True-North-Intelligent-Algorithms / napari-easy-augment-batch-dl

A plugin for deep learning labeling, augmenting, training and predicting on 2d image sets. Well suited for training specialist networks using a small number of labels.

napari-easy-augment-batch-dl

A plugin to perform unet based deep learning with a small number of labels and augmentation

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

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

Stardist

Windows

    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

Linux

    pip install tensorflow[and-cuda]
    pip install stardist
    pip install gputools
    pip install edt

Pytorch

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

Cellpose

SAM (Segment Anything)

(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

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-easy-augment-batch-dl" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.