bioimageflow-spot-tools
Tools for puncta and spot quantification.
Tools
AtlasSpotDetection: wraps the external Atlas CLI for adaptive 2D TIFF spot detection.DetectSpots: detects local maxima after DoG/LoG-compatible filtering and returns one dataframe row per spot plus a label image.AssignSpotsToLabels: samples a label image at each detected spot coordinate.SpotSummary: aggregates spot counts and intensities per label.FilterSpots: filters spot dataframe rows by intensity, score, radius, and mask.RenderSpots: renders coordinate rows to binary mask or label images.SpotsToLabels: converts spot coordinates or masks into label images.SpotColocalization: matches two upstream spot dataframes between channels by distance.SpotQualityMetrics: computes SNR, local background, and nearest-neighbor distances.
ATLAS is the primary external spot detection method used by the FISH and parameter-space exploration workflows. The local spot table utilities support assignment, rendering, filtering, and summary after detection.
Example
See the FISH spot-counting and parameter-space exploration workflows in the main workflow catalog.
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