I want to measure volume of Drosophila tracheal tube. I need to normalize 3-D objects (that spans 6-11 z-stacks) with the volume of selected area in trachea in order to get objects per unit volume.
I am facing two problems here-
- Problem in 3-D object count- since my objects spans 6-11 z-stacks, one object is being counted as 11 while thresholding the image.
- Analyzing the volume of the selected area of tube- I am not sure what plugin I should use in Fiji and whether I should normalize the objects with volume or not (as volume will also include hollow space of the tube)
Can anyone advice me how to do volumetric analysis of such structures or any other ways to get a normalized value of objects per unit area so that I can compare change in object count in a control with a knockdown?