1. Yakir Luc Gagnon
Education
03/2006–10/2010 Ph.D. Integrative Zoology, Cell & Organism Biology, Lund University,
Lund, Sweden.
Researching the optical properties of fish lenses using mathematical computer
modeling based on experiments done on various fish species
03/2002–02/2006 MSc Marine Biology, Marine Biology, Lund University, Helsingborg,
Sweden.
Studying the fundamentals of biology in the marine environment
Positions
01/2016–present Parental leave, Sweden.
01/2016–present Adjunct Postdoctoral Research Fellow, Sensory Neurobiology Group,
Queensland Brain Institute, University of Queensland, Brisbane, QLD,
Australia.
Researching the sighting distance, vision, and representation of polarization
06/2013–12/2015 Postdoctoral Research Fellow, Sensory Neurobiology Group,
Queensland Brain Institute, University of Queensland, Brisbane, QLD,
Australia.
Understanding the circular polarization vision of stomatopod crustaceans
11/2010–05/2013 Postdoctoral Research Fellow, Biology, Duke University, Durham, NC,
USA.
Discovering how the camouflage of cephalopods works
Publications
Refereed Journal Articles
1 Thomas W. Cronin, Yakir Luc Gagnon, Sönke Johnsen, N. Justin
Marshall, and Nicholas W. Roberts. Comment on “open-ocean fish reveal
an omnidirectional solution to camouflage in polarized environments”.
Science, 353(6299):552–552, 2016.
2 Yakir Luc Gagnon and N. Justin Marshall. Intuitive representation
of photopolarimetric data using the polarization ellipse. Journal of
Experimental Biology, 219(16):2430–2434, 2016. Cover image.
3 Yakir Luc Gagnon, Daniel C. Osorio, Trevor J. Wardill, N. Justin Marshall,
Wen-Sung Chung, and Shelby E. Temple. Can chromatic aberration
enable color vision in natural environments? Proceedings of the National
Academy of Sciences, 1:1–2, 2016.
4 Yakir Luc Gagnon, David Wilby, and Shelby Eric Temple. Losing
focus: how lens position and viewing angle affect the function of
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

2. multifocal lenses in fishes. Journal of the Optical Society of America A,
33(9):1901–1909, 2016. Cover image.
5 Sönke Johnsen, Yakir Luc Gagnon, N. Justin Marshall, Thomas W.
Cronin, Viktor Gruev, and Sam Powell. Polarization vision seldom
increases the sighting distance of silvery fish. Current Biology,
26:752–754, 2016.
6 Eric C. Orenstein, Justin M. Haag, Yakir Luc Gagnon, and Jules S.
Jaffe. Automated classification of camouflaging cuttlefish. Methods in
Oceanography, 15–16:21–34, 2016.
7 Daniel I. Speiser, Yakir Luc Gagnon, Raghav K. Chhetri, Amy L.
Oldenburg, and Sönke Johnsen. Examining the effects of chromatic
aberration, object distance, and eye shape on image-formation in the
mirror-based eyes of the bay scallop argopecten irradians. Integrative
and Comparative Biology, 56(5):796–808, 2016.
8 Yakir L. Gagnon, Tracey T. Sutton, and Sönke Johnsen. Corrigendum
to “visual acuity in pelagic fishes and mollusks” [vis. res. 92 (2013) 1–9].
Vision Research, 115, Part A:155–156, 2015.
9 Yakir Luc Gagnon, Rachel Marie Templin, Martin John How, and
N. Justin Marshall. Circularly polarized light as a communication signal
in mantis shrimps. Current Biology, 25:3074–3078, 2015.
10 Darcy A. A. Taniguchi, Yakir Luc Gagnon, Benjamin R. Wheeler, Sönke
Johnsen, and Jules S. Jaffe. Cuttlefish Sepia officinalis preferentially
respond to bottom rather than side stimuli when not allowed adjacent
to tank walls. PLoS ONE, 10:1–18, 2015.
11 Yakir Luc Gagnon, Daniel I. Speiser, and Sönke Johnsen. Simplifying
numerical ray tracing for characterization of optical systems. Applied
Optics, 53(21):4784–4790, 2014.
12 Amanda L. Holt, Sanaz Vahidinia, Yakir Luc Gagnon, Daniel E. Morse,
and Alison M. Sweeney. Photosymbiotic giant clams are transformers of
solar flux. Journal of The Royal Society Interface, 11(101):1–13, 2014.
