CellProfilerPelkmans

A customized-version of CellProfiler1.0 maintained by members of Pelkmans Lab.

Major differences to the original version:

• many additional custom modules

How to install?

CellProfilerPelkmans is part of each iBRAIN_UZH release in iBRAIN/tools/CellProfilerPelkmans.

Please follow the instructions in the iBRAIN_UZH User Guide

Dependencies

Some CellProfilerPelkmans modules depend on Matlab code that resides outside of this repository - specifically in PelkmansLibrary. This is also part of each iBRAIN_UZH release.

After installation

Now you are ready to go.

Open your Matlab application and type:

CellProfiler

This will start the CellProfiler program and open the GUI window.

Reference Documentation

Reference documentation is found in several locations:

• Modules API Documentation. It is updated automatically daily, and contails all modules.
• CellProfiler manual. Standard modules only.
• CellProfilerPelkmans Wiki. Custom modules only.
• List of Standard Modules. Standard modules only.

Further documentation can be found in the actual Matlab functions (.m files). This information can also be queried from the GUI using the ? button.