I am pretty new to cellprofiler. I have been trying to create a pipeline for automatic cell counts. We use a confocal microscope to take z-stack (3d) images that are saved in an .oib file. Currently we are using three channels (DAPI, Alexa488, Alexa594) so I am trying to separate the individual channels from that one big .oib file and then use “MakeProjection” to create a flattened image of the z-stack per channel.
Then I used the “EnhanceOrSurpress” on the DAPI images so far and they came out pretty good.
The problem I am encountering is when I try to use “IdentifyPrimaryObject” for some reason I cannot get the advanced settings tweaked to pick up anything from my image. Whenever I change it to not use advanced settings it picks up some particles but I would like to use the advanced settings to pick up all of my cells.
Thank you very much for all your help!
Here is my .oib picture that I am trying to work on:
CellCount_Test_pipeline.cpproj (1.0 MB)