NIH-sponsored zebrafish and Aquatic Models working groups have recommended the creation of web based anatomy, histology and pathology atlases as a community resource. The principal investigators propose to generate and digitize reference glass slides for web-based virtua/microscopy and 3D at as of the zebrafish. This atlas will be available through the Zebrafish Information Network (ZFIN) of the University of Oregon (http://zfin.org/ZFIN/). In virtual microscopy, any computer with a web browser and fast internet connection can function as a microscope, using annotated virtual slide files on a remote server. Virtual slides are GB size, compressed composites of high magnification image tiles or strips;image packets are sent to the remote user according to user-chosen field-of-view and magnification. In the 3D anatomy atlas, selected anatomical structures can be viewed and rotated. The atlases will include normal, and some abnormal, embryos, larvae, juveniles and adults. The experimental features of the zebrafish have made it a premier model for functional genomics. High-throughput mutant, antisense knockdowns (""""""""morphants""""""""), fluorescent transgenic, and chemical screens have already yielded thousands of potential models of human disease affecting a variety of biological functions at a variety of stages of growth and development. A web-based, comprehensive reference atlas of normal zebrafish would greatly facilitate this work. Remote annotation of and access to such atlases will facilitate the growth of the atlas as a resource, as well as individual and collaborative investigations.
Specific Aim 1 is to generate a registry of serial, stained paraffin and plastic sections of normal zebrafish embryos, larvae, juveniles, and adults.
Specific aim 2 is to scan these sections to create virtual slides. Illustrative pairs of annotated fields will be generated.
Specific Aim 3 is to digitally outline histologically identifiable structures in zebrafish embryos, larvae, juveniles, and adults for 3D reconstructions. The resultant infrastructure will be complementary to, adaptable to, and coordinated with those of other model systems. The atlas will support the zebrafish community across multiple disciplines, and address the missions of nearly all Institutes of the NIH.
| Copper, Jean E; Budgeon, Lynn R; Foutz, Christina A et al. (2018) Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish. Comp Biochem Physiol C Toxicol Pharmacol 208:38-46 |
| Kapp, Friedrich G; Perlin, Julie R; Hagedorn, Elliott J et al. (2018) Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche. Nature 558:445-448 |
| Booth, Jennifer L; Peng, Xuwen; Baccon, Jennifer et al. (2013) Multiple complex congenital malformations in a rabbit kit (Oryctolagus cuniculi). Comp Med 63:342-7 |
| Canfield, Victor A; Berg, Arthur; Peckins, Steven et al. (2013) Molecular phylogeography of a human autosomal skin color locus under natural selection. G3 (Bethesda) 3:2059-67 |
| Cheng, Keith C; Hinton, David E; Mattingly, Carolyn J et al. (2012) Aquatic models, genomics and chemical risk management. Comp Biochem Physiol C Toxicol Pharmacol 155:169-73 |
| Cheng, Keith C; Xin, Xuying; Clark, Darin P et al. (2011) Whole-animal imaging, gene function, and the Zebrafish Phenome Project. Curr Opin Genet Dev 21:620-9 |
| Titarenko, Valeriy; Titarenko, Sofya; Withers, Philip J et al. (2010) Improved tomographic reconstructions using adaptive time-dependent intensity normalization. J Synchrotron Radiat 17:689-99 |
| Kawasaki, Kazuhiko (2009) The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues. Dev Genes Evol 219:147-57 |
| Spitsbergen, Jan M; Blazer, Vicki S; Bowser, Paul R et al. (2009) Finfish and aquatic invertebrate pathology resources for now and the future. Comp Biochem Physiol C Toxicol Pharmacol 149:249-57 |
| Sabaliauskas, Nicole A; Foutz, Christina A; Mest, Jason R et al. (2006) High-throughput zebrafish histology. Methods 39:246-54 |
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