Problem with RescaleIntensity module

Usage & Issues
,
#1

I just start a pipeline using CellProfiler 2 but there seems to have a problem with the RescaleIntensity module. We have 12 bits image saved in 16 bits, so we have to rescale the histogram.
When I apply the rescale intensity, I get this error message:

Error while processing RescaleIntensity:
too many values to unpack

Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 792, in do_step
File “cellprofiler\modules\rescaleintensity.pyc”, line 214, in run
ValueError: too many values to unpack

I’m using v.9777 of CellProfiler
It was working fine with CellProfiler 1
Is there something I should do different ?

Thanks,
Daniel

#2

Hi Daniel,

We have noticed this behavior ourselves and corrected it. If you download our newest beta build from our website, your pipeline should work (I believe we’ve just placed a new beta without increasing the version number so it’s still v9777).

As a side note, we noticed this behavior when loading a CP1.0 pipeline in CP2.0. If this is what is occurring with you, you can get around this by adding the RescaleIntensity module yourself in CP2.0, with these settings:

  • Select rescaling method:Choose specific values to be reset to the full intensity range

  • Use the minimum intensity value as the lower limit?:No

  • Use the maximum intensity value as the upper limit?:No

  • Enter the intensity range for the input image:0,0.0625

  • Select method for rescaling pixels below the lower limit:Set to custom value

  • Enter custom value for pixels below lower limit:0

  • Select method for rescaling pixels above the upper limit:Set to custom value

  • Enter custom value for pixels below upper limit:1

Regards,
-Mark

#3

Thank you for the fast answer.
I just downloaded the last CellPorfiler and it solves the problem if I use the exactly the same parameters you mentioned.
Unfortunately, I also have to use (in another pipeline) these two parameters:
Use the minimum intensity value as the lower limit?:Yes
Use the maximum intensity value as the upper limit?:Yes

When I check yes for these two parameters, I get the same error message as before.

Daniel

#4

Hi Daniel,

We have also fixed this behavior as well, and it will be included in the next release. When we release it, I’ll notify you on this post.

Regards,
-Mark

#5

In the meantime, there is a workaround: use the ‘Stretch each image to use the full intensity range’ option.