Problem with export modules

cellprofiler

#1

Hello,
We are setting up a pipeline to analyze wound healing assays we are doing using fluorescence.
Here is the pipeline we would like to use

LoadImages
SubtractBackground
RescaleIntensity
Smooth
MeasureImageAreaOccupied
ExportToExcel

The pipeline was running fine without the SubstractBackground module but as soon as we add the SubstractBackground, we get an error message telling: “Cell contents reference from a non-cell array object in the ExportToExcel module”. We got the same message with the ExportToDatabase module.

As we get best results with the SubstractBackground it would be nice to keep this module. So, we are wondering what can can be done to avoid this error.

Thank you for your help.
Daniel


#2

Hello,
I am looking into this issue for you. In the mean time, have you tried using the ‘Export To Excel’ or ‘Export To Database’ option from the DataTools? (Click Data Tools >> Export To Excel >> select the output file).

thanks for your patience,
martha


#3

I just tried both Export to Excel or to Database from DataTools and I got the same error…

Daniel


#4

Hi,
What operating system are you using?

thanks,
martha


#5

I’m using Windows XP with the last version of CellProfiler.

Daniel


#6

Looks like a bug in SubtractBackground. This bug is only harmful if SubtractBackground is followed by an Export Module, and thus rare. It will be corrected in the next release, but until then you can modify these lines in the code to fix it (assuming you have the Developer’s version of CellProfiler!)

Line 189 should read:
handles.Measurements.Image.IntensityToShift{handles.Current.SetBeingAnalyzed}(:,NewPos) = MinimumTenthMinimumPixelValue;

And line 192 should read:
handles.Measurements.Image.IntensityToShift{handles.Current.SetBeingAnalyzed} = MinimumTenthMinimumPixelValue;

Let us know if this helps.
Cheers,
Dave


#7

Hi Dave,

as we don’t own Matlab, would it be possible to send me by email the compiled fixed module.

Thank you.


#8

Hi,
I will recompile it on Monday.
~martha


#9

If somebody could send me the compile module with the correction it would be really appreciated.

Thank you
Daniel


#10

Hi,
I am in the process of recompiling the software. It will be available online soon.
~martha