Segment 2 Channel Nueral Cells Images with CellProfiler


Hi, Dear all:

I am a postdoc researcher working with the bio-imaging group of Bio-informatics Institute of Singapore. Currently, I am working with IMB to process some neural cell images. I am using the CellProfiler to segment the two-channel images. The results is quite nice. Thanks a lot for your effort sand make this software free for the researchers as us.

During the use of CellProfiler, there are several intermediate figures we want to save. I attached two images(each two channels “w2” and “w1”) and the pipeline file I created. The procedure is “loading images”->“RescaleIntensity” of two channels->“IdentifyPrimAutomatic”->“IdentifySecdary”->“SaveImages”.

My question is that after I finish the “IdentifyPrimAutomatic” and “IdentifySecdary”, how can I save the picture of the segmentation results automatically? (as attached “picture 1. png” and “picture 2.png”). Since I have thousand images to process, it is impossible for me to save them manually. I read the manual of CellProfile, it was said that:

“Because CellProfiler usually performs many image analysis steps on many
groups of images, it does not save any of the resulting images to the
hard drive unless you use the SaveImages module to do so. Any of the
processed images created by CellProfiler during the analysis can be
saved using this module.”

I also tried to input the module number, instead of the “image name” in SaveImages, but can not. Then I tried to add a print at the end of IdentifySecdary.m, but it only print the CellProfiler interface. Could please let me know how to configure the CellProfile such that we can save the segmentation results automatically?

Thanks a lot and best regards

Yours sincerely,
YU Weimiao


I’m glad you like CellProfiler!

The answer is probably simple: In the Identify module, one of the last settings is “What do you want to call the outlines?” (or something similar). Just give the outlines a name (like “PrimaryOutlines” or “SecondaryOutlines”) then use an OverlayImages module to place those outlines on top of the original image (or maybe even make a color image of your originals to put the outlines on top using GrayToColor, if you like). Then use SaveImages as usual. If you want to save the random-colored objects (not the outlines), use the ConvertToImage module to convert your objects into an image, then use the SaveImages module as usual. As you noticed, you can save the entire figure window by entering the figure number in SaveImages, but it only allows saving in “fig” format, which can only be opened in CellProfiler or MATLAB.

Best wishes,