Neighbors cellprofiler


I would like to quantify the distance between microglia and blood vessels. Do you have any pipeline suggestion that I can use to quantify this?

Many Thanks,

I would recommend providing a sample image, or at least some idea of how you are generating your data.

  1. Brightfield or IF?
  2. 2D or 3D?
  3. Edge to edge or center to center? Or center to edge?
  4. How large are your images?


Thank you very much for your quick reply.

Please find attached the images (including nuclei)
The image is for IF (2D) and I would like to calculate the distance center to center.

Many Thanks,

Snap-07_b0c0x0-692y0-520.tiff (166.8 KB) Snap-07_b0c0x0-692y0-520.tiff_metadata.xml (335 Bytes) Snap-07_b0c1x0-692y0-520.tiff (190.4 KB) Snap-07_b0c1x0-692y0-520.tiff_metadata.xml (335 Bytes) Snap-07_b0c2x0-692y0-520.tiff (205.9 KB) Snap-07_b0c2x0-692y0-520.tiff_metadata.xml (335 Bytes)

Great! Hopefully someone conversant with CellProfiler will be along to help you :slight_smile: I don’t actually use it, but wanted to make sure enough information was available for someone to help!

Hi @mtaga5510,

I don’t have already existing pipeline. But the workaround could be like this,

  1. Segment the nuclei (using IdentifyPrimary Object)
  2. Segment the microglia (using IndentifySecondary object), check thislink.
  3. Segment your bloodvessels (using IdentifyPrimary Object)
  4. To measure the distance between object you could use “RelateObjects” module.
    In case you are beginner with the CP, the example pipeline could help you start with.


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