napari-stress
Interactive surface analysis in napari for measuring mechanical stresses in biological tissues
This plugin provides tools for the analysis of surfaces in Napari, such as utilities to determine and refine the surface-representation of objects using a ray-casting approach and calculate the curvature of surfaces. It re-implements code in Napari that was written for Gross et al. (2021): STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses and has been made open source in this repository.
Usage¶
Functionality in this repository is divided in two groups: Recipes and plugins.
Recipes
Receipes are workflows for processing images, points and surface data step-by-step.
Recipe | Description |
---|---|
![]() | Confocal data (.tif), 3D+t: Interactive tutorial on how to extract surfaces from intensity image data |
![]() | Confocal data (.tif), 3D+t: Interactive tutorial on how to extract curvature from surfaces |
![]() | Confocal data (.tif), 3D+t: Jupyter notebook for processing single channel data and extracting gaussian curvature. |
Plugins
All functions in napari-stress are documented separately for interactive usage from the napari viewer as well as Jupyter notebooks.
Function | Links |
---|---|
![]() | Fit spherical harmonics: Interactive Code |
![]() | Surface tracing: Code |
![]() | Reconstruct surface: Code |
Utilities
Data to be used for this plugin is typically of the form [TZYX]
(e.g., 3D + time).
Napari-stress offers convenient ways to use functions from other repositories (which are often made for 3D data) on timelapse data with the frame_by_frame
function and the TimelapseConverter
class.
Both are described in more detail in this notebook.
Installation¶
Create a new conda environment with the following command. If you have never used conda before, please read this guide first.
conda create -n napari-stress Python=3.9 napari jupyterlab -c conda-forge
conda activate napari-stress
You can then install napari-stress using pip:
pip install napari-stress
Issues¶
To report bugs, request new features or get in touch, please open an issue or tag @EL_Pollo_Diablo
on image.sc.
See also¶
There are other napari plugins with similar / overlapping functionality
Contributing¶
Contributions are very welcome. Tests can be run with pytest, 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-stress" is free and open source software
Acknowledgements¶
This project was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC2068 - Cluster of Excellence "Physics of Life" of TU Dresden.
Version:
- 0.0.15
Release date:
- 16 June 2022
First released:
- 02 June 2022
License:
- BSD-3-Clause
Supported data:
- Information not submitted
Plugin type:
- Information not submitted
GitHub activity:
- Stars: 5
- Forks: 0
- Issues + PRs: 20
GitHub activity:
- Stars: 5
- Forks: 0
- Issues + PRs: 20
Requirements:
- numpy
- vedo
- napari (<=0.4.15)
- vispy (<=0.9.6)
- matplotlib
- tqdm
- scipy
- pandas
- scikit-image
- napari-tools-menu (>=0.1.15)
- napari-process-points-and-surfaces (>=0.2.0)
- aicsimageio
- napari-segment-blobs-and-things-with-membranes
- mpmath
- pyshtools