Tricks for handling biomedical imaging data

Tools

• ImageJ - a simple image processing tool
• MeVisLab - a visual programming interface for medical data

Convert image stack into Raw/TIFF volume (ImageJ)

• load image stack Import > ImageSequence by pointing to the folder that contains your images
• save volume as TIFF or .raw image

Extracting a mesh from a segmentation stack (MeVisLab)

1. use this MeVisLab network
2. load your volume as a TIFF file into the Image Load module
3. set the segmentation id you want to extract as a mesh in the Threshold module