Hi guys,
So I have been trying to measure the area of keratinocyte cells in zebrafish using IMARIS. The only way that I was able to figure out how to do so, is by creating Isosurfaces. But when I tried to do so, the system marked the mucus/goblet cells that have brighter expressions than the actual cells of interest. I have played with the parameters, but have not been able to figure out what the issue is and I have tried with ImageJ before but it was taking too long.
Appreciate any help!
Hi Kiarash. I think you first have to segment the cells and then you can measure the area. If your image is 2d then segmentation will be easy for your image. But in 3d it will be super complex. I am sure that Imaris have a way to segment the cells based on ROI. If you cannot find then I can suggest QuPath which has very nice algorithm based on watershed there you can segment most of the cells with choosing the watershed parameters. Once you have segmented mask object then you can import in ImageJ which can calculate all the morphometric properties of the cells.
Ankit Agrawal Thanks for your help. I am not sure how to segment the cells but will give that a shot. I have tried using ImageJ but a similar issue arises, in that case, I am able to manually calculate the are but it takes forever.
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