Neurite length + Colocalize quantification

Dear All

I am totally newbie in using CellProfiler. I a looking for pipeline that can automatically measure neurite length and count the co-localising cell (if possible).

According to an attached picture, I would like to quantify neurite length in green channel, also counting nuclei that have red+DAPI and DAPI alone.

I am trying to explore several ImageJ plugin such as NeuriteTracer and Morphoneuronet but I seem cannot follow an instruction well enough and cannot get through to get result.

Any comment and suggestion is truly appreciate.

Cheers !!!


Hi @NopJong,

In ImageAnalysis each problem has its own specification, so there is no one pipeline that is suitable for all kinds of images. Nevertheless, Cellprofiler have some example pipelines from basic to advanced pipeline which might help you to start with.

With respect to your sample images, though I don’t have direct pipeline I could suggest with rough workflow.

  1. Segmentation of Nuclei (examples from Basic pipelines)
  2. Segmentation of Neurites (Check the documentation, where you can enhance the neurites before segmentation. This facilitates your neurite segmentation better)
  3. Segmentation from the Red channel
  4. To relate DAPI with Red you could try β€œRelate objects” module (check Colocalisation pipeline)
  5. Measure features (Check the example pipelines)

In addition, this thread might be useful too.

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Dear Lakshmi

Many thanks for your suggestion. I would need to learn more about CP and will try to follow your suggestion. I will let you know an outcome soooon.

Many Thanks > /\ <

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