Metadata-Version: 2.3
Name: spfluo
Version: 0.0.9rc14
Summary: SPFluo package
Project-URL: Repository, https://github.com/jplumail/spfluo.git
Author-email: Jean Plumail <jplumail@unistra.fr>
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Requires-Dist: array-api-compat>=1.6
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: ome-types
Requires-Dist: scikit-image>=0.21
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: tqdm
Requires-Dist: typing-extensions; python_version < '3.10'
Provides-Extra: ab-initio-reconstruction
Requires-Dist: simpleitk; extra == 'ab-initio-reconstruction'
Provides-Extra: all
Requires-Dist: albumentations; extra == 'all'
Requires-Dist: napari-bbox-spfluo; extra == 'all'
Requires-Dist: napari<0.4.19,>=0.4.18; extra == 'all'
Requires-Dist: numpy<2; extra == 'all'
Requires-Dist: simpleitk; extra == 'all'
Requires-Dist: tensorboard; extra == 'all'
Provides-Extra: manual-picking
Requires-Dist: napari-bbox-spfluo; extra == 'manual-picking'
Requires-Dist: napari<0.4.19,>=0.4.18; extra == 'manual-picking'
Requires-Dist: numpy<2; extra == 'manual-picking'
Provides-Extra: picking
Requires-Dist: albumentations; extra == 'picking'
Requires-Dist: tensorboard; extra == 'picking'
Provides-Extra: visualisation
Requires-Dist: napari-bbox-spfluo; extra == 'visualisation'
Requires-Dist: napari<0.4.19,>=0.4.18; extra == 'visualisation'
Requires-Dist: numpy<2; extra == 'visualisation'
Description-Content-Type: text/markdown

# SP-Fluo

This repository contains code for picking and single particle reconstruction in fluorescence imaging.

Pipeline :
1. [picking](spfluo/picking)
2. for centrioles only : [cleaning with segmentation](spfluo/segmentation) and [alignement](spfluo/alignement)
3. [reconstruction ab-initio](spfluo/ab_initio_reconstruction/)
4. [refinement](spfluo/refinement/)

## Installation

```bash
git clone https://github.com/jplumail/spfluo
```

```bash
cd spfluo
pip install .
```

## Run tests

To test for python 3.9, 3.10 and 3.11:
```bash
hatch test spfluo
```

For python 3.8:
```bash
hatch env run -e hatch-test-38 pytest -- spfluo
```