Count Nuclei



Is there workflow that:

  1. Segments nuclei in a fluorescence image, e.g. applying a threshold followed by a connected components analysis.
  2. Counts the number of nuclei in each image and measures their area.
  3. Generates an overlay of the segmentation and the input image for quality control.

Thank you very much!

Hi Christian there a various such workflows and modules that could be used.

Module: Cell Analyzer, Particle Analyzer 2D, 3D Segmentation and Analysis

Workflows: Cell Counter and Analyzer, Count Particles or Objects (see image)

and even some more depending on what do you excatly what to achieve. I am not sure there is an overlay in the end, but this sounds doable.

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Thank you very much!

I got it working!

I ran the analysis for three input images and got three results, so that is nice :slight_smile:


Is there a way to batch download the results for all the images?

Hi Christian, I think that this is not possible yet, but I will check.

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