Linking HitTable to per_object table to examine classified cells


I’m having a problem understanding how to link tables together in the Analyst tool.

I have trained the classifier to recognize two different cells populations (positive or negative) and scored all of my images for these phenotypes. Now that I have done this, I would like to use the scatter plot, histogram, and heatmap features to examine per object measurements for each of my classes (positive or negative). I want to do this to see (and show) the important measurements for defining my phenotypes.

My problem is that my ‘HitTable’ (created from scoring all images after training) is not linked to the per_objects table, and I have no clue how to achieve this. I have tried many different variations of linking using the “OTHER TABLE” option in the drop down menus in the heatmap/scatterplot options, but none seem to work for me. Perhaps I am missing a step somewhere?

Also, a minor problem I have observed is that when you are setting a gate in the heatmap/scatterplot options on some data filtered by plate/well/ image, and you request to see the cells in that gate, the filters do not apply to the cells you are shown. i.e. when I filter by my mutant and request cells in a gate, the program will show me cells from my wild-type images too. Perhaps I am missing something here too?

Thanks for any help you can provide.


Nice to hear from you! I’m afraid we don’t have much knowledge in the group on that functionality anymore :cry: Your best bet is to peruse the help/documentation but if something isn’t working properly, it’s entirely possible it’s not you… it’s a bug. Wish I had better news!

Thanks for the response Anne. I appreciate it.

I’ll play around some more and if I figure it out I’ll post what I did here.

Excellent software by the way, made lots of my experiments much easier to analyse!

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For anyone interested, I managed to fix the problem. Not sure if this is the best way to go though.

Essentially, CellProfiler Analyst was generating the classification per_object table after classification but not specifying a reasonable name to it (it was simply called “MyExpt_”). So I accessed the properties file (with notepad) and renamed the table output (under the section “Output per-object classes” to be ‘MyExpt_classified’. Doing this overcame the error of CellProfiler Analyst not recognizing that these tables were linked. You can name the classification table prior to opening the properties file in analyst.

Hope this helps some people.


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That’s fantastic!! Thanks so much for reporting back.