Installing CellPose on the HPC Cluster (nemo)

To install CellPose to run properly on a Jupyter notebook on the HPC cluster (nemo), follow these steps:

⚠️ Be sure to use a GPU node while installing!

Download the files install_cellpose_0525.sh and Cellpose_GPU_Check.ipynb to a folder on nemo

(e.g., labname/working/username/cellpose0525).
Open an OnDemand desktop session on a GPU node.
Open a terminal window in OnDemand.
Navigate in the terminal to the folder where you downloaded the files.
Run the install script:
```
./install_cellpose_0525.sh
```
Wait a few minutes for everything to install.
If it installs suspiciously quickly, something likely went wrong.
After installation, open a Jupyter session on OnDemand on a GPU node.
Open the notebook Cellpose_GPU_Check.ipynb from the folder where you saved it.
Run the two cells. If both return True, CellPose is successfully installed.

Demo Notebook

For a demonstration of running Cellpose-SAM on images, please see this notebook: