3D Foci Identification


I am a novice image analyst currently working on creating a cell profiler pipeline for 3D analysis of foci within segmented nuclei using data generated on a high throughput imager.
I am trying to compare my 3D outputs (nuclei and foci segmentation) to segmentation on 2D MIP projection images. However, I am unable to do the following.

  1. Create a 3D Z stack for visualization, so I don’t have to compare each Z-slice to the 2D output.
  2. Annotate/ Number the foci or nuclei on the output 3D image for validation
    I was able to label the foci using Watershed and exported the data as a spreadsheet, but I wanted to label the count on the image for comparison to the 2D pipeline.
  3. obtain volumetric measurements for foci intensity and size

Looking forward to any guidance on how to approach these issues! Thanks!

Hi @liqw,

Here are some suggestions,

  1. 3D visualization is not possible using Cellprofiler. You can save the segmented objects as a tif image and use the visualization tool from other softwares like Fiji/ImageJ.
  2. If the pipeline is 3D, it is difficult to get the display whereas in 2D you can try “DisplaydataonImage” module.
  3. In case of 3D pipleline, “MeasureObjectSizeShape” module will give the volumetric measurements. check these links,


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