Dear all,
I just learned that our resource allocation request on the NSF's XSEDE HPC 
infrastructure to create a science gateway for 3D quantitative phenotyping is 
approved. When implemented, this will be a cloud platform where registered 
users can upload their imaging datasets and use the provided R and associated 
mesh/image analysis on the virtual HPC cluster. In addition, we will also make 
the ANTs diffeomorphic deformable image registration library and its R package 
available on this gateway. Provided tools will enable generation of a 
population template from a set of volumetric images [1-2]. Average anatomical 
templates (or atlases) provide a least-biased coordinate system to study 
structure-function relationships [3]. They operate as a reference frame for 
understanding the variation in anatomy, and as a probabilistic space into which 
structural features are mapped. In more practical terms, templates can aid in 
the automated or semi-automated segmentation of complex morphology [4], or 
landmarking [5-6].  Our goals is to facilitate morphometric analysis of large 
structural datasets using open standards and analytical pipeline.
I expect the gateway in its rough form will be available by fall of this year. 
This year we have enough allocations to process about ~1000 medium resolution 
(i.e. 512^3 voxels or less) dataset. If you are interested, please get in touch 
with me at<>. I am particularly interested in 
hearing from developmental biologist or people working on model organisms.
[1] For volumetric dataset
[2] For mesh based dataset

MORPHMET may be accessed via its webpage at
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 

Reply via email to