fishtank.scripts.detect_spots

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fishtank.scripts.detect_spots#

fishtank.scripts.detect_spots(input, fov, ref_series, common_bits, reg_bit='beads', output='spots', file_pattern='{series}/Conv_zscan_{fov}.dax', color_usage='{input}/color_usage.csv', filter=None, filter_args=None, spot_min_sigma=2, spot_max_sigma=20, spot_threshold=1000, spot_radius=5, exclude_bits=['DAPI', 'empty'], include_series=None, z_drift=False, max_drift=100, reg_min_intensity=1000, reg_color=None, reg_z_slice=None, reg_clip_pct=None, scale_factor=None, z_slices=None, **kwargs)#

Detect spots in an image and quantify their intensity.

fishtank detect-spots -i input -f 1 –ref_series H0M1 –common_bits DAPI,empty -o spots

Parameters:

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

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

  • ref_series (str | int) – Reference series for drift correction.

  • common_bits (list[str]) – Common bits used for spot detection.

  • reg_bit (str (default: 'beads')) – Bit used for series registration.

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

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

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

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

  • filter_args (Optional[dict] (default: None)) – Additional filter arguments.

  • spot_min_sigma (int (default: 2)) – Minimum sigma for spot detection.

  • spot_max_sigma (int (default: 20)) – Maximum sigma for spot detection.

  • spot_threshold (int (default: 1000)) – Minimum intensity threshold for spot detection.

  • spot_radius (int (default: 5)) – Spot radius for intensity quantification.

  • exclude_bits (list[str] (default: ['DAPI', 'empty'])) – Bits to exclude from intensity quantification.

  • include_series (Optional[list[str]] (default: None)) – Series to include in intensity quantification.

  • z_drift (bool (default: False)) – Do drift correction in z.

  • max_drift (int (default: 100)) – Maximum allowed drift between series.

  • reg_min_intensity (int (default: 1000)) – Minimum intensity for registration channel to consider drift valid.

  • reg_color (Optional[int] (default: None)) – Color name for registration channel (overrides reg_bit if provided).

  • reg_z_slice (Optional[int] (default: None)) – Z slice to use for registration (overrides z_drift if provided).

  • reg_clip_pct (Optional[float] (default: None)) – Percentile to clip registration image intensities.

  • scale_factor (Optional[float] (default: None)) – Factor to convert pixel coordinates to microns. If None, will use micron_per_pixel from image metadata.

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

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