NA-MIC NCBC Collaboration:3D+t Cells Lineage:GoFigure

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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 due to its transparency and the ability to obtain rapid feedback. To monitor alterations in gene expression in normal and mutant embryos, we will develop new techniques for in situ hybridization that permit simultaneous analysis of multiple marker genes in a sensitive and potentially quantitative manner. Our goal is to combine real-time analysis of gene expression on a genome-wide scale coupled with the ability to mutate genes of interest and examine global alterations in gene expression as a result of gene loss. The vast amount of quantitative, in vivo data obtained through this program will serve as the basis for creating a "digital fish" that models


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. GoFigure is build on top of ITK and VTK toolkits.


  1. Distributed Image database
  2. Very large datasets (200+ Go)
  3. Segmentation of cells in 2D+t, 3D and 3D+t datasets
  4. Real time visualization
  5. New Data structure for 2-Manifolds (itkQE)
    1. Core
    2. Euler Operators
    3. Port of VTK filters to ITK
  6. New Data structure for 3-Manifolds
  7. New Segmentation algorithms


  1. beta version available
  2. itkQE's core in review for integration in ITK
  3. cmake-compliant configuration/compilation
  4. packaging (cpack)
  5. Dashboard (dart2)

To Do:

Key Investigators:

  • Sean Megason (Caltech)
  • Titus Brown (Caltech)
  • Alex. Gouaillard (Caltech)


  1. Center For Excellence in Genomics (caltech)
  2. GoFigure software website
  3. GoFigure and itkQuadEdgeMesh Dashboard
  4. 4-block ppt for NAMIC Project Week will be added here