bioimageflow-spot-tools¶
bioimageflow-spot-tools provides a focused puncta workflow: detect spots,
assign spot coordinates to label images, and summarize spot counts/intensities
per object. It is intended for FISH-like, smFISH-like, synapse, vesicle, or
small puncta examples where a lightweight and deterministic baseline is enough.
Core libraries are imageio, NumPy, pandas for dataframe tools, and BioImageFlow core APIs. SciPy is used opportunistically for LoG scoring when available; a NumPy fallback keeps default tests runnable. Big-FISH remains a future optional evaluation backend, not a current default dependency.
Tools¶
AtlasSpotDetection: external Atlas CLI-backed adaptive spot detection for 2D TIFF intensity images.
DetectSpots: LoG, DoG, or local-maxima spot detection.
AssignSpotsToLabels: sample label values at spot coordinates.
SpotSummary: aggregate assigned spot counts and intensities per label.
FilterSpots: filter spot dataframe rows by numeric thresholds and masks.
RenderSpots: render coordinates to label or mask images.
SpotsToLabels: create spot label images from dataframe rows or masks.
SpotColocalization: match two upstream spot dataframes by distance.
SpotQualityMetrics: compute SNR, local background, and nearest-neighbor distances.
Workflow Use¶
Use AtlasSpotDetection in the FISH spot-counting and parameter-space exploration workflows.
Use assignment and summary tools to connect spot tables to segmented nuclei or other label images.