13 Yakir Luc Gagnon, Tracey T. Sutton, and Sönke Johnsen. Visual acuity
in pelagic fishes and mollusks. Vision Research, 92:1–9, 2013.
14 Yakir Luc Gagnon, Bo Söderberg, and Ronald H. H. Kröger. Optical
advantages and function of multifocal spherical fish lenses. Journal of
the Optical Society of America A, 29:1786–1793, 2012.
15 Thomas Nørgaard, Yakir Luc Gagnon, and Eric J. Warrant. Nocturnal
homing: Learning walks in a wandering spider? PLoS ONE, 7(11):1–7,
2012.
16 Yakir Luc Gagnon, Nadav Shashar, and Ronald H. H. Kröger. Adaptation
in the optical properties of the crystalline lens in the eyes of the
lessepsian migrant Siganus rivulatus. Journal of Experimental Biology,
214:2724–2729, 2011.
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

3. 17 Yakir Luc Gagnon, Ronald H. H. Kröger, and Bo Söderberg. Adjusting a
light dispersion model to fit measurements from vertebrate ocular media
as well as ray-tracing in fish lenses. Vision Research, 50(9):850–853,
2010.
18 J. Marcus Schartau, Bodil Sjögreen, Yakir Luc Gagnon, and Ronald
H. H. Kröger. Optical plasticity in the crystalline lenses of the cichlid
fish Aequidens pulcher. Current Biology, 19:122–126, 2009.
19 Yakir Luc Gagnon, Bo Söderberg, and Ronald H. H. Kröger. Effects of
the peripheral layers on the optical properties of spherical fish lenses.
Journal of the Optical Society of America A, 25(10):2468–2475, 2008.
20 Yakir Luc Gagnon, Nadav Shashar, Eric J. Warrant, and Sönke J. Johnsen.
Light scattering by selected zooplankton from the gulf of aqaba. Journal
of Experimental Biology, 210(21):3728–3735, 2007.
Conference Abstracts
1 S Johnsen, Yakir L Gagnon, NJ Marshall, and TW Cronin. Another
beautiful hypothesis slain by an ugly fact: Polarization vision does not
increase the sighting distance of silvery fish. In Annual Meeting of
the Society-for-Integrative-and-Comparative-Biology (SICB), volume 56,
pages E103–E103. 2016.
2 Yakir Luc Gagnon, Martin J. How, and N. Justin Marshall1. Circular
polarization vision as a covert signal in stomatopods. In Australian Coral
Reef Society. 2014.
3 Yakir Luc Gagnon, Martin J. How, and N. Justin Marshall1. The possible
usage of circular polarization vision for covert signals in stomatopods.
In International Congress of Neuroethology. 2014.
4 N. Justin Marshall, Yakir Luc Gagnon, Hanne H. Thoen, Rachell Templin,
Thomas Cronin, Nicholas Roberts, Martin How, Shelby E. Temple,
Viktor Gruev, and Sam Powell. Polarisation vision: the new currency of
communication. In International Congress of Neuroethology. 2014.
5 Rachel Templin, Martin How, Yakir Luc Gagnon, Nicholas Roberts,
and N. Justin Marshall. Circular polarisation vision in the stomatopod
gonodactylaceus falcatus. In International Congress of Neuroethology.
2014.
6 Y. L. Gagnon and S. Johnsen. Visual acuity in deep-sea fish and mollusks.
In The Society for Integrative and Comparative Biology. 2013.
7 A. L. Holt, Y. L. Gagnon, S. Vahidinia, D. E. Morse, and A. M. Sweeney.
Photonic enhancement of symbiotic photosynthesis in giant clams. In
The Society for Integrative and Comparative Biology. 2013.
8 A. M. Sweeney, S. Johnsen, Y. L. Gagnon, D. E. Morse, and D. Stramski.
Jurassic marine photonics: Squid dynamic iridescence and predation
by large extinct marine reptiles. In The Society for Integrative and
Comparative Biology. 2013.
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

4. 9 Yakir Luc Gagnon, Daniel Speiser, and Alison Sweeney. The visual
function of the fluorescent lenses of Greeneye fish. In The Society for
Integrative and Comparative Biology. 2012.
