ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari
ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari¶
Authors: Rocco D'Antuono, Giuseppina Pisignano¶
What you can do with ZELDA plugin for napari¶
Segment objects such as cells and organelles in 2D/3D.
Segment two populations in 2D/3D (e.g. cells and organelles, nuclei and nuclear spots, tissue structures and cells) establishing the "Parent-Child" relation: count how many mitochondria are contained in each cell, how many spots localize in every nucleus, how many cells are within a tissue compartment.
Example: cell cytoplasms (parent objects) and mitochondria (child objects)
Parent cell cytoplasms
Children labelled by Parents
Plot results within napari interface.
Customize an image analysis workflow in graphical mode (no scripting knowledge required).
Custom image analysis workflow
Import and Export Protocols (image analysis workflows) in graphical mode (share with the community!).
Import and Export of ZELDA Protocols
Option A. You can install
napari-zelda via pip. For the best experience, create a conda environment and use napari!=0.4.11, using the following instructions:
conda create -y -n napari-env python==3.8 conda activate napari-env pip install "napari[all]" pip install napari-zelda
Option B. Alternatively, clone the repository and install locally via pip:
pip install -e .
Option C. Another option is to use the napari interface to install it (make sure napari!=0.4.11):
Plugins / Install/Uninstall Package(s)
ZELDA is installed
Contributions are 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-zelda" is free and open source software
If you encounter any problems, please [file an issue] along with a detailed description.
- 10 August 2023
- 17 October 2021
- Information not submitted
- Stars: 16
- Forks: 3
- Issues + PRs: 4