I’m hoping someone can help me with this issue.
I have a 96 z-stack image of some micro-particles and I want to measure the volume, surface area, diameter, etc of these particles. The protocol is as follow:
- open .tiff image with bio-formats (96 stacks image)
- go to slice number 48 (which should be the most focused slice)
- adjust threshold using Otsu thresholding & create a binary image
- image segmentation with MorphoLibJ
- open the segmented image with 3D ROI manager and get my measurements
What I have noticed however, is that based on the slice of my z-stack I select in step 2 (so the slice on which the thresholding is based upon), my measurements will change at the end, so for instance the value for the volume, surface area, etc.
Unfortunately the microscope I am using is not automatized so most of the time the most focused slice ends up being number 48 (as it should be); however sometimes it is number 50 or 52 for instance and so my measurements at the end would not be correct.
My question is, is there a way to automatically pre-select the most focused slice (e.g. the slice with the brightest point) so that I do not have to manually check which slice I should select prior to running my image segmentation protocol?
Hope it makes sense & Thanks in advance!