Open ian-coccimiglio opened 5 hours ago
Linux installation:
conda create -n napari_EABDL python=3.10
conda activate napari_EABDL
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 throws: reikna 0.9.0 incompatibility with numpy version. Doesn't seem to impact functionality
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/bnorthan/napari-easy-augment-batch-dl.git # this one fails, private repo perhaps?
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
Mac M1 installation:
conda create -n napari_EABDL python=3.10
conda activate napari_EABDL
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 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/bnorthan/napari-easy-augment-batch-dl.git # this one doesn't work - private repo?
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
Testing on Python=3.10 first. Tests are being performed on Linux, Windows 10, and Mac M1 architectures. I'm using the env name napari_EABDL, though the name probably should change to something easier to type.
Any changes/deviations from existing instructions are written in comments.
General notes: