Metadata-Version: 2.4
Name: bioimageflow-common-tools
Version: 0.1.9
Summary: Common bioimage analysis tools for BioImageFlow
Project-URL: Homepage, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Documentation, https://bioimageflow.readthedocs.io/latest/
Project-URL: Repository, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Issues, https://github.com/Inria-SAIRPICO/bioimageflow/issues
Author: BioImageFlow Contributors
License-Expression: BSD-4-Clause
License-File: LICENSE
Keywords: bioimage-analysis,bioimageflow,microscopy,workflow
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Requires-Dist: bioimageflow-core<0.3,>=0.1.6
Requires-Dist: bioimageflow<1,>=0.1.6
Requires-Dist: imageio>=2.31.0
Requires-Dist: numpy>=1.23.5
Requires-Dist: pandas>=2.0.0
Requires-Dist: pillow>=9.5.0
Description-Content-Type: text/markdown

# 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.
- `ExtractChannel`, `ConnectedComponents`, `LabelOverlaps`, `Mosaic`: small
  common image and reporting helpers.

## Dependencies

Install-time libraries are BioImageFlow, pandas, imageio, NumPy, and Pillow.
`ConnectedComponents` uses SimpleITK and tifffile from its isolated `EnvironmentSpec` runtime rather than requiring them in the main process.
New domain-specific tools should live in their own packages instead of expanding this package's scope.

## Tests

```bash
uv run pytest packages/bioimageflow-common-tools/tests
```

Package-owned docs live in `docs/`, with one page per public tool under
`docs/tools/`.
