DisplayHistogram question

Hello,

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,

David


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.

Regards,
-Mark

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

David

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.
-Mark