cellpose_container.recipe

Bootstrap: docker
From: ubuntu:18.04

%labels
        AUTHOR: Shilpita Mitra-Behura, Reto Fiolka, Stephan Daetwyler

%files
        /home/vagrant/python_main.py /mnt

%post
        #Downloads the latest package lists.
        apt-get update -y

        #Install python and other tools.
        #Non-interactive is used to ensure prompts are not needed.
        DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
        python3 python3-pip\
	python3-setuptools

        #Update pip
        python3 -m pip install --upgrade pip==21.2.4

        #Install python libraries needed for Cellpose to run
        python3 -m pip install wheel==0.37
        python3 -m pip install --no-cache-dir torch==1.8.1
        python3 -m pip install opencv-python-headless==4.5.3.56
        python3 -m pip install cellpose==0.6.5

%runscript
        exec /usr/bin/python3 /mnt/python_main.py "$@"

%help
        This is a Singularity container to segment images using Cellpose.
        To run this container, use, for example, 'singularity run cellpose_container.sif --filedir /folder/where/files/to/segment/are --savedir /folder/where/segmented/files/should/be/saved --pretrained_model cyto --chan 2 --chan2 1 --save_tif'  

	The user must put the folder where the files to be segmented are after the flag “--filedir.”  
	The directory where the user wants to save their files is optional, with the tag “--savedir.” If this tag is not provided, the files will save to the directory denoted in "--filedir".
	The flag “--pretrained_model” is required and must have either the input “cyto” or “nuclei.”  
	The flags “--chan” and “--chan2” are optional and allude to the channels of the image that will be segmented. 
	The flag “--diameter” is optional and can be added for the user to specify the diameter of the nuclei in image.  
	The flags “--flow_threshold”, “--cellprob_threshold” are further optional flags to specify cellpose parameters.
	The flags “--save_png” and “--save_tif” are used to denote what filetype the segmented files are saved as. The default is to save as a Tiff.