- Senior software Engineer, Key Staff, Caltech.
- Main mission: Lead of "GoFigure" software development.
- Other objectives: assist biologists with various Image processing problem.
- Side project: integration of more mesh processing in ITK (QuadEdgeMesh project)
Center For Excellence In Genomics
Imaging for System Biology
Imaging is becoming a very important approach for doing systems biology because of its unique ability to capture quantitative, longitudinal data at cellular resolution from living organisms. However, the use of imaging for systems biology presents unique and significant challenges for image analysis. We have recently established a Center of Excellence in Genomic Science at Caltech to develop the technology (imaging hardware, image analysis software, and genetic/molecular tools) to develop an imaging based platform for deciphering zebrafish embryogenesis.
In Toto imaging
In Toto Genomic Analysis of Vertebrate Development
This Center of Excellence in Genomic Science (CEGS) assembles a multidisciplinary group of Caltech investigators, Sean Megason, Niles Pierce, Scott Fraser and Marianne Bronner-Fraser, to develop innovative technologies with the goal of imaging and mutating every developmentally important vertebrate gene. Novel "in toto imaging" tools will make it possible to analyze gene expression and function in developing vertebrate embryos in time and space, digitizing in vivo data in a systematic, high-throughput, and quantitative fashion.
Key technologies will be developed and tested in the zebrafish embryo since it is ideal for both imaging and genetics. We are generating FlipTraps to fluorescently mark protein expression and gene function on a genome wide scale, and developing new techniques for in situ hybridization using HCR that permit simultaneous analysis of multiple marker genes. In toto imaging will be used to digitize this marked data quantitatively at cellular resolution throughout embryogenesis. The vast amount of quantitative, in vivo data obtained through this project will serve as the basis for creating a "digital fish" that models the molecular and cellular orchestra that transforms an egg into an embryo.
GoFigure is an image analysis software package specifically designed for visualizing, tracking, and analyzing cells in multidimensional confocal/two-photon image sets. Eventually GoFigure will be able to analyze time-lapse series of confocal image stacks (xyzt) and to automatically segment and track cells in 2D, 2D+time, 3D, 3D+time, and 3D+time+cell division.
GoFigure now runs on the Microsoft Windows platform. GoFigure utilizes a MySql database back-end so it can handle extremely large image sets.
- old website
- Insight Journal Publication (MICCAI 2007)
- NAMIC's wiki page at 5th NA-MIC's Project week (MIT, June 29, 2007).
- Publicly available dataset
- integration of a QuadEdge Data structure in ITK (ITK 3.4?)
- development of an Euler operator implementation for the above mentioned data structure.
- integration of optimized, state of the art, discrete surface processing algorithms in ITK.
Past and current collaborators
- Remy Prost [France - Creatis]
- Sebastien Valette [France - Creatis]
- Christophe Odet [France - Creatis]
- Eric Boix [France - CNRS - ENS ]
- Takashi Kanai [Japan - U. of Tokyo]
- Arnaud Gelas [Singapore - BIL]
- Xianfeng Gu [USA - SUNY STony Brook]
- Marc Janier [France - Animage]
- Emmanuel Chereul [France - voxcan]
- Sean Megason [USA - CEGS]
- Titus brown [USA - CEGS]