napari-morphodynamics
This plugin offers an interface for the Morphodynamics package which allows to study the shape and intra-cellular dynamics of cells imaged as time-lapses by fluorescence microscopy. The plugin offers a single place to perfrom segmentation, windowing (partition cells into small regions of interests that are tracked over time) and results visualization. The software depends on napari-convpaint a pixel-classifier and/or on cellpose for segmentation.
Installation
You can install the plugin via pip with:
pip install napari-morphodynamics
To install latest development version :
pip install git+https://github.com/guiwitz/napari-morphodynamics.git
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-morphodynamics" is free and open source software
Authors
This plugin has been developed by Guillaume Witz and Ana Stojiljkovic at the Data Science Lab, University of Bern, in collaboration with Lucien Hinderling and Olivier Pertz from the Pertz Lab, University of Bern. Development has been partially funded by a Chan Zuckerberg Initiative grant.
Issues
If you encounter any problems, please file an issue along with a detailed description.
1 maintainer
Metadata
1 maintainer
Release files for napari-morphodynamics 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| napari-morphodynamics-0.1.2.tar.gz | 37.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| napari_morphodynamics-0.1.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 37.3 MB
Release files / napari-morphodynamics-0.1.2.tar.gz
| Download URL | napari-morphodynamics-0.1.2.tar.gz |
|---|---|
| Size | 37.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f4c5793ed3ce2403e093c8f808ea5d4b2399e3620cc85b278c38b0492b1bf089
|
|
BLAKE2b-256 checksum How to use checksums |
c8ab2199dac3762595151c22839c8bed752ea2e2bd1303c9a8f50a4a832080f5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.12.1
|
Release files / napari_morphodynamics-0.1.2-py3-none-any.whl
| Download URL | napari_morphodynamics-0.1.2-py3-none-any.whl |
|---|---|
| Size | 17.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
f13060f7fca03b63dd99bede9045492e0557c6b30fea52686ba369a06ecd68a5
|
|
BLAKE2b-256 checksum How to use checksums |
7057f2dff19e26f224f31b3029d9f016f4d5a784ddc5bcdd4299083cfc91c43a
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.12.1
|
