First, follow the instructions at https://github.com/MouseLand/cellpose#system-requirements to install cellpose and jupyter. Other than cellpose, the other packages required by the notebook are below:
- matplotlib
- scikit-image
In Terminal, navigate to where you want the code to live. Then, type the following line and press Enter:
git clone https://github.com/superresolusian/cellpose.git
The files inside this repository should then be with you. In Terminal, while still in this directory, then type in jupyter notebook and a browser window with the current directory's file structure should then open. Click on run_pretrained.ipynb and you're good to go!
We installed all the packages into a conda environment called 'cellpose'. Before launching the notebook from your cellpose folder, make sure you're in the correct environment by typing conda activate cellpose into Terminal. You can do this either before or after you navigate to the folder with the notebook in it, as long as it's before you actually launch the notebook itself.
There is only one bit of code that you need to check before running the notebook, which is in the second cell. This is where you tell the code where your images are and where you want to save them. Once you're happy with that, then go to Kernel > Restart & run all in the jupyter menu. You should get some output printed at the bottom which will let you know how everything's progressing.
I've set up the notebook to output the following into the save directory specified in the code: png files of the masks and outputs (useful for quick visual evaluation), seg.npy file of the segmentation results which can be reloaded into cellpose at a later date, should you wish, and a txt file with outlines that can be loaded as ImageJ ROIs. To load the outlines into ImageJ, paste the code from https://github.com/MouseLand/cellpose/blob/master/imagej_roi_converter.py into a new macro in ImageJ, set the language to Python, and run the macro.
If you want to check for new updates in this repository, while inside the inner cellpose folder (where the notebook is saved) in Terminal, type git pull origin. If you've already made some changes, it might get angry - a total reset to what's inside this repo would require you typing the line git reset --hard origin/master (note this will get rid of any changes you made to filepaths etc). What might be a good idea is to duplicate the notebook and work on the duplicate, as I don't think git will be annoyed by changes in a file that has a different name to the notebook in here. It just gets alarmed when we've both made changes to the same-named file.