About

What is CERAMICCA?

Advances in Biomedical Imaging have enabled scientists to acquire exquisite images of human anatomy and function and these images are vital to understand the onset and progression of a wide range of human diseases. Modern scanners are exquisite cameras - they can observe exquisite detail of internal anatomy and function that are provided in the form of raw images. The availability of large scale imaging databases, containing hundreds of thousands to millions of images, has now shifted the bottleneck in understanding diseases from the acquisition of data to the analysis and interpretation of data. In the 'omics' era of "biomedical big data", where databases containing several terabytes of imaging data are commonly available, computational algorithms, tools and software for the analysis of large scale multimodal and multivariate datasets are essential to discover useful patterns, identify outliers and interpret each image in the context of variability in normal and diseased states. In addition, the ability of process tens-of-thousands to hundreds-of-thousands of images through computational models and tools requires the ability to harness the compute power of geographically-distributed clusters in an automated manner, for it is manually unfeasible to manage the required order of millions of jobs to perform the many steps in measurements needed in large scale processing.

CERAMICCA - Cloud Engine Resource for Accelerated Medical Image Computing for Clinical Applications - is a web portal for the secure high-throughput analysis of largescale imaging databases by leveraging the computational power of multiple large compute clusters in a transparent manner to the end-user. CERAMICCA manages secure data upload, submission, transmission, processing, monitoring and cleanup from one central web-location thereby hiding the tedium and complexities of interacting with multiple compute cluster environments and providing a unified, fast, simple, secure and highly-automated pipeline for the analysis of imaging databases. Currently CERAMICCA connects researchers to ready made MRI analysis modules developed at Simon Fraser University in the Functional & Anatomical Imaging & Shape Analysis Lab of Professor Mirza Faisal Beg. However, it is a general purpose system that is designed to allow end-users to bring their computational modules as plugins into CERAMICCA and harness the aggregated bandwidth of multiple distributed compute clusters in an automated manner.

What can CERAMICCA do for me?

The modules currently available on CERAMICCA are mainly dedicated to brain imaging (MR). Rapid development is taking place in the background to provide modules for retina OCT imaging as well as other imaging modalities (CT). The brain-specific modules currently available allow users to perform whole-brain and subcortical segmentation and registration as well as visualize the results of the each stage of processing for easy inspection before downloading. CERAMICCA processes images and notifies you by email when processing is complete.

Can CERAMICCA process images already on Compute Canada/NIACAL systems?

Provided your data is housed on Cedar, then there is no need to re-upload the images. For more information, please visit the documentation page. There are Unix permissions issues with this procedure, so be sure to contact us to establish a collaboration.

How can users provide feedback?

Contact us with suggestions, bug reports, or inquiries.