DisplayHistogram question


First, I want to say thanks so much for making this incredibly useful tool.

I am slowly getting used to CP 2.0 and have encountered a problem in displaying my data using the >Data tools > DisplayHistogram function. In tests using images of stained nuclei I can easily set up the pipeline to identify individual nuclei. I then run ‘MeasureObjectIntensity’ and export the data to a spreadsheet.

After the process is complete, I click ‘Data tools’ and select ‘DisplayHistogram’ and select the .mat file produced from my analysis. The dropdown boxes are selected for: Nuclei, Intensity, IntegratedIntensity, DAPI (as the source image), bins = 100, no, linear. The resulting histogram does not appear to account for all the identified nuclei - there were around 355K nuclei identified in the analysis, the histogram is attached to this post.

Could you please let me know what I am doing incorrectly here as well as tell me what the scale is on the y-axis (I assume that is the ‘real value’ in number of nuclei instead of say, 16K, 14K, etc.)?

Thanks very much,


Hi David,

You are using the data tool correctly; however, the help is misleading: the tool is plotting the values for only the first cycle. I have filed a bug report and will post here when a fix is completed.


I was just curious as to the status of the “Display Histogram” bug fix. I noticed it is not fixed in version r11710.


Version 11710 only deals with a couple of specific bugfixes; see the “News” section on cellprofiler.org under the 2/27/2012 dateline. We do not yet have a timeline for the next release which will incorporate this bugfix, among others.