Hi,
I acquired multiple confocal stack images of olfactory epithelium from rostral to caudal position from 1 slide. I want to create 3d reconstruction by adding all the z stacks to look at expression pattern of few neuronal markers. I am able to add multiple stacks by selecting "add slice" option. However, there is a distance of 50 micron between every 2 slices. 2 questions:
1) Can I add blank space of 50 micron between every 2 slices?
2) How to align for x-y drift between different z stacks?
Thank you
Raghu
1) If you are using ImageJ, you can add any slice spacing in 3D Project settings
Image/Stacks/3D Project >> adjust slice spacing parameter
https://imagej.net/Z-functions
2) alignment of 2d slices should be performed before creation of the 3D stack, either by yourself (e.g., in Elasticks), or can be done using available imageJ toolkits (http://bigwww.epfl.ch/thevenaz/stackreg/)
Hi,
Thank you very much for the reply!
I tried the first option in Image J to add space between to image stacks, but it looked like I can add space between 2 slices of the same z stack but not between 2 different z stacks. I am trying to work on the 2nd option you talked about.
Besides this, I worked on Imaris again, as we have the software available and now I am able to do it! I can add specific distance between 2 z stacks and create a 3d reconstruction of organ from rostral to caudal.
Raghu Ram Katreddi Hi Raghu. I am having the same issue now. May I ask how you adjust slice spacing parameter in Imaris?
Thank you
Bests
Ziming Chen Hi, I don't remember the exact steps/options as its been a while and I am not using Imaris for the past 1 and half year. But I am sure there are options to add particular distance between 2 slices. I added 8-10 z stacks and added equal z distance between each slice. You can also adjust x and y distance. Sorry, I am not able to be helpful at this point