Welcome to the 3D-Quantitative Phenotyping Gateway (3D-QPG)!

3D-QPG is a computational platform that provides open-source image analytics for processing and analyzing 3D imagery (e.g., CT, microCT, OPT, OCT and/or MR) from model organisms. Of particular interest to the potential users is the availability of the Advanced Normalization Tools (ANTs) ecosystem and its associated anatomical template building tools, R package for statistical analysis, and open-source biomedical visualization suite 3D-Slicer.

For the convenience of the community, 3D-QPG provides a virtual HPC environment at no cost to the users through a resource allocation from NSF/XSEDE to Dr. Murat Maga (TG-BIO180006). To use the platform, please get in touch with me via e-mail (maga@uw.edu) with the subject line 3D-QPG, and a brief description of your project, image format and sample sizes. I will get back to you in 24-48h with information about how to access the resources and necessary steps to get your data in.

 

Some examples of the potential use of 3D-QPG are:

Template-based automated landmarking:

https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-015-0127-8

Construction of de-novo anatomical templates for model organism:

https://onlinelibrary.wiley.com/doi/abs/10.1111/joa.12645