FIJI 3D cell density measurement

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Max-Heart-nuclei.tif (141.4 KB)

Hi,

Hi,

I want to measure the cell density in the attached images of hearts (nuclei labelled).

I can derive the number of cells using 3D manager, but I am unable to derive the surface area of the whole heart.

Also, I can’t seem to find a way of numbering each counted nuclei in 3D manager (I can do that it in 3-OC)

Any insights will be hugely appreciated @ThomasBoudier

Thanks,Heart-nuclei.tif (7.0 MB)

Hi @Priya,

First for the second question, are you referring to putting labels on the image ? There is a button “labels” in 3D Manager that will do that. Here the results :
nuclei-1 Objects-1

Best,

Thomas

2 Likes

Hi @Priya,

Regarding the first question, here a simple protocol to extract (what I think is :wink: ) the surface of the heart:

  • 3d median filter 4x4x2
  • 3d maximum filter 4x4x2
  • 3d minimum filter 4x4x2
  • thresholding
  • add to 3D manager and measure volume, surface, …

Best,

Thomas

3 Likes