A plugin to perform unet based deep learning with a small number of labels and augmentation
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
To install latest development version :
pip install git+https://github.com/bnorthan/napari-easy-augment-batch-dl.git
You will also need to install the latest development version of tnia-python:
pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git
You will need to install napari and for augmentation you will need albumentations library. Also explicitly install numpy 1.26. (We have not tested with numpy 2.0 so it is a good idea to explicitly install numpy 1.26 to avoid another dependency installing numpy 2.x)
pip install numpy==1.26
pip install napari[all]
pip install albumentations
pip install matplotlib
You will also need one or more of stardist, cellpose, segment-everything or Yolo
conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
pip install "tensorflow<2.11"
pip install stardist==0.8.5
pip install gputools
pip install edt
pip install tensorflow[and-cuda]
pip install stardist
pip install gputools
pip install edt
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
pip install pytorch-lightning
pip install monai
pip install scipy
pip install tifffile
pip install cellpose
pip install segment-everything
(more details to come on installing dependencies)
(Coming soon) You can install napari-easy-augment-batch-dl via pip:
pip install napari-easy-augment-batch-dl
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.
Distributed under the terms of the BSD-3 license, "napari-easy-augment-batch-dl" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.