downsample (Optional[int] (default: None)) – Downsampling factor.

  • do_3D (bool (default: False)) – Use 3D segmentation.

  • model_args (Optional[dict] (default: None)) – Additional model arguments (e.g., key1=val1,key2=val2).

  • clear_border (bool (default: False)) – Remove cells touching the image border.

  • min_size (int (default: 1000)) – Minimum area or volume for a cell to be kept.

  • filter (Optional[str] (default: None)) – Filter to apply to the image before segmentation.

  • filter_args (Optional[dict] (default: None)) – Additional filter arguments (e.g., key1=val1,key2=val2).

  • gpu (bool (default: False)) – Use GPU.

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