## Install from environement

On Windows:

in terminal:

Z:

cd Z:\Imaging\_Analysis\ImageAnalysis_pipeline

conda env create -f environment.yml

conda activate cellpose_2.0

python -m pip install cellpose --no-deps

On Linux:

in terminal:

cd ~/EBlabDrive/Imaging/_Analysis/ImageAnalysis_pipeline/

conda env create -f environment.yml

conda activate cellpose_2.0

python -m pip install cellpose --no-deps

## Install MatlabRuntime

On Windows:

go to \ImageAnalysis_pipeline folder:

launch MyAppInstaller_web.exe

follow instruction on the gui

save matlabRunTime as default

BUT save the pkg (BaxTrack) in your own local folder (e.g. in D: or E:)

in terminal (cellpose_2.0 env):

D: or E:

cd D:\path\to\BaxTrack\application or E:\path\to\BaxTrack\application (same path as above)

python setup.py install

On Linux:

go to /ImageAnalysis_pipeline folder:

launch MyAppInstaller_web.exe

follow instruction on the gui

save matlabRunTime as default

BUT save the pkg (BaxTrack) in your own local folder (e.g. ~/)

in terminal (cellpose_2.0 env):

cd ~/path/to/BaxTrack/application

python setup.py install

open ~/.bashrc in a TextEditor and copy the lines below:

# MATLAB RunTime

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/MATLAB_Runtime/v912/runtime/glnxa64

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/MATLAB_Runtime/v912/bin/glnxa64

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/MATLAB_Runtime/v912/sys/os/glnxa64

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/MATLAB_Runtime/v912/sys/opengl/lib/glnxa64

Save and close