GSoC/GCI Archive
Google Summer of Code 2015

Department of Biomedical Informatics, Stony Brook University

License: Apache License, 2.0

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Mailing List:!forum/stonybrookbmigsoc

The Department of  Biomedical Informatics (BMI) is the home of biomedical informatics research and education at Stony Brook University. The department has a key role in delivering innovative informatics concepts and implementations to enhance scientific investigations and healthcare delivery as well as to train next generation of biomedical informatics researchers. The department carries out cutting edge research in a wide range of informatics areas, including Clinical Informatics, Translational Informatics, Imaging Informatics, Pathology Informatics, Bioinformatics, Public Health Informatics, and Computational Science, and drive the development of novel Biomedical Informatics concepts, methods, and tools. The education mission of the department is to train and prepare students and postdoctoral researchers to become leaders in the field of biomedical informatics and shape the informatics research and applications to advance biomedical research and healthcare delivery.


  • High performance vessel analysis tools:3D vessel reconstruction & analysis In this project under Google Summer of Code 2015, an efficient and scalable version of HPC implementation will be done using C++ programming language leveraging the powerful and rich open source libraries such as openCV, openSlide, VTK etc. to study 3D whole-slide microscopy image datasets and reconstruct 3D vessel structure to analyze serial liver slices.
  • Large scale image viewing/editing module in 3D Slicer Description: create an extension in C++ for the cross-platform imaging framework 3D Slicer that enables viewing and editing of large two-dimensional images. This proyect will utilize QT for its GUI, VTK for displaying and visualizing the images, and libraries such as openSlide and bigTiff to read and write the images from and to files. An initial prototype for reading and interacting with these large scale images was made using QT Creator. Available at the provided URL.
  • Visualization of Multivariate Analysis of TCGA data using WebGL I will develop a interactive browser application that visualizes similarities between patients based on the molecular and clinical patient data, which should serve as a visual aid in the analyzation of TCGA data. In agreement with the architecture of the OpenHealth app, the analytical processing of the data will take place in the browser on the client side. Javascript will be used for the numerical and algorithmic aspect and WebGL for the illustration.