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 source and label.FilterSpots: filters spot dataframe rows by intensity, score, radius, and mask.RenderSpots: renders coordinate rows to binary mask or label images.SpotsToLabels: combines spot-coordinate rows into one label image.MaskToLabels: converts each mask row into a connected-component label image.SpotColocalization: computes a maximum-cardinality, minimum-total-distance one-to-one match between two spot tables.SpotQualityMetrics: computes annular-background SNR and indexed 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.
All coordinate consumers use finite (y, x) values and the same nearest-pixel rule: exact half values round upward.
Example
See the FISH spot-counting and parameter-space exploration workflows in the main workflow catalog.
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