ca_tracker 0.2.11

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

Installation instructions for dzne compute server. –tested on python version 2.7.7– Christoph Moehl, [e-mail]

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

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

9. now you can run ca_tracker_1 and ca_tracker_2

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