Skip to main content Accessibility help

Imaging the adult zebrafish cone mosaic using optical coherence tomography

  • Please note a correction has been issued for this article.


Zebrafish (Danio rerio) provide many advantages as a model organism for studying ocular disease and development, and there is great interest in the ability to non-invasively assess their photoreceptor mosaic. Despite recent applications of scanning light ophthalmoscopy, fundus photography, and gonioscopy to in vivo imaging of the adult zebrafish eye, current techniques either lack accurate scaling information (limiting quantitative analyses) or require euthanizing the fish (precluding longitudinal analyses). Here we describe improved methods for imaging the adult zebrafish retina using spectral domain optical coherence tomography (OCT). Transgenic fli1:eGFP zebrafish were imaged using the Bioptigen Envisu R2200 broadband source OCT with a 12-mm telecentric probe to measure axial length and a mouse retina probe to acquire retinal volume scans subtending 1.2 × 1.2 mm nominally. En face summed volume projections were generated from the volume scans using custom software that allows the user to create contours tailored to specific retinal layer(s) of interest. Following imaging, the eyes were dissected for ex vivo fluorescence microscopy, and measurements of blood vessel branch points were compared to those made from the en face OCT images to determine the OCT lateral scale as a function of axial length. Using this scaling model, we imaged the photoreceptor layer of five wild-type zebrafish and quantified the density and packing geometry of the UV cone submosaic. Our in vivo cone density measurements agreed with measurements from previously published histology values. The method presented here allows accurate, quantitative assessment of cone structure in vivo and will be useful for longitudinal studies of the zebrafish cone mosaics.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the or variations. ‘’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Imaging the adult zebrafish cone mosaic using optical coherence tomography
      Available formats

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Imaging the adult zebrafish cone mosaic using optical coherence tomography
      Available formats

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Imaging the adult zebrafish cone mosaic using optical coherence tomography
      Available formats


This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Corresponding author

*Address correspondence to: Ross Collery, PhD, Department of Cell Biology, Neurobiology, and Anatomy; Medical College of Wisconsin, 8701 W. Watertown Plank Rd, Milwaukee, WI 53226-0509. E-mail:


