BacSeg
Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
Installing BacSeg¶
Create a virtual environment and then activate it:
conda create –-name napari-bacseg python==3.9
conda activate napari-bacseg
Install napari-bacseg
via pip:
pip install napari-bacseg
Launch Napari:
Napari
Select napari-bacseg from the Plugins dropdown menu
Installing BacSeg From GitHub¶
conda create –-name napari-bacseg python==3.9
conda activate napari-bacseg
conda install -c anaconda git
conda update --all
pip install napari[all]
pip install git+https://github.com/piedrro/napari-bacseg.git
Updating BacSeg From Github¶
Once you have installed the plugin, you can update the plugin by running the following commands:
pip install git+https://github.com/piedrro/napari-bacseg.git
GPU Installation¶
Once you have installed the plugin, you can install the GPU version of the plugin by running the following commands:
pip uninstall torch
conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia
If the latest CUDA versions don't work, try an older version like cuda 11.3:
pip uninstall torch
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch -c nvidia
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-bacseg" is free and open source software
Issues¶
If you encounter any problems, please file an issue along with a detailed description.
Version:
- 1.0.6
Last updated:
- 06 May 2023
First released:
- 24 February 2023
License:
- BSD-3-Clause
Supported data:
- Information not submitted
Plugin type:
GitHub activity:
- Stars: 2
- Forks: 1
- Issues + PRs: 0
GitHub activity:
- Stars: 2
- Forks: 1
- Issues + PRs: 0
Python versions supported:
Requirements:
- napari (>=0.4.17)
- numpy (==1.23.5)
- qtpy
- cellpose[all] (>=2.1.1)
- numba (>=0.43.1)
- scipy
- torch
- opencv-python-headless
- natsort
- tqdm
- imagecodecs
- tifffile
- pandas
- mat4py
- glob2
- matplotlib
- scikit-image
- roifile
- openpyxl
- shapely
- colicoords
- psutil
- xmltodict
- astropy
- tiler
- imageio-ffmpeg