Napari-EpySeg
Napari plugin to segment epithelia with EpySeg
napari-epyseg
Plugin to run EpySeg directly in Napari. Can handle temporal data (movie) or single time point (image).
Installation
To install it from Napari, go into the Plugins
menu, select Install/Uninstall Plugins..
and look for napari-epyseg in the plugins list.
To install it directly outside of napari, create/reuse and activate a python environement, e.g epyseg_env
and install it with pip
:
pip install napari-epyseg
[!IMPORTANT]
epyseg
is compatible until python 3.10 (included), but not for versions of python above. Thus,napari-epyseg
is also compatible with python versions until 3.10
Usage
In Napari, go to Plugins>napari-epyseg
to start it.
It will open an interface in the left part of the main window.
You must select the layer (image or movie, single color channel) on which to run EpySeg
.
For this, in the Pick an Image
parameter, select the corresponding layer (you should open the image/movie independantly of the plugin).
To run EpySeg
with default parameters, press directly Segment
once you have selected the image.
When processing is finished, a new layer called Segmentation
will be added in the right panel of the interface.
You can save the result with the Save segmentation
button that appears on the left part of the interface.
Choose where to save the file and the file name with the Segmentation filename
parameter, and click the button to save it.
Remark
This plugin was tested on python 3.10, with epyseg version 0.1.52, napari version 0.4.19, tensorflow 2.14
Troubleshooting
- On Linux Ubuntu, python 3.10, epyseg don't run with tensorflow 2.15 and output the error:
DNN not found
. Downgrading tensorflow to 2.14 worked. tifffile versions
compability: some versions of tifffile where not compatible with epyseg, but recent versions are now fine.tifffile <= 2021.11.2
are fine andtifffile==2025.1.10
also.
License
This plugin is distributed under the BDS-3 license.
If you use this plugin, please cite Epyseg and the plugin with its doi:
Version:
- 0.0.8
Last updated:
- 2025-09-03
First released:
- 2025-02-12
License:
- BSD-3-Clause
Python versions supported:
Operating system:
- Information not submitted
Requirements:
- epyseg
- napari<=0.6.1
- numpy
- magicgui
- tifffile
- pillow
- tox; extra == "testing"
- pytest; extra == "testing"
- pytest-cov; extra == "testing"
- pytest-qt; extra == "testing"
- napari; extra == "testing"
- pyqt5; extra == "testing"