Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

Software for Fluorescence Molecular Tomography (FMT)

Dr. Vasilis Ntziachristos

This project is a collaboration between Center for Integrative Biomedical Computing and Dr. Vasilis Ntziachristos, Director of the Laboratory for Biooptics and Molecular Imaging (LBMI), in the Center for Molecular Imaging Research (CMIR) at Massachusetts General Hospital (MGH). The primary interest of the LBMI is the development of novel optical imaging and spectral techniques that allow non-invasive or minimally invasive interrogations of molecular function and gene-expression in tissues.

Dr. Ntziachristos is one of the leaders in the field of optical molecular imaging, and the CMIR, under the direction of Dr. Ralph Weissleder, is one of the leading sites in the world for research into molecular imaging. Dr. Ntziachristos was named by Technology Review magazine as one of the TR100 top young innovators for 2004. His group has recently published advanced methods for visualizing proteases and apoptotic responses to treatment in Nature Medicine and PNAS respectively using imaging systems developed in-house.

The work of the LBMI primarily involves what is called Fluorescence Molecular Tomography (FMT), in which fluorescence reporters (molecular beacons, tagging agents, fluorescent proteins) are resolved tomographically through whole animal bodies. The technique illuminates tissue from different view points, or projections, using light at the fluorochrome excitation wavelengths and detects light at both the excitation and emission wavelengths using a CCD camera and appropriate filters. Then, light propagation models are used to reconstruct the location and strength of the tagged fluorescent sources in the tissue. The work is primarily done in animals (mice) and the lab has developed quite sophisticated hardware and matching forward models to accomplish this work.

The longer-term goals of the lab are to improve our understanding of the molecular and genetic responses of cancer in vivo and to invent tools to aid and accelerate the development of appropriate targeted pharmaceutical therapies. Examples of current applications include: imaging of enzyme expression patterns in various tumor cell lines, imaging of apoptosis or imaging of gene expression associated with viral transfection and the in vivo evaluation of disease response to drugs.

Prof. Brooks, along with a colleague at Northeastern University, Prof. Eric Miller, is currently co-supervising a PhD student, Mr. Damon Hyde, who is working in Dr. Ntziachristos's lab. The immediate direction of Mr. Hyde's current work is to understand and characterize the various noise sources in their imaging system. The goal is to develop appropriate advanced reconstruction algorithms to improve the robustness, accuracy, and sensitivity of the reconstructions. Dr. Ntziachristos is currently submitting a proposal to NIH to develop systems for gene-expression imaging that require high detection sensitivity with low SNR. This is a particular area in which the collaboration with Center for Integrative Biomedical Computing will be invaluable.