So I am trying to learn a bit more about how I can apply clij to analyse my images. I am not doing images on a light-sheet microscope, but I am trying to improve my skills with the image I have. I am trying to understand the pipe line you guys suggested on the paper that you guys describe as
1)push data - I think this part I understood from the little tutorial on clij website
2)Gaussian blur filter - I assumed it means executing the following in my image Plugins > ImageJ on GPU (CLIJ) > Filter > 3D Blur on GPU. Is there a logic to the parameter (sigma) choice?
3)Gaussian blur filter - is this a second round of blurring? In what image I do it, there resulted from step 2 or the original? Do I set the same parameters for the Blur?
4)pixel wise subtraction - what image do I subtract what from?
5)reslicing - Reslicing part was a bit confusing for me… why do we do it? and is it top, right, down, etc???
6)maximum projection - I assumed this is the max projection of the resliced image… correct?
7)pull data- I guess I learned that on the tutorial again
8)spot detection. Is this the 3D spot segmentation?
As you can see my questions are very naive… but I really would love to learn more about it.
Thank you so much,