Rescale Intensity error

cellprofiler

#1

Hi all,

I have a pipeline setup to analyse many images.

Currently I have the rescaledintensity module to be of method (E) - enter min and max, set at AA for both. However, since each field of view may be different, I would like to do AE, so to calculate the min and max for each image, as opposed to all.

however I get this error when I want to use AE

There was a problem running the image analysis. Sorry, it is unclear what the problem is. It would be wise to close the entire CellProfiler program in case something strange has happened to the settings. The output file may be unreliable as well. Matlab says the error is: Undefined function or method ‘min’ for input arguments of type ‘cell’. in the RescaleIntensity module, which is module #02 in the pipeline.

Stack:
CPrescale in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CPsubfunctions/CPrescale.m (103)
RescaleIntensity in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/Modules/RescaleIntensity.m (141)
AnalyzeImagesButton_Callback in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (9409)
gui_mainfcn in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (11138)
CellProfiler in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (55)

thanks for your help

Tim


Rescale intensity
#2

Hi Tim,

Unfortunately, what you’re describing is a bug in the code.

If you’re using the compiled version of CellProfiler (an executable which doesn’t require MATLAB), we don’t have a workaround for you, but we’ll correct it with the next release.

If you’re using the developer’s version (which requires MATLAB and the image processing toolbox), we can provide you with the fix. Just let us know.

Regards,
-Mark