Summary: Imports non-DICOM image sequences (TIF/PNG/JPG/BMP) generated by the Bruker/Skyscan Nrecon software into 3D Slicer and orients the data to match the canonical anatomical planes.

User needs to locate the _REC.LOG file generated by the Nrecon software. All necessary fields (such as voxel spacing, image dimensions and file prefix) are obtained from the log file. It is important that image sequence is unmodified after the reconstruction (i.e., no renaming, or changing the slice numbers, or post-processing with any software)

A transformation is applied to the image to align it with respect to the anatomical coordinates shown in Slicer. It is assumed that specimen is aligned in the scanner using this convention: Anterior of the specimen is into the scanner, and dorsal (superior) surface is facing up. See below:

Memory consumption during import is higher than ImageStacks. Also, no downsampling or subsetting is possible. If those are important, please use ImageStacks module instead.

https://github.com/SlicerMorph/Tutorials/tree/main/SkyscanReconImport