This is the development repository for our NSF ABI grant

SlicerMorph enable biologists to retrieve, visualize, measure and annotate high-resolution specimen data both from volumetric scans (CTs and MRs) as well as from 3D surface scanners effectively within 3D-Slicer. It also provides a Generalized Procrustes Analysis (GPA) module as well as tools to visualize PCA decomposition of the GPA results.

To install SlicerMorph, please first install the Preview Release of 3D-Slicer. Open the application and use the Extensions Manager module to install the SlicerMorph extension. After restarting 3D-Slicer, all SlicerMorph modules will be available in the application.

• ConvertMorphologikaLandmarks: Imports a Morphologika formatted landmark file that may contain multiple subjects and exports a Slicer .FCSV landmark file for each individual to a directory specified by the user.
• GPA: Performs generalized Procrustes analysis (GPA) with or without scaling and principle component analysis (PCA) of shape from landmark data and provides visualizations of statistical output.
• ImportSurfaceToSegment: Imports a 3D surface model as a segmentation and prompts the user to edit it using the Segment Editor module.
• MorphoSource: MorphoSource is a publicly available repository for 3D media representing biological specimens. This module provides convenient access and data import from M/S directly into Slicer.
• ReadLandmarkFile: Imports IDAV landmark editor files with header length specified by the user.
• SkyscanReconImport: Imports an image stack from Bruker/Skyscan reconstruction software (Nrecon) with correct voxel spacing and orientation as a 3D volume.

This project is supported by a NSF Advances in Biological Informatics Collaborative grant to Murat Maga (ABI-1759883), Adam Summers (ABI-1759637) and Doug Boyer (ABI-1759839).

See License.md