bioimageflow-common-tools
bioimageflow-common-tools provides lightweight workflow glue for BioImageFlow.
It focuses on source tables, table reshaping, simple joins, small image helpers, and report-friendly exports.
Domain-heavy segmentation, restoration, tracking, spot detection, and large-format IO belong in the specialized optional packages.
Tools
Files: create a source table from an explicit ordered file list or a directory scan.TableFromCsv: load CSV or TSV metadata into a source table.Generate: create a source table from literal values.InnerJoin,CrossJoin,JoinOnColumn,Concat,Collect: combine workflow tables.FilterTableRows: keep rows matching a column/operator/value predicate.SelectColumns: keep and optionally rename table columns.WriteTable: persist an upstream table to CSV or TSV.ConnectedComponents,LabelOverlaps,Mosaic: small common image and reporting helpers.
Dependencies
Install-time libraries are BioImageFlow and pandas.
Image-processing tools import imageio, scikit-image, NumPy, and Pillow only inside worker methods and obtain them from the shared GENERAL_ENV.
New domain-specific tools should live in their own packages instead of expanding this package's scope.
Migration
ExtractChannel has moved out of this package.
Use SelectChannel from bioimageflow-io-tools for channel selection.
Tests
uv run pytest packages/bioimageflow-common-tools/tests
Package-owned docs live in docs/, with one page per public tool under docs/tools/.
1 maintainer
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