Exporting image stacks from TrakEM2

Exporting aligned image stacks from TrackEM2 ist an important feature, allowing it to make use of semi-automatic segmentation tools available in others Open Source Software packages (such als MIB, Drishti, Ilastik…) as well as commercial packages (Amira, Imaris, VGstudio…).The export ist easily done after the alignment (see here), either as export of the complete canvas (everything visible in the […]

Aligning an image stack in TrackEM2

This a very brief, compact introduction on how to align image stacks in TrakEM2. 1.open Fiji (download: https://imagej.net/Fiji/Downloads) : choose File in the sidebar –>Import –> Image Sequence 2. Choose the folder with all your images (mac) or open the folder and click on the first image (PC) and select the open button below. 3. the following […]