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AnniekStok committed Aug 13, 2024
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[![codecov](https://codecov.io/gh/AnniekStok/napari-segmentation-correction/branch/main/graph/badge.svg)](https://codecov.io/gh/AnniekStok/napari-segmentation-correction)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-segmentation-correction)](https://napari-hub.org/plugins/napari-segmentation-correction)

A basis for a napari plugin for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.

The plugin heavily relies on several very useful open source packages and other napari plugins:
- orthogonal view widget: [napari multiple viewer widget](https://github.com/napari/napari/blob/e490e5535438ab338a23b17905a1952f15a6d27a/examples/multiple_viewer_widget.py)
- table widget: [napari-skimage-regionprops](https://github.com/haesleinhuepf/napari-skimage-regionprops)
A collection of functions for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.
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This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
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## Usage
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
- explore label properties in a table widget, based on [napari-skimage-regionprops](https://github.com/haesleinhuepf/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).
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