TABLE 2.

Code used for establishing a sandbox container. Please note that copying text from the table might introduce some errors, particularly for the hyphens. In case of errors, we suggest typing the code newly in the command line.

Code	Project title
Code 21	vagrant@vagrant>sudo singularity build --sandbox nameofdir/ docker://ubuntu:18.04
Code 22	vagrant@vagrant> sudo singularity exec --writable nameofdir/ /bin/bash
Code 23 (alternatively)	vagrant@vagrant> sudo singularity shell --writable nameofdir/
Code 24	Singularity>
Code 25	Singularity> apt-get update -y
Code 26	Singularity> apt-get install -y python3
Code 27	Singularity> apt-get install python3-pip
Code 28	Singularity> python3 -m pip install --upgrade pip==21.2.4
Code 29	Singularity> pip install cellpose==0.6.5
Code 30	vagrant@vagrant> sudo cp python_main.py nameofdir/mnt/
Code 31	vagrant@vagrant> singularity exec nameofdir/ python3 /mnt/python_main.py --filedir /home/vagrant/cellpose_testdata --pretrained_model nuclei --chan 1 --save_tif
Code 32	vagrant@vagrant> sudo singularity build containername.sif nameofdir/
Code 33	vagrant@vagrant> singularity exec containername.sif python3 /mnt/python_main.py --filedir /home/vagrant/cellpose_testdata --savedir /home/vagrant/cellposedata/masks --pretrained_model nuclei --chan 1 --save_tif