Metadata-Version: 2.5
Name: bioimageflow-measurement-tools
Version: 0.2.2
Summary: Lightweight measurement 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<0.6,>=0.5.0
Requires-Dist: bioimageflow<1,>=0.9.0
Requires-Dist: numpy>=1.23.5
Requires-Dist: pandas>=2.0.0
Description-Content-Type: text/markdown

# bioimageflow-measurement-tools

Optional BioImageFlow package for object measurements, label counting, table summaries, and segmentation benchmark metrics.

Worker-side image tools use imageio, NumPy, and scikit-image through BioImageFlow's general environment.
Main-process table tools use BioImageFlow, NumPy, and pandas, which remain package dependencies.
The two tool families live in separate modules so worker imports never depend on the orchestrator package.

Label inputs must be finite, non-negative, integer-valued 2D rasters; `0` is background.
Table tools reject empty or duplicate selections, nonnumeric selected values, and output-name collisions.

## Tools

- `RegionProperties`
- `ShapeProperties`
- `IntensityProperties`
- `CountLabels`
- `SummarizeTable`
- `LabelBenchmark`
- `ObjectMatchingMetrics`
- `DiceIoU`
- `AggregatePerImage`
- `NormalizeFeatures`

## Tests

Run package tests with:

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

The tests use generated label images, intensity images, and tables with exact expected values.
Public-data workflow tests should assert stable ranges rather than commit large datasets.
