Conidie
A segmentation tool to get conidie and hyphe
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.
Version:
- 1.0.2
Last updated:
- 2024-04-29
First released:
- 2022-12-15
License:
- BSD-3-Clause
Operating system:
- Information not submitted
Requirements:
- numpy
- magicgui
- qtpy
- pandas
- h5py
- scikit-image
- napari
- matplotlib
- tox ; extra == 'testing'
- pytest ; extra == 'testing'
- pytest-cov ; extra == 'testing'
- pytest-qt ; extra == 'testing'
- napari ; extra == 'testing'
- pyqt5 ; extra == 'testing'