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Package for cell segmentation, tracking, classification into asc negative and asc positive cells and calcium intensity measurements over time

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Installation instructions for dzne compute server. –tested on python version 2.7.7– Christoph Moehl, christoph.moehl@dzne.de

  1. Install x forwarding software on you client computer, e.g. http://xquartz.macosforge.org/landing/ (if not installed yet)

2. log in to one of the dzne compute servers e.g. ssh -Y compute-04.dzne.de

3. load the python module module load python

4. install virtualenv in your home directory (if not installed yet) easy_install -d /home/[username]/.python27 –user virtualenv

5. cerate a project directory and a new virtual environment (here with name venv - other names are possible) mkdir my_project cd my_project /home/[username]/.local/bin/virtualenv venv

6. activate the virtual environment and install python packages numpy, six, pandas ans scipy source venv/bin/activate pip install numpy==1.8.1 pip install six pip install pandas pip install scipy

7. finally install ca_tracker pip install ca_tracker

  1. edit the file config.json to set the analysis parameters

  2. now you can run ca_tracker_1 and ca_tracker_2

you can check what modules are already installed with the command pip freeze

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