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

From NAMIC
Revision as of 19:47, 16 May 2007 by Agouaillard (talk | contribs)

Jump to: navigation, search
Home < NA-MIC NCBC Collaboration:3D+t Cells Lineage:GoFigure

Scientific Background

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

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.

Open Source and Open Software

Even if the Beta version of GoFigure is still only distributed on-demand, the project embrace the OpenSource and OpenData philosophy. We want the software and the data not only to be at the disposition of the researchers but we also want the researchrs to be able to make they own modifications and enhancements to it. the transition phase from the Alpha version (prototype) to a full open source software is almost complete now. The (actual) beta version is based on the following NA-MIC kits:

  • VTK
  • ITK
  • CMake
  • CTest
  • CPack

and on the following OpenSource software and technologies:

  • svn
  • track
  • wiki, mailing list, ...

We have postdoctoral positions to fill related to GoFigure development, please consult this page

Objective:

  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

Progress:

  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)

Links:

  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