A collection of functions for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install napari-segmentation-correction via pip:
To install latest development version :
pip install git+https://github.com/AnniekStok/napari-segmentation-correction.git
This plugin aims to help you correct segmentation results. It can work with 3D arrays, 4D arrays, or 4D virtual arrays. There are several functionalities:
- explore label properties in a table widget, based on napari-skimage-regionprops
- filter labels by size
- select/delete labels with point layer selection
- copy labels from a nD array with multiple segmentation options to your current label layer. For this you have to add a special labels layer for which you need to select a folder that contains subfolders for the different options. In each subfolder, there should be one 3D image per time point (or just one image if there is only one time point).
- erode/dilate labels
- smooth labels
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the BSD-3 license, "napari-segmentation-correction" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.