Create virtual environment for calculating features on fluorescence microscopy images using pyslic #python #slic #pyslic

pyslic.sh

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#uses python global packages if found
virtualenv --system-site-packages pyslic

#move into newly created directory
cd pyslic

#activate virtual environment
. ./bin/activate

#install all pyslic dependencies
pip install numpy
pip install scipy
pip install pymorph
pip install mahotas
pip install milk

#install pyslic
pip install pyslic

#make folder to hold data
mkdir data

#deactivate newly created environment
deactivate