10 Amanda L. Holt, Yakir Luc Gagnon, A. M. Sweeney, and D. E. Morse.
A monte-carlo model of photon transport in symbiotic giant clams. In
The Society for Integrative and Comparative Biology. 2012.
11 Daniel Speiser, Yakir Luc Gagnon, R. K. Chhetri, A. L. Oldenburg, and
Sönke Johnsen. Optical coherence tomography (OCT) reveals that
scallop eyes may have bifocal optics. In The Society for Integrative and
Comparative Biology. 2012.
12 Alison M. Sweeney, Amanda L. Holt, Yakir Luc Gagnon, and Daniel E.
Morse. Giant clam iridocytes optimize photosynthetic symbiosis. In The
Society for Integrative and Comparative Biology. 2012.
13 A.M. Sweeney, A.L. Holt, Y. L. Gagnon, and D.E. Morse. Bio-photonics
and monte carlo modeling of the tridacnid giant clam symbiosis. In NASA
Space Science DiVision meeting, Ames Research Center (Mountain View,
CA). 2011.
14 Yakir Luc Gagnon, R. H. H. Kröger, and B. Söderberg. Light dispersion
in the lens of the cichlid fish Astatotilapia Burtoni. In The Association
for Research in Vision and Ophthalmology. 2009.
15 Yakir Luc Gagnon and R. H. H. Kröger. Gradient index models of
monofocal and multifocal spherical fish lenses. In The Association for
Research in Vision and Ophthalmology. 2006.
Media Coverages
1 Science Daily. Marine animals use new form of secret light communication.
ScienceDaily, 1:1, 2015.
2 Nature research. Polarized light as a secret signal. Nature research
highlights, 527:278, 2015.
3 Madeleine van der Linden. Shrimp communicate using ’secret’ light code.
Australian Geographic, 1(1):1, 2015.
4 Ed Yong. Why mantis shrimp send secret messages using twisted light.
National Geographic, 1(1):1, 2015.
5 Susan Milius. Fish’s eyes apparently glow to pick up hard-to-detect hues.
Science News, 181(3):10, 2012.
6 Elizabeth Pennisi. Light in the deep. Science, 335(6073):1160–1163,
2012.
Invited talks
10/2014 Lab seminar, Prof. Thomas Cronin’s laboratory at the University of
Maryland, Baltimore County, MD, USA.
Circularly polarized light as a communication signal in mantis shrimps
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

5. 10/2012 Biology Departmental Seminar, Western Carolina University, USA.
The visual function of the fluorescent lenses of Greeneye fish
11/2008 Limnology Departmental Seminar, Lund University, Sweden.
Light scattering by selected zooplankton from the Gulf of Aqaba
Awards and Grants
2009 Venture Cup Southern Sweden (2nd place), The Bokelund travel-grant,
The Foundation of Charlotte Wollmars Donation, Fokus Verifiering
2008 Paper selected for the November, 2008 issue of Virtual Journal of
Biological Physics Research as well as the December, 2008 issue of the
Virtual Journal for Biomedical Optics, The Royal Physiographic Society
in Lund, The Müllerska fund, The innovation prize, The Venture Cup
Research Challenge
2007 The Hierta-Retzius Fund, The Royal Physiographic Society in Lund
2006 The Royal Physiographic Society in Lund, The Carl Swartz Fund
2004 Travel and Scholarship Grant for studies at the BMS, University of British
Columbia
Supervision of Graduate Students
06/2013–12/2015 Co-supervised a PhD student and a MSc student
09/2010–03/2013 Co-supervised a MSc student
Teaching Activities
06/2013–12/2015 Associate Lecturer, Department of Biology, Queensland University,
Brisbane, Australia.
From Brain to Behavior, 1st
–4rd
year students
09/2006–09/2009 Associate Tutor, Faculty of Science, Lund University, Lund, Sweden.
Sensory Biology, 3rd
year students
09/2006–09/2009 Associate Tutor, Faculty of Science, Lund University, Lund, Sweden.
Human Physiology, 3rd
year students
09/2006–09/2009 Associate Tutor, Faculty of Science, Lund University, Lund, Sweden.
Heart Pathology, biomedical 1st
year students
Academic Outreach & Service
02/2016 How to be an academic?, (Via Skype) Colorado College, Colorado
Springs, CO, USA.
Explain about the difficulties and hurdles of becoming an academic
10/2015 Eyes Wide Open, National Geographic documentary.
