Let me just start with a small introduction: I’m a student at the ETH working in the Pelkmans lab, working with another PhD student on setting up the image analysis for high throughput analysis of amongst others virus entry. The modular build of the CellProfiler and the fact that it is written in MatLab is interesting for us because this would allow us to experiment easily with different analysis methods and combinations. We therefore set out to create our own module for the CellProfiler which could do some final statistics and data analysis using the measurements and objects created by stadard CP modules.
So, we have been trying to add our own module in CP. We have figured out how to access the measurements and object (properties) created by several CP modules, and we are now trying to establish a new module. We have created a file in the Modules dir with a name that corresponds to its function name, and in the CellProfiler.m file we have inserted a reference to our module at the following position:
line 36: "%#function …"
line 3760: created a new modulename toolhelp
line 3789 (line numbering is altered from original file): We have added this module to the handles.Current.ModuleFilenames array
line 8761: we have added it to the load_listbox function, in the ‘OtherFiles’ array.
Doing the previous allowed us to add our new module to pipelines. Apart from a revisionnumber error message, and the fact that we can not remove this new module after adding it we get an error stating that this module is not valid because it appears to have no variables. There are several textVars present in the module, and ofcourse also just plain variables used for storing data (cells, matrices). Perhaps we are going totally the wrong way about this - if so, please tell us To keep a long story short, our questions are the following:
- Is there any documentation on how to add your own modules, and reference internal values of CP?
- If yes, then we will RTFM; If not, could you explain the ‘no-variables’ error we get and possible give us some hints how to go about setting up our own module?
Thanx in advance.