License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: November 02, 2022
Last Modified: November 02, 2022
Protocol Integer ID: 72198
Abstract
How to use ImageJ in our 3D-workflow from data manipulation, import, alignment, segmentation and export as OBJ-file.
•Open Image J and import your Image Sequence
•It is possible in Image J to transform stacks into Images Sequences and vice versa
•Make sure your Image Sequence starts with 1 and choose Use virtual stack to save RAM
•You can scale your data set down too
•Make sure your data set is processablefor your computer
•Binning is easy and suitable for reducing data size, here bin2 from 14.3 to 3.4 GB
•Only bin x and y not z
•Save binned data set
•For the alignment or registration of your virtual stack
•Go to Plugins – Registration – Register Virtual Stack Slices