I am trying to montage two stacks of ~ 1000 slices (.TIF SEM greyscale images). One stack is an overview of an area and the other stack is a region of interest within that overview (both collected from the same sample). Both stacks have nearly the same number of pixels (6k x 5k), however one stack has a pixel size of 50 nm and the other stack has a pixel size of 11.5 nm. I’ve set these properties for the stacks using FIJI (->Image->Properties; I’ve tried using nm, um, and pixels as units). Yet, when I import the stacks into TrakEM2, they open as though they are the same scale. For example (note these two images are from different regions in the stack - this is just for illustration purposes):
It appears as though TrakEM2 is just registering the number of pixels, and not their respective scale. Here is an example of what I’m hoping to achieve (I did this by approximately scaling the second image, also just for illustration):
Is there a way to get TrakEM2 to recognize the different pixel scales? Or perhaps I haven’t properly set the pixel sizes in the image metadata?
Thanks so much!
(PS I am able to ‘trick’ TrakEM2 by cropping and resampling the overview stack using Amira. When resampling from 50 nm to 11.5 nm, the Amira resample module adds pixels to the image so that when I load it into TrakEM2 it appears to be the correct scale. This is very cumbersome and time consuming however, and it requires decent computational power…)