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qin-yu/stardist-setup.md

Last active September 14, 2021 12:25
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stardist-setup.md

Setup Conda Environment for StarDist

$ conda create --name stardist-gpu python=3.7  # Although now we have 3.9 but Conda's `gputools` requires 3.7 or less
$ conda activate stardist-gpu
$ conda install -c anaconda tensorflow-gpu
$ conda install -c talley gputools
$ conda install -c anaconda git  # Just to `git checkout dev` for the `dev` branch
$ conda install -c anaconda natsort colorcet
$ git clone git@github.com:stardist/stardist.git
$ git checkout dev
$ python setup.py install

If Jupyter Notebook is needed:

$ conda install -c conda-forge notebook
$ conda install -c conda-forge ipywidgets
$ CUDA_VISIBLE_DEVICES=7 nohup jupyter notebook --no-browser --port=8901 &> /g/kreshuk/yu/.lognohup/jupyter_stardist.log &
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