Metadata-Version: 2.4
Name: leica_roi_finder
Version: 0.0.4
Summary: Automatic ROI detection using cellpose, exports to .rgn files
Author: KJ van Beem
License: GPL-3.0
Project-URL: Homepage, https://github.com/JvB22/Leica_ROI_finder
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: cellpose==3.1.1.2
Requires-Dist: numpy>=2.0.2
Requires-Dist: pyshortcuts>=1.9.5
Requires-Dist: PyQt6>=6.9.0
Requires-Dist: lxml>=5.4.0
Requires-Dist: pyqtgraph>=0.13.7
Requires-Dist: superqt>=0.7.3
Requires-Dist: scikit-image>=0.25.2
Requires-Dist: pandas>=2.2.3
Dynamic: license-file

# Leica_ROI_finder
Automatic ROI finder for Leica Stellaris 8
- Automatic segmentation using cellpose 3
- ROI filtering using intensity, size and circularity
- Exports ROIs to Leica .rgn files, can be imported into LAS X navigator

![](./assets/images/leica_roi_finder.png)

## Installation
Leica ROI finder is available on PyPi and can be installed as follows:
```shell
pip install leica-roi-finder
```

# Workflow
Load LIF image into ROI finder:

![](./assets/images/image_loaded.png)

Perform segmentation using cellpose, filter ROIs using intensity, size and circularity:

![](./assets/images/segmentation.png)

Export ROIs to Leica .rgn format and import into LAS X Navigator:

![](./assets/images/regions_loaded.png)

Perform imaging on all regions:

![](./assets/images/experiment.png)
