The retina Is composed of the neural retina and retinal pigmented epithelium. This multilayered structure conveys visual information to the brain.


You can explore the different regions of the zebrafish retina by selecting one of the images below. The specific layers and structures referenced in this tutorial are highlighted in white. You can click on an image to see which transgenic lines or antibodies label each specific layer or the neural retina. For a more general overview of the neuroanatomy of the zebrafish retina please read on. 

Retina Regions

The Eye

The eye is a compound organ that functions as the sensory apparatus of the visual system.  It detects information in the form of refracted light and together with visual centres in the brain it provides visual perception of the surrounding environment.The eye is composed of the retina, optic nerve, lens, cornea and iris. These structures derive from three types of tissue during embryogenesis: neural ectoderm, extraocular mesenchyme and surface ectoderm. The neural ectoderm gives rise to the retinal derivatives (neural retina, ciliary margin zone (CMZ), retinal pigmented epithelium (RPE), and optic stalk/nerve); the extraocular mesoderm gives rise to the corneal endothelium, iris, and other extraocular structures; the surface ectoderm gives rise to the lens and the corneal epithelium.  For the sake of this neuroanatomical atlas, we concentrate on the parts of the eye that are derived from the neural plate, which evaginate from the region of the forebrain called the diencephalon. 

The neural Retina

Vision, one of the most important senses, begins when a photon strikes opsin molecules located in the photoreceptor outersegments.  Photoreceptors translate this physical stimulus into an electrochemical signal that is transmitted and refined through the interneurons of the retina.  Within milliseconds, this message converges on the retinal ganglion neurons that retinotopically project their axons to specific locations in the optic tectum, the visual processing center of the zebrafish brain. These retinotopic projections preserve the nasal-temproal and dorsal-ventral spatial resolution of the image detected by the eye.

Like most classes of extant vertebrates, the zebrafish neural retina is composed of six major cell types, five types of neurons and a single glial cell, the Müller glia.  The cells are arranged in three basic layers: the innermost ganglion cell layer, inner nucler layer, and the outer photoreceptor layer, and these are separated by two intervening layers of synapses, the inner and outer plexiform layers. The cell bodies of the rod and cone photoreceptors reside in the outer nuclear layer while those of bipolar cells, horizontal cells, and amacrine cells, as well as the Muller glia, are found in the inner nuclear layer.  All retinal ganglion cell bodies, along with those of displaced amacrine cells occupy the ganglion cell layer.  The five major classes of neurons can be subdivided into numerous subpopulations based on morphological, immunohistochemical and physiological profiles, and a more detailed description of the immunolabeling patterns for many of these subpopulations and structures can be found in Yazulla and Studholme, 2001.

The neural retina is composed of the following general types of cells, starting from apical to basal:


Photoreceptor cells span the outer nuclear layer as well as the outer and inner segment layers. The light sensing cells of the retina, the cone and rod photoreceptors, are located in the apical-most layer of the retina, and display a stereotypical subcellular organization with their nuclei basal to the inner segment (cell body or soma) and outer segment, which abuts the retinal pigmented epithelium (RPE) and is full of membrane invaginations packed with light-sensitive cell-specific opsins.  All photoreceptors have opsin-containing outersegments, which are replaced on a daily basis.  The older membrane and protein debris is shed from the distal tip of the outersegment and phagocytosed by the adjacent RPE cells.  Because zebrafish are diurnal, their retinae contains a large number of bright-light sensitive cone subtypes in addition to dim-light sensitive rod photoreceptors, all of which are organized into regular mosaic patterns that can best be visualized in tangential sections.  Below is more detailed information about the distinct types of photoreceptors found in zebrafish.


Cones are required for bright light vision and can be subdivided into four classes based on opsin expression and morphology.  The paired long double cones express both red and green opsin, the long single cones express blue opsin, and the short single cones express uv-sensitive opsin.  Antibodies generated against each of the 4 cone opsins or rhodopsin label the outer segments of individual cones or rods, respectively; in situ hybridization of the opsin transcripts label the inner segments. Several transgenic lines, which use various opsin promoters to drive expression of fluorophores (see below), reveal the location and morphology of specific photoreceptor subtypes.


Rods are utilized mainly for dim-light vision, and their cell bodies are located vitreal to the cone nuclei, and in the light-adapted retina, the thin rod inner and outer segments project beyond the cones, interdigitating between the apical microvilli of the adjacent retinal pigmented epithelia (RPE)l cells.

Retinal Inner-nuclear layer cell types:

Horizontal Cells

Horizontal cells are second order neurons that mediate the process of lateral inhibition in the outer retina, and are therefore electrically coupled by connexin-positive gap junctions.  Horizontal cell nuclei have a flattened appearance in retina sections.

Bipolar Cells

Bipolar cells are interneurons that transmit information from photoreceptors to the inner retina.  Bipolar cells are classified by three main criteria:  the type of photoreceptor that provides input, dendritic and axonal morphologies, and the polarity of their responses (e.g., depolarizing or hyperpolarizing). 

Amacrine Cells

Amacrine cell are interneurons with soma that reside primarily in the inner nuclear layer and send processes into the inner plexiform layer.  Amacrine cells mediate motion selectivity and modulate input into the inner retina.  Amacrine cells are classified based upon neurotransmitter expression and morphology. 


Müller glia

Müller cells are radial glia that perform a wide variety of support functions for retinal neurons. Immunolabeling for carbonic anhydrase or glutamine synthetase shows that the Müller cell bodies are positioned in a row in the middle of the inner nuclear layer.  Müller glial processes, which are positive for the glial fibrillary acidic protein (GFAP), extend radially across the thickness of the retina and compose parts of the outer and inner limiting membranes.  The outer limiting membrane is formed by the tight junctions that connect Müller glia (MG) apical processes and photoreceptors cell bodies while the inner limiting membrane contains the MG end feet.  


Retinal ganglion cells

Ganglion cells (RGCs) are the final output neurons of the vertebrate retina.  The ganglion cell axons form the nerve fiber layer of the inner retina as they coalesce to form the optic nerve head, which is composed of ganglion cell axons and glia that migrate into the optic nerve as well as astrocytes that are derived from the optic stalk. RGC axons cross the midline at the optic chiasm and arborize in distinct arborization fields or AFs. These neuropil areas correspond to 10 different retinorecipient brain nuclei the largest of which is the midbrain optic tectum. For a complete description of all the AFs and a lot more information on the neuroanatomy and function of RGCs see Robles et al., 2014).  

CLick button below for a bonus in depth description of Eye Development in zebrafish


Author: Kara Cerveny

Key Publications

Robles, E., Laurell, E., Baier, H. (2014) 
The Retinal Projectome Reveals Brain-Area-Specific Visual Representations Generated by Ganglion Cell Diversity.
Current biology : CB. 24(18):2085-96.