A segmentation tool to get conidie and hyphe

License BSD-3 PyPI Python Version tests codecov napari hub

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.


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

1 - Install latest development version :

git clone

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




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-conidie" is free and open source software


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


  • 1.0.2

Last updated:

  • 29 April 2024

First released:

  • 15 December 2022


Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 0
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:


  • numpy
  • magicgui
  • qtpy
  • pandas
  • h5py
  • scikit-image
  • napari
  • matplotlib