Hide All
Allison, W.T., Barthel, L.K., Skebo, K.M., Takechi, M., Kawamura, S. & Raymond, P.A. (2010). Ontogeny of cone photoreceptor mosaics in zebrafish. Journal of Comparative Neurology 518, 41824195.
Allison, W.T., Haimberger, T.J., Hawryshyn, C.W. & Temple, S.E. (2004). Visual pigment composition in zebrafish: Evidence for a rhodopsin-porphyropsin interchange system. Visual Neuroscience 21, 945952.
Bailey, T.J., Davis, D.H., Vance, J.E. & Hyde, D.R. (2012). Spectral-domain optical coherence tomography as a noninvasive method to assess damaged and regenerating adult zebrafish retinas. Investigative Ophthalmology & Visual Science 53, 31263138.
Bell, B.A., Xie, J., Yuan, A., Kaul, C., Hollyfield, J.G. & Anand-Apte, B. (2014). Retinal vasculature of adult zebrafish: In vivo imaging using confocal scanning laser ophthalmoscopy. Experimental Eye Research 129, 107118.
Branchek, T. & Bremiller, R. (1984). The development of photoreceptors in the zebrafish, Brachydanio rerio. I. Structure. Journal of Comparative Neurology 224, 107115.
Cheng, Y.H., Yu, J.Y., Wu, H.H., Huang, B.J. & Chu, S.W. (2010). Spectral ophthalmoscopy based on supercontinuum. In Proceedings of SPIE, ed. Farkas, D.L., Nicolau, D.V. & Leif, R.C., pp. 75680F. San Francisco, CA: SPIE.
Chhetri, J., Jacobson, G. & Gueven, N. (2014). Zebrafish- on the move towards ophthalmological research. Eye 28, 367380.
Chiu, S.J., Lokhnygina, Y., Dubis, A.M., Dubra, A., Carroll, J., Izatt, J.A. & Farsiu, S. (2013). Automatic cone photoreceptor segmentation using graph theory and dynamic programming. Biomedical Optics Express 4, 924937.
Choi, J.H., Law, M.Y., Chien, C.B., Link, B.A. & Wong, R.O. (2010). In vivo development of dendritic orientation in wild-type and mislocalized retinal ganglion cells. Neural Development 5, 29.
Clark, B.S., Winter, M., Cohen, A.R. & Link, B.A. (2011). Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Developmental Dynamics 240, 24522465.
Collery, R.F., Veth, K.N., Dubis, A.M., Carroll, J. & Link, B.A. (2014). Rapid, accurate, and non-invasive measurement of zebrafish axial length and other eye dimensions using SD-OCT allows longitudinal analysis of myopia and emmetropization. PLoS One 9, e110699.
Cooper, R.F., Wilk, M.A., Tarima, S. & Carroll, J. (2016). Evaluating descriptive metrics of the human cone mosaic. Investigative Ophthalmology & Visual Science 57(7), 29923001.
de la Zerda, A., Prabhulkar, S., Perez, V.L., Ruggeri, M., Paranjape, A.S., Habte, F., Gambhir, S.S. & Awdeh, R.M. (2015). Optical coherence contrast imaging using gold nanorods in living mice eyes. Clinical & Experimental Ophthalmology 43, 358366.
Duval, M.G., Chung, H., Lehmann, O.J. & Allison, W.T. (2013). Longitudinal fluorescent observation of retinal degeneration and regeneration in zebrafish using fundus lens imaging. Molecular Vision 19, 10821095.
Ferrara, D., Mohler, K.J., Waheed, N., Adhi, M., Liu, J.J., Grulkowski, I., Kraus, M.F., Baumal, C., Hornegger, J., Fujimoto, J.G. & Duker, J.S. (2014). En face enhanced-depth swept-source optical coherence tomography features of chronic central serous chorioretinopathy. Ophthalmology 121, 719726.
Flatter, J.A., Cooper, R.F., Dubow, M.J., Pinhas, A., Singh, R.S., Kapur, R., Shah, N., Walsh, R.D., Hong, S.H., Weinberg, D.V., Stepien, K.E., Wirostko, W.J., Robison, S., Dubra, A., Rosen, R.B., Connor, T.B. Jr. & Carroll, J. (2014). Outer retinal structure after closed-globe blunt ocular trauma. Retina 34, 21332146.
Fraser, B., Duval, M.G., Wang, H. & Allison, W.T. (2013). Regeneration of cone photoreceptors when cell ablation is primarily restricted to a particular cone subtype. PLoS One 8, e55410.