Presented the circular polarization vision of mantis shrimps in the context of a
documentary about the evolution of eyes
10/2014 Show and tell, Department of Biology, Queensland University, Brisbane,
Queensland, Australia.
Present research done at the Queensland Brain Institute to high school students
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

6. 07/2013 Crown-of-thorns starfish population control, Lizard Island Research
Station, Great Barrier Reef, Australia.
Find and exterminate starfishes by using scuba
08/2008 Linnaeus day, Lund University, Lund, Sweden.
Explained visual systems to the general public using visual illusions
2007–present Reviewer.
Journal of Experimental Biology, the Journal of the Optical Society of America,
PLOS One, Vision Research, and Applied Optics
09/2007–09/2009 Ph.D. Representative in the Departmental Board of Directors,
Lund University, Lund, Sweden.
Ensured proper representation of the financial and organisational needs of Ph.D.
students in the Board’s decisions
09/2006–10/2009 Logistical organizer for Sensory Ecology, Lund University, Lund,
Sweden.
Coordinated the arrival and presentations of foreign postgraduate students
Research Expeditions
08/2015–09/2015 Field work, Lizard Island Research Station, Great Barrier Reef, Australia.
Polarization vision in mantis shrimps (funded by AFOSR)
05/2015 Field work, Lizard Island Research Station, Great Barrier Reef, Australia.
Polarization vision in mantis shrimps (funded by AFOSR)
02/2014–03/2014 Field work, Lizard Island Research Station, Great Barrier Reef, Australia.
Polarization vision in mantis shrimps (funded by AFOSR)
01/2014 Field work, Lizard Island Research Station, Great Barrier Reef, Australia.
Polarization vision in mantis shrimps (funded by AFOSR)
07/2013 Field work, Lizard Island Research Station, Great Barrier Reef, Australia.
Polarization vision in mantis shrimps (funded by AFOSR)
05/2012-06/2012 Research cruise, Hawaii, USA.
Visual acuity in pelagic animals (funded by ONR)
03/2012–04/2012 Field work, Palau International Coral Reef Center, Palau.
Giant clams photonics (funded by ONR)
09/2011 Research cruise, Rhode Island, USA.
Visual acuity in pelagic animals (funded by ONR)
06/2011–07/2011 Research cruise, Sea of Cortez, Mexico.
Visual acuity in pelagic animals (funded by ONR)
09/2008 Field work, Inter University Institute, Eilat, Israel.
Light scattering from zooplankton (funded by Lund Physiographic Society)
Analysis Skills
Problem Solving Designing algorithms and models with object oriented programming,
strongly typed programming, constrained and non-constrained
optimization procedures (numerical analysis), symbolic math (analytical
analysis), memory allocation procedures, and parallel computing
Optics Ray tracing, polarization, dispersion, Monte Carlo simulations, IOPs,
gradient lenses, irregular and/or asymmetric optics
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008

7. Image analysis Image statistics, video processing, filtering and transformations
(e.g. Kalman, Fourier, Radon, Hough), edge detection, registration,
segmentation, tracking, classification
Statistics t-test, m/anova, pca, large data, linear, non-linear, multiple regression
analysis, multivariable non-normal non balanced (permanova, anosim),
Generalized Linear Mixed Models (glmm), Markov chain Monte Carlo
(mcmc)
Data sampling Interfacing signal processing and hardware communication (ccd, cmos,
actuator motors, etc.), photospectrometers (absolute and wavelength
calibrations), microtome cryostat, lasers, optical tables and setups,
interference, light, confocal microscopes, dslrs
Computer skills
OS Linux, Windows Programming Julia, Matlab, R (some
proficiency in c++,
Python, and Haskell)
Reports LATEX, pgf, TikZ,
beamer, Adobe CS,
GIMP, Inkscape
Diverse Vim, pdftk,
ImageMagick, ssh,
screen, gnu parallel,
dcraw
Other
Languages Completely fluent in English, Hebrew, and Swedish
Diving scuba (Advanced PADI, AAUS, ADAS, blue water, Nitrox, +Dry suit)
and free diving (Thailand, Egypt, Israel, Sweden, England, Australia,
and West Coast Canada)
Falkenbergsgatan 8B – Malmö, Skåne, 21424, Sweden
 +46 (0)728 379 876 •  12.yakir@gmail.com
ORCID: 0000-0003-2512-4520 • ResearcherID: C-2665-2008