bioimageflow-spot-tools
Tools for puncta and spot quantification. Main-process dataframe tools require BioImageFlow, ImageIO, NumPy, pandas, and SciPy from the host; processing tools obtain scikit-image from their worker environment.
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.
1 maintainer
Metadata
1 maintainer
Release files for bioimageflow-spot-tools 0.2.2
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Source distribution (sdist)
| File | Size | Uploaded | |
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| bioimageflow_spot_tools-0.2.2.tar.gz | 32.7 kB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bioimageflow_spot_tools-0.2.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 54.9 kB
Release files / bioimageflow_spot_tools-0.2.2.tar.gz
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Release files / bioimageflow_spot_tools-0.2.2-py3-none-any.whl
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