napari-conidie

A segmentation tool to get conidie and hyphe

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

This plugin is a use case for obtaining conidia and hyphae surface from images. This plugin is a private tool dedicated exclusively to the work of the QUASAV team.

Installation

This private tool cannot be found in the built-in napari. The installation therefore follows two steps:

1 - Install latest development version :

git clone https://github.com/hereariim/napari-conidie.git

Getting started

As prerequisite, user must have installed ilastik in its computer.

Before using the plugin, you must have two data:

• The ilastik model
• The compressed file contained your images structured as followed :

└── Compressed file
    ├── Folder1
    │   ├── img0_1.jpg
    │   ├── img0_2.jpg
    │   ...
    │   └── img0_n.jpg
    │ 
    ├── Folder2
    │   ├── img1_1.jpg
    │   ├── img1_2.jpg
    │   ...
    │   └── img1_n.jpg
    ...
    │
    └──  Foldern
        ├── imgn_1.jpg
        ├── imgn_2.jpg
        ...
        └── imgn_n.jpg

Plugin

Contributing

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.

License

Distributed under the terms of the BSD-3 license, "napari-conidie" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.