Per_Object filtering

Is it possible to set filter for object and not only for image?
I have 3 types of objects identified in the image:

  1. nuclei - DAPI positive
  2. nuclei - GFP positive
  3. H2AX foci - labeled in red

In multiwell plate, some columns are not transfected with green protein - they serve as control. Other columns are transfected with GFP but efficiency of transfection is not complete but only around 20-50 percent.
Cells in all columns are stained for H2AX foci. My task is to find how many H2AX foci are in GFP positive and how much in GFP negative cells in those columns which received transfection mixture with GPF fused protein.
See image which documents the setup I used.

The problem I have is how to filter nuclei of certain (low) green intensity (threshold set using background level of green from GFP non-transfected wells) in box-plot chart which displays H2AX foci number per nucleus? There is “add filter” selection but there is not possibility of “per object” (=nucleus in my case) selection but only “per image” selection. In all images (37 images per well in my case) there are green positive (transfected) and green negative cells (non-transfected) so filtering of “per image” does not have sense here. There are multiple choices in “per_image” filter option as visible from image attached , but does any of these help in my analysis? Pipeline project is attached.

Thank you

pipeline.cpproj (2.13 MB)


Unfortunately, filters are only image filters. This thread has more info on the same question: viewtopic.php?f=12&t=3514&p=9879&hilit=filter+per_object&sid=2f5fcee7a318b5a929de99b2ae73b051#p9879

So you can try Gates as decribed above, but the most straightforward way to filter a per_object table (though not necessarily the easiest, nor the most “database-y”) is to create a new column for “green_positive” objects (or whatever) and then use a little SQL to filter the rows. But that does require some SQL knowledge.

And if you simply want counts of, say, green positive objects, then you can do something like this command, in any SQL tool (SQLyog or SequelPro for Windows and Mac, respectively):

SELECT COUNT(*) FROM <your_per-object_table_name> WHERE Nuclei_Intensity_MeanIntensity_RecQL4_green > 0.0072
Hope that helps!