Brain atlas of juvenile zebrafish

The aim of this open-source atlas is to provide a comprehensive referencefor the juvenile zebrafish brain, available for the scientific community. This atlas is based on a single 3-week old zebrafish brain stained with DAPI. All brains are registered to this common reference brain, allowing for consistent across samples.

 

Each displayed brain is an average of multiple stained brains. These samples are first registered to the reference and then averaged. Stainings were performed using a modified Hybridization Chain Reaction (HCR) in situ hybridisation technique (Molecular Instruments), with imaging conducted via light-sheet microscopy.

 

How to use the Atlas

To explore different planes, click on the yellow and/or purple lines in the Horizontal section, then drag the lines to view the area of interest. You can select one line at a time and overlay a mask to enhance visualisation.

 

Legend of Masks

The brain is segmented into distinct anatomical regions, guided by DAPI and brain stainings. The masks were created using the terminology from “Neuroanatomy of the Zebrafish Brain” as a reference.

dENT: Entopeduncular Nucleus dorsal part, DL: Lateral zone of Dorsal telencephalic area, GC: Griseum Centrale, Hb: Habenula, Hc: Caudal zone of Hypothalamus, Hd: Dorsal zone of Hypothalamus, IPN: Interpeduncular Nucleus, LC: Locus Coeruleus, LR: Lateral Recess of diencephalic ventricle, NLV: Nucleus Lateralis Valvulae, NMLF: Nucleus of the Medial Longitudinal Fascicle, OB: Olfactory Bulb, OT: Optic Tectum, P: Pallium, PGZ: Periventricular Gray Zone of Optic Tectum, PPa: Parvocellular Preoptic Nucleus anterior part, PPd: Parvocellular Preoptic Nucleus dorsal part, PPv: Parvocellular Preoptic Nucleus ventral part, PrT: Pretectum, PT: Posterior Tuberculum, PVO: Paraventricular Organ, sbP: SubPallium, SR: Superior Raphe, TSc: Nucleus of Torus Semicircularis, vENT: Entopeduncular Nucleus ventral part. 

 

Information

Contact us. For question or inquiries, please email us at e.dreosti@ucl.ac.uk

Access raw data. All imaging files are accessible for download from the DreostiLab GitHub repository.

Funding. This project was supported by a Wellcome Trust grant.

Contribute to the atlas. We welcome collaborations! If you have additional markers, tools, or reagents for new stainings, or if you'd like to help with brain area annotations, please get in touch.

 

Other zebrafish atlases available:

Larval stage:

  1. mapZebrain - A larval zebrafish atlas, offering detailed annotations and markers for neuroanatomy studies.

  2. ZebrafishBrain - This atlas provides insights into early brain development and includes high-resolution transgenic images.

  3. Z-Brain Atlas - Comprehensive larval stage atlas focused on functional anatomy and brain connectivity.

Adult stage:

  1. 3D Adult Zebrafish Brain Atlas (AZBA) - A detailed 3D reference for the adult zebrafish brain.