V1.0.4303 not listing modules and hangs


I have installed the v1.0.4303 source code (un-edited) on a Linux machine, started Matlab and then CellProfiler. I could upload a pipeline and have it run to completion. However, I was not able to add new modules into the pipeline as there are no modules listed in the AddModule window (The same un-edited version works on a Windows machine).

When I edited the program by adding in the function names and its menus, I was able to get the module listing. The problem with this version is that it does not allow me to add the ExportToDatabase module: it reports the following error in the Matlab window:

??? Error using ==> fgets
Invalid file identifier.

Error in ==> CellProfiler>PutModuleInListBox at 6236
output = fgetl(fid);

Error in ==> CellProfiler>AddModuleListBox_Callback at 9399

Error in ==> CellProfiler>gui_mainfcn at 10290

Error in ==> CellProfiler at 64
gui_mainfcn(gui_State, varargin{:});

??? Error using ==> fig=guidata(gcf);val=get(fig.ModulesListBox,‘Value’);if (~isempty(val)); set(fig.ModulesListBox,‘Value’,val(1));end;CellProfiler(‘AddModuleListBox_Callback’,gcbo,],guidata(gcf));clear val fig
Error using ==> fgets
Invalid file identifier.

??? Error while evaluating uicontrol Callback

When this program was compiled, I was able to load a pipeline but hangs when I try to execute it.

Any suggestions?


Batch processing on a Single machine

Have you tried going to File > Set Preferences and specifying the folder where your modules are stored?

It sounds to me like CellProfiler can’t find the modules properly - even though it finds them well enough for running pipelines, they are not on the expected path, and I think it makes sense based on how the code works for it to be producing the error you note.

Let us know if that fixes the problem!


The settings/file paths were properly set. The error occurs in the compiled verison of CellProfiler on a Linux system (and I did not pursue this further to find a fix). As I only need CellProfiler to generate a batch pipeline for the clusters, I could use the uncompiled version running within MATLAB to create the pipeline that incorporates some of our modules.

I now create the new modules in the MATLAB_CPCluster directory so that both CellProfiler and CPCluster would access the same modules. The compile version of CPCluster appears to work.