Projecting 2D gene expression data into 3D and 4D space

Abstract

Video games typically generate virtual 3D objects by texture mapping an image onto a 3D polygonal frame. The feeling of movement is then achieved by mathematically simulating camera movement relative to the polygonal frame. We have built customized scripts that adapt video game authoring software to texture mapping images of gene expression data onto b-spline based embryo models. This approach, known as UV mapping, associates two-dimensional (U and V) coordinates within images to the three dimensions (X, Y, and Z) of a b-spline model. B-spline model frameworks were built either from confocal data or de novo extracted from 2D images, once again using video game authoring approaches. This system was then used to build 3D models of 182 genes expressed in developing Xenopus embryos and to implement these in a web-accessible database. Models can be viewed via simple Internet browsers and utilize openGL hardware acceleration via a Shockwave plugin. Not only does this database display static data in a dynamic and scalable manner, the UV mapping system also serves as a method to align different images to a common framework, an approach that may make high-throughput automated comparisons of gene expression patterns possible. Finally, video game systems also have elegant methods for handling movement, allowing biomechanical algorithms to drive the animation of models. With further development, these biomechanical techniques offer practical methods for generating virtual embryos that recapitulate morphogenesis. Developmental Dynamics 236: 1036 -1043, 2007.

Prototipe Desain Gedung Kuliah 1 Universitas Klabat Dengan Tampilan First Person View Menggunakan Metode UV Mapping

“…Pembuatan prototipe ini menggunakan konsep 2D yang nantinya dapat dikonversi menjadi 3D dengan membuat rancangan objek 2D yang disusun sehingga membentuk objek 3D. metode ini disebut dengan UV Mapping [7] [8].…”

Eye Field Specification in Xenopus laevis

“…The relatively slow generation time (1-2 years) and pseudotetraploid genome of X. laevis has lead to the more recent use of the smaller and more rapidly developing (as short as 4 months) diploid Xenopus tropicalis, allowing for the rapid generation of breeding lines (Amaya et al, 1998;Bisbee et al, 1977;Graf and Kobel, 1991). These new technologies, the ever expanding computer based and online Xenopus resources (http://www.xenbase.org/), coupled with the powerful "old school" embryological manipulation, make Xenopus an ideal model system for identifying the mechanism driving eye field specification Gerth et al, 2007;Gilchrist et al, 2009;Pollet et al, 2000Pollet et al, , 2003Pollet et al, , 2005Segerdell et al, 2008;Vize, 2001). The sequencing of the X. tropicalis genome has been completed and there is an initiative to sequence the X. laevis genome.…”