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.
- Create a 3D Z stack for visualization, so I don’t have to compare each Z-slice to the 2D output.
- 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.
- obtain volumetric measurements for foci intensity and size
Looking forward to any guidance on how to approach these issues! Thanks!