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 from PyPi
Create a new conda environment:
conda create --name napari-bacseg python==3.9
conda activate napari-bacseg
conda install -c anaconda git
conda update --all
Install napari-bacseg
via pip:
pip install napari-bacseg
Launch Napari:
napari
Install latest version of 'napri-bacseg' from pip:
pip install napari-bacseg --upgrade
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 torchvision torchaudio -y
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu118
If the latest CUDA versions don't work, try an older version like cuda 11.3:
pip uninstall torch torchvision torchaudio -y
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu113
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:
- 1.1.2
Last updated:
- 2024-11-13
First released:
- 2023-02-24
License:
- Unavailable
Operating system:
- Information not submitted
Requirements:
- napari[all]==0.5.0
- torch
- torchvision
- cellpose==3.0.1
- opencv-python
- picassosr==0.7.3
- bactfit>=0.1.6
- numpy
- pyqt5
- pyqt6
- qtpy
- scipy
- natsort
- tqdm
- imagecodecs
- tifffile
- pandas
- mat4py
- glob2
- matplotlib
- scikit-image
- roifile
- openpyxl
- shapely
- colicoords
- psutil
- xmltodict
- astropy
- tiler
- imageio-ffmpeg
- aicspylibczi
- czifile
- omnipose
- h5py
- pyqtgraph
- tox; extra == "testing"
- pytest; extra == "testing"
- pytest-cov; extra == "testing"
- pytest-qt; extra == "testing"
- napari; extra == "testing"
- pyqt5; extra == "testing"