Dependencies

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)

You will also need stardist, cellpose, segment-everything and Yolo. On Windows you will likely need to create separate environments for Stardist and the Pytorch dependencies (Cellpose, SAM and YOLO).

In addition to the popular deep learning toolkits these tutorials use 4 helper and widget libraries. (Note that Yolo is installed via the vendored version of MobileSam installed through segment-everything)

tnia-python: General image processing and deep learning helpers.
napari-easy-augment-batch-dl: Napari widgets for labelling and running deep learning workflows on image series.
segment-everything: Helper to run YOLO and SAM variations and work with lists representing (possibly overlapping) labels.
napari-segment-everything: Napari GUI for segment-everything.

Linux

    conda create -n I2K2024_dl python=3.10
    conda activate I2K2024_dl
    pip install numpy==1.26 # 
    pip install "napari[all]" # requires quotation marks to parse the square brackets on Linux, not sure if generalizes
    pip install albumentations
    pip install matplotlib
    pip install "tensorflow[and-cuda]" # as above, requires quotation marks
    pip install stardist 
    pip install gputools==0.2.15 # I think numpy v2.1.2 gets installed here for me
    pip install edt # pip throws: numba v0.60.0, tensorflow v2.18.0 require lower versions of numpy. Should still work but iffy.
    pip 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 git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git 
    pip install git+https://github.com/True-North-Intelligent-Algorithms/segment-everything.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-easy-augment-batch-dl.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-segment-everything.git

Mac M1

    conda create -n I2K2024_dl python=3.10
    conda activate I2K2024_dl
    pip install numpy==1.26 # 
    pip install "napari[all]" # also requires quotes on Mac
    pip install "tensorflow[and-cuda]" # as above, requires quotation marks. Pip throws a bunch of conflicts, but whatever.
    pip install stardist
    pip install gputools==0.2.15 # pip dependency incompatibilities
    pip install edt 
    pip install torch torchvision torchaudio # remove the index flag url
    pip install pytorch-lightning
    pip install monai
    pip install scipy
    pip install tifffile
    pip install cellpose
    pip install git+https://github.com/True-North-Intelligent-Algorithms/segment-everything.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-easy-augment-batch-dl.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git 
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-segment-everything.git

Windows

Note that to use GPU with Stardist in Windows we need two different environments because Windows needs an older version of tensorflow, which is not compatible wither newer version of pytorch based toolkits.

Windows stardist environment

    conda create -n I2k2024_stardist python=3.10
    conda activate I2k2024_stardist
    pip install numpy==1.26
    pip install "napari[all]"
    pip install albumentations
    pip install matplotlib
    conda install -c conda-forge cudatoolkit=11.8 cudnn=8.1.0
    pip install "tensorflow<2.11"
    pip install stardist 
    pip install gputools==0.2.15 
    pip install edt
    pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git 
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-easy-augment-batch-dl.git

Windows pytorch environment

    conda create -n I2k2024_pytorch python=3.10
    conda activate I2k2024_pytorch
    pip install numpy==1.26
    pip install "napari[all]"
    pip install albumentations
    pip install matplotlib
    pip 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 git+https://github.com/True-North-Intelligent-Algorithms/segment-everything.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-easy-augment-batch-dl.git
    pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git 
    pip install git+https://github.com/True-North-Intelligent-Algorithms/napari-segment-everything.git