PennState University has developed a phenomenal resource for zebrafish researchers. It is a web-based anatomical and pathological atlas of the zebrafish. The atlas serves as a resource of reference images of ‘normal’ zebrafish at different stages of development.

The atlas is comprised of two-dimensional histology images taken from serially sectioned specimens, and also includes three-dimensional reconstructions. New additions to the atlas include microCT scans. The atlas can be used as a reference tool, a resource to become more familiar with zebrafish anatomy, and it can serve as a tool for comparing different imaging techniques.

The slides in the Zebrafish Atlas allow the user to choose his or her own field of view and magnification, view labeled sections of the zebrafish, and view sections from different stages of development. The authors report on the Zebrafish Atlas website that they plan to add embryonic, larval, and juvenile sections, as well as comparisons (mutant vs. normal, diseased vs. normal, etc) in the future.

Depending on your area of study, you can select a region of interest to learn more about. For example, the Zebrafish Atlas provides a very useful overview of the (adult) Zebrafish brain in the anatomical reference section.

Credits: http://zfatlas.psu.edu/, NIH grant 5R24 RR01744, Jake Gittlen Cancer Research Foundation, and PA Tobacco Settlement Fund.

Zebrafish are increasing in popularity in countless research areas. Having made its debut in developmental biology, Danio rerio is swimming through research areas spanning from behavioral neuroscience to cardiac or oncological studies. There are few disciplines I can think of where zebrafish have not yet been used, but with the recent surge in zebrafish research there is also a need for good literature on the topic. Here is a brief list of useful resources for zebrafish research:

The Zebrafish Book

Already in its 5th edition, the Zebrafish Book by Westerfield (2007) is certainly not a new kid on the block, but it is by far the most basic and necessary resource for anyone venturing into zebrafish research. You can either purchase a print version of the book, but you can also access all of the content in the 4th edition of the book online (for free!).
The Zebrafish Book covers general methods for zebrafish care, breeding, embryonic and larval culture, cellular and molecular methods, and protocols.

ZFIN Protocol Wiki

ZFIN has built a Wiki with protocols for zebrafish research. Whether you are using Danio rerio for gene cloning, protein analysis, or microscopic observations… ZFIN has a protocol for it.
As it is a wiki, users can load protocols to the site as well. When using protocols, it is worth keeping in mind that although it being a useful resource it is not peer reviewed. Some of the protocols are based on peer reviewed papers.

ZFIN model organism database

ZFIN is a phenomenal database for all things zebrafish. ZFIN has a database with zebrafish lines and also a page with job listings for people in the field.

Zebrafish Neurobehavioral Protocols

Zebrafish are relatively new in behavioral neuroscience. As a consequence, standardized protocols are still in being developed by the different groups in this field. There is a remarkable need for good protocols, and this book covers a number of protocols that have successfully been used in previous studies.

This list is by no means comprehensive, if you know of some other great resources for beginners in zebrafish research, or for those who have used this model organism for decades, feel free to share it in the comments!