Hi,

First, thank you for these amazing tools.
I have used both QhickNII and VisuAlign to get a great registration of my imaging stack to the mouse Allen CCF.
I then used Nutil to feed in a segmentation image (from Ilastik) and got the right results in terms of looking with the online MeshView
Attached is an example (slide1.png).

However I have a problem, I have other information relating to each one of these cells, and I want to know which one of the cells in the output report is which from the input.

Is there a way to know what is the order in which cells were detected?
Can I feed a label image which each cell having a different number to keep identity?

As I have already thresholded and trained a second Ilastik object based network I don't want to lose that information.
Any advice would be appreciated.

Thanks again,
Boaz