Virtual microscopy of zebrafish as a community resource

  • Cheng, Keith (PI)

Project: Research project

Project Details


DESCRIPTION (provided by applicant): 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 ( 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.
Effective start/end date7/1/048/31/12


  • National Center for Research Resources: $544,756.00


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