napari-BacSEG
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.
1 maintainer
Release files for napari-bacseg 1.1.2
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_bacseg-1.1.2.tar.gz | 143.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| napari_bacseg-1.1.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 298.5 kB
Release files / napari_bacseg-1.1.2.tar.gz
| Download URL | napari_bacseg-1.1.2.tar.gz |
|---|---|
| Size | 143.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.0
|
Release files / napari_bacseg-1.1.2-py3-none-any.whl
| Download URL | napari_bacseg-1.1.2-py3-none-any.whl |
|---|---|
| Size | 155.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.0
|
