Overlaying traces from simple neurite tracer to an other image (had to register it using SIFT because it was disaligned)

plugin
overlay
fiji
segmentation
Tags: #<Tag:0x00007fd542e35bd8> #<Tag:0x00007fd542e35a98> #<Tag:0x00007fd542e35958> #<Tag:0x00007fd542e357f0>

#1

Hi,
One of my images skewed when imaging it and so the end image I have has shifted. I’ve used SIFT to register it together. Previously, I had traced quite a lot of it using SNT but every time I open it, it opens on to the unaligned image. When I open traces with the aligned version open, I get the image below (see traces on top left corner).

Does anyone know if there’s a way to open the traces over the shifted image?

Thank you,
Mimi


#2

Welcome to the forum @MimiB!

The simplest way would be to export your tracings as SWC, then re-import using “File> Load Traces/(e)SWC…”, selecting the “Apply offset to SWC file co-ordinates” option and specifying the X, Y and Z offsets.
Alternatively, one would have to write a small script that applies the offsets to all the coordinates of the traced paths.