Garrioch, R., Langlo, C., Dubis, A.M., Cooper, R.F., Dubra, A. & Carroll, J. (2012). Repeatability of in vivo parafoveal cone density and spacing measurements. Optometry and Vision Science 89, 632643.
Garvin, M.K., Abramoff, M.D., Wu, X., Russell, S.R., Burns, T.L. & Sonka, M. (2009). Automated 3-D intraretinal segmentation of macular spectral-domain optical coherence tomography images. IEEE Transactions on Medical Imaging 28, 14361447.
Goldsmith, J.R. & Jobin, C. (2012). Think small: Zebrafish as a model system of human pathology. Journal of Biomedicine and Biotechnology, e817341.
Hayashi, A., Naseri, A., Pennesi, M.E. & de Juan, E.J. (2009). Subretinal delivery of immunoglobulin G with gold nanoparticles in the rabbit eye. Japanese Journal of Ophthalmology 53, 249256.
Hood, D.C., Fortune, B., Mavrommatis, M.A., Reynaud, J., Ramachandran, R., Ritch, R., Rosen, R.B., Muhammad, H., Dubra, A. & Chui, T.Y. (2015). Details of glaucomatous damage are better seen on OCT en face images than on OCT retinal nerve fiber layer thickness maps. Investigative Ophthalmology & Visual Science 56, 62086216.
Huckenpahler, A., Wilk, M.A., Cooper, R.F., Carroll, J., Link, B. & Collery, R.F. (2016). Imaging the adult zebrafish cone photoreceptor mosaic using optical coherence tomography (OCT). In ARVO Annual Meeting, p. 2196. Seattle, WA: Association for Research in Vision and Ophthalmology.
Jian, Y., Zawadzki, R.J. & Sarunic, M.V. (2013). Adaptive optics optical coherence tomography for in vivo mouse retinal imaging. Journal of Biomedical Optics 18, 56007.
Lawson, N.D. & Weinstein, B.M. (2002). In vivo imaging of embryonic vascular development using transgenic zebrafish. Developmental Biology 248, 307318.
Levine, E., Zawadzki, R.J., Cheng, H., Simon, S., Pugh, E. & Burns, M. (2013). Early indications of pending degeneration in a mouse model of photoreceptor light damage. Investigative Ophthalmology & Visual Science 54, 4179.
Li, Y.N., Tsujimura, T., Kawamura, S. & Dowling, J.E. (2012). Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. Journal of Comparative Neurology 520, 37863802.
Link, B.A. & Collery, R.F. (2015). Zebrafish models of retinal disease. Annual Review of Vision Science 1, 125153.
Lozano, D.C. & Twa, M.D. (2013). Development of a rat schematic eye from in vivo biometry and the correction of lateral magnification in SD-OCT imaging. Investigative Ophthalmology & Visual Science 54, 64466455.
Lu, R., Levy, A.M., Zhang, Q., Pittler, S.J. & Yao, X. (2013). Dynamic near-infrared imaging reveals transient phototropic change in retinal rod photoreceptors. Journal of Biomedical Optics 18, 106013.
McLellan, G.J. & Rasmussen, C.A. (2012). Optical coherence tomography for the evaluation of retinal and optic nerve morphology in animal subjects: Practical considerations. Veterinary Ophthalmology 15, 1328.
Mitchell, D.M., Stevens, C.B., Frey, R.A., Hunter, S.S., Ashino, R., Kawamura, S. & Stenkamp, D.L. (2015). Retinoic acid signalling regulates differential expression of the tandemly-duplicated long wavelength-sensitive cone opsin genes in zebrafish. PLoS Genetics 11, e1005483.
Mohammad, F., Wanek, J., Zelkha, R., Lim, J.I., Chen, J. & Shahidi, M. (2014). A method for en face OCT imaging of subretinal fluid in age-related macular degeneration. Journal of Ophthalmology 2014, 720243.
Odell, D., Dubis, A.M., Lever, J.F., Stepien, K.E. & Carroll, J. (2011). Assessing errors inherent in OCT-derived macular thickness maps. Journal of Ophthalmology 2011, 692574.
Parthasarathy, M.K. & Bhende, M. (2015). Effect of ocular magnification on macular measurements made using spectral domain optical coherence tomography. Indian Journal of Ophthalmology 63, 427431.
Pickart, M.A. & Klee, E.W. (2014). Zebrafish approaches enhance the translational research tackle box. Translational Research 163, 6578.
