Abstract
In developmental biology an overwhelming amount of experimental data concerning patterns of gene expression is produced revealing the genetic layout of the embryo and finding evidence for anomalies. Genes are part of complex genetic cascades and consequently their study requires tools for handling combinatorial problems. Gene expression is spatio-temporal and generally, imaging is used to analyze expression in four dimensions. Reporting and retrieving experimental data has become so complex that printed literature is no longer adequate and therefore databases are being implemented. Zebrafish is a popular model system in developmental biology. We are developing a 3D digital atlas of the zebrafish embryo, which is envisaged as standard allowing comparisons of experimentally induced and normally developing embryos. This 3D atlas is based on microscopical anatomy. From serial sections 3D images are reconstructed by capturing section images and registering these images respectively. This is accomplished for all developmental stages. Data management is solved using XML which is platform independent, ASCII-based, interchangeable and allows easy browsing. Applying supervised segmentation accomplishes a completely anatomically annotated 3D image. It divides the image into domains required for comparison and mapping. Experts provided with dedicated software and Internet-access to the images review annotations. Complete annotation and review is stored in a database.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of SPIE - The International Society for Optical Engineering |
| Publisher | Society of Photo-Optical Instrumentation Engineers |
| Pages | 242-252 |
| Number of pages | 11 |
| Volume | 3964 |
| State | Published - 2000 |
| Externally published | Yes |
| Event | Proceedings of the 2000 Internet Imaging - San Jose, CA, USA Duration: Jan 26 2000 → Jan 28 2000 |
Other
| Other | Proceedings of the 2000 Internet Imaging |
|---|---|
| City | San Jose, CA, USA |
| Period | 1/26/00 → 1/28/00 |
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ASJC Scopus subject areas
- Electrical and Electronic Engineering
- Condensed Matter Physics
Cite this
Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. / Verbeek, Fons J.; den Broeder, M. J.; Boon, P. J.; Buitendijk, B.; Doerry, Eckehard; van Raaij, E. J.; Zivkovic, D.
Proceedings of SPIE - The International Society for Optical Engineering. Vol. 3964 Society of Photo-Optical Instrumentation Engineers, 2000. p. 242-252.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data
AU - Verbeek, Fons J.
AU - den Broeder, M. J.
AU - Boon, P. J.
AU - Buitendijk, B.
AU - Doerry, Eckehard
AU - van Raaij, E. J.
AU - Zivkovic, D.
PY - 2000
Y1 - 2000
N2 - In developmental biology an overwhelming amount of experimental data concerning patterns of gene expression is produced revealing the genetic layout of the embryo and finding evidence for anomalies. Genes are part of complex genetic cascades and consequently their study requires tools for handling combinatorial problems. Gene expression is spatio-temporal and generally, imaging is used to analyze expression in four dimensions. Reporting and retrieving experimental data has become so complex that printed literature is no longer adequate and therefore databases are being implemented. Zebrafish is a popular model system in developmental biology. We are developing a 3D digital atlas of the zebrafish embryo, which is envisaged as standard allowing comparisons of experimentally induced and normally developing embryos. This 3D atlas is based on microscopical anatomy. From serial sections 3D images are reconstructed by capturing section images and registering these images respectively. This is accomplished for all developmental stages. Data management is solved using XML which is platform independent, ASCII-based, interchangeable and allows easy browsing. Applying supervised segmentation accomplishes a completely anatomically annotated 3D image. It divides the image into domains required for comparison and mapping. Experts provided with dedicated software and Internet-access to the images review annotations. Complete annotation and review is stored in a database.
AB - In developmental biology an overwhelming amount of experimental data concerning patterns of gene expression is produced revealing the genetic layout of the embryo and finding evidence for anomalies. Genes are part of complex genetic cascades and consequently their study requires tools for handling combinatorial problems. Gene expression is spatio-temporal and generally, imaging is used to analyze expression in four dimensions. Reporting and retrieving experimental data has become so complex that printed literature is no longer adequate and therefore databases are being implemented. Zebrafish is a popular model system in developmental biology. We are developing a 3D digital atlas of the zebrafish embryo, which is envisaged as standard allowing comparisons of experimentally induced and normally developing embryos. This 3D atlas is based on microscopical anatomy. From serial sections 3D images are reconstructed by capturing section images and registering these images respectively. This is accomplished for all developmental stages. Data management is solved using XML which is platform independent, ASCII-based, interchangeable and allows easy browsing. Applying supervised segmentation accomplishes a completely anatomically annotated 3D image. It divides the image into domains required for comparison and mapping. Experts provided with dedicated software and Internet-access to the images review annotations. Complete annotation and review is stored in a database.
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M3 - Conference contribution
VL - 3964
SP - 242
EP - 252
BT - Proceedings of SPIE - The International Society for Optical Engineering
PB - Society of Photo-Optical Instrumentation Engineers
ER -