Error in identifying primary objects following image J

Hi,

I got an error massage “Index out of bounds” while identifying primary objects, after using image J module (Subtracting background using rolling ball). When I use Image J directly (without the cellProfiler) , saving the file in tiff format and then applying the cellProfiler on this image the pipeline runs smoothly. Since this is time consuming I prefer to use only cellProfiler if possible. (I have tried to add a second pipeline of ImgJ just to save the image in tiff format but it did not solve the problem.)

Thank you,
Reinat

Hi Reinat,

Would you mind posting your pipeline plus an example image in which you get this error message? Also, the same rolling ball background subtraction can be achieved in CellProfiler by using the EnhanceOrSupressFeatures module, using Speckles as the feature type.

Regards,
-Mark

Thank you for your answer.
I have attached a pipeline with the example

Thank you,
Reinat





Speckle_ImgJ.cp (10.7 KB)

Hi Reinat,
A couple of extra points:

  • The error you encountered is because CellProfiler is expecting pixel values from 0 - 1, and the output of RunImageJ is producing negative-valued pixels. This is causing IdentifyPrimaryObjects to error.
  • For an example of an assay much the same same as yours, check out cellprofiler.org/examples.shtml#Speckles

Cheers,
-Mark