Ramsey, M. & Perkins, B.D. (2013). Basal bodies exhibit polarized positioning in zebrafish cone photoreceptors. Journal of Comparative Neurology 521, 18031816.
Rao, K.D., Verma, Y., Patel, H.S. & Gupta, P.K. (2006). Non-invasive ophthalmic imaging of adult zebrafish eye using optical coherence tomography. Current Science 90, 15061510.
Raymond, P.A., Colvin, S.M., Jabeen, Z., Nagashima, M., Barthel, L.K., Hadidjojo, J., Popova, L., Pejaver, V.R. & Lubensky, D.K. (2014). Patterning the cone mosaic array in zebrafish retina requires specification of ultraviolet-sensitive cones. PLoS One 9, e85325.
Robinson, J., Schmitt, E.A., Harosi, F.I., Reece, R.J. & Dowling, J.E. (1993). Zebrafish ultraviolet visual pigment: Absorption spectrum, sequence, and localization. Proceedings of the National Academy of Sciences of the United States of America 90, 60096012.
Salbreux, G., Barthel, L.K., Raymond, P.A. & Lubensky, D.K. (2012). Coupling mechanical deformations and planar cell polarity to create regular patterns in the zebrafish retina. PLoS Computational Biology 8, e1002618.
Sallo, F.B., Peto, T., Egan, C., Wolf-Schnurrbusch, U.E., Clemons, T.E., Gillies, M.C., Pauleikhoff, D., Rubin, G.S., Chew, E.Y., Bird, A.C. & MacTel Study Group. (2012). The IS/OS junction layer in the natural history of type 2 idiopathic macular telangiectasia. Investigative Ophthalmology & Visual Science 53, 78897895.
Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. (2012). NIH image to ImageJ: 25 years of image analysis. Nature Methods 9, 671675.
Scoles, D., Flatter, J.A., Cooper, R.F., Langlo, C.S., Robison, S., Neitz, M., Weinberg, D.V., Pennesi, M.E., Han, D.P., Dubra, A. & Carroll, J. (2016). Assessing photoreceptor structure associated with ellipsoid zone disruptions visualized with optical coherence tomography. Retina 36, 91103.
Tarboush, R., Chapman, G.B. & Connaughton, V.P. (2012). Ultrastructure of the distal retina of the adult zebrafish, Danio rerio . Tissue and Cell 44, 264279.
Tschopp, M., Takamiya, M., Cerveny, K.L., Gestri, G., Biehlmaier, O., Wilson, S.W., Strähle, U. & Neuhauss, S.C. (2010). Funduscopy in adult zebrafish and its application to isolate mutant strains with ocular defects. PLoS One 5, e15427.
Verma, Y., Rao, K.D., Suresh, M.K., Patel, H.S. & Gupta, P.K. (2007). Measurement of gradient refractive index profile of crystalline lens of fisheye in vivo using optical coherence tomography. Applied Physics B: Lasers and Optics 87, 607610.
Wan, J. & Goldman, D. (2016). Retina regeneration in zebrafish. Current Opinion in Genetics & Development 40, 4147.
Wang, J.L., Kardon, R.H., Kupersmith, M.J. & Garvin, M.K. (2012). Automated quantification of volumetric optic disc swelling in papilledema using spectral-domain optical coherence tomography. Investigative Ophthalmology & Visual Science 53, 40694075.
Watanabe, K., Nishimura, Y., Oka, T., Nomoto, T., Kon, T., Shintou, T., Hirano, M., Shimada, Y., Umemoto, N., Kuroyanagi, J., Wang, Z., Zhang, Z., Nishimura, N., Miyazaki, T., Imamura, T. & Tanaka, T. (2010). In vivo imaging of zebrafish retinal cells using fluorescent coumarin derivatives. BMC Neuroscience 11, 116.
Weber, A., Hochmann, S., Cimalla, P., Gärtner, M., Kuscha, V., Hans, S., Geffarth, M., Kaslin, J., Koch, E. & Brand, M. (2013). Characterization of light lesion paradigms and optical coherence tomography as tools to study adult retina regeneration in zebrafish. PLoS One 8, e80483.
Zhang, Q.X., Lu, R.W., Curcio, C.A. & Yao, X.C. (2012). In vivo confocal intrinsic optical signal identification of localized retinal dysfunction. Investigative Ophthalmology & Visual Science 53, 81398145.



Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed

A correction has been issued for this article: