DOI: 10.5061/dryad.31v01
title: Data from: Three-dimensional midwater camouflage from a novel two-component photonic structure in hatchetfish skin

description: The largest habitat by volume on Earth is the oceanic midwater, which is
 also one of the least understood in terms of animal ecology. The organisms
 here exhibit a spectacular array of optical adaptations for living in a
 visual void that have only barely begun to be described. We describe a
 complex pattern of broadband scattering from the skin of Argyropelecus
 sp., a hatchetfish found in the mesopelagic zone of the world's
 oceans. Hatchetfish skin superficially resembles the unpolished side of
 aluminum foil, but on closer inspection contains a complex composite array
 of sub-wavelength-scale dielectric structures. The superficial layer of
 this array contains dielectric stacks that are rectangular in
 cross-section, while the deeper layer contains dielectric bundles that are
 elliptical in cross-section; the cells in both layers have their longest
 dimension running parallel to the dorsal-ventral axis of the fish. Using
 the finite-difference time-domain approach and photographic radiometry, we
 explored the structural origins of this scattering behavior and its
 environmental consequences. When the fish’s flank is illuminated from an
 arbitrary incident angle, a portion of the scattered light exits in an arc
 parallel to the fish's anterior-posterior axis. Simultaneously, some
 incident light is also scattered downward through the complex birefringent
 skin structure and exits from the ventral photophores. We show that this
 complex scattering pattern will provide camouflage simultaneously against
 the horizontal radially symmetric environmental light in this habitat, the
 predatory bioluminescent searchlights that are ubiquitous here. The
 structure also directs light incident on the flank of the fish into the
 downwelling, silhouette-hiding counterillumination of the ventral
 photophores.
description: 3D FDTD hatchetfish
 nearfield scattering calculationsFolder containing all
 files and data necessary to model and plot Figure 4, the 3D nearfield
 scattering calculations from the hatchetfish skin using FDTD and
 MEEP.Meep3DNearfieldBackscatter_AH_March2017.zipMeepFarFieldFluxsetup_AH_March2017Folder containing files for calculating and plotting figure 2c,2d and 2e, the farfield backscatter from hatchetfish skin.MeepScatteringCalculationSetup_ER_march2017Folder containing all files necessary to calculate and plot Figure 3b, the scattering phase functions of different types of single cells.Threshold Camouflage CalculationMatlab file used to calculate threshold detection for bioluminescent searchlight predator in Figure 5bthresholdWarrant.mBRDF plot, Figure 2aMatlab file for opening BRDF data called S17_grn_BRDF_around_incTheta_8.mat and plotting like Figure 2a. Requires S17_grn_BRDF_around_incTheta_8.mat.percentanisotropic.mBRDF dataMat file to be used with percentisotropic.m for plotting BRDF data from Figure 2a.S17_grn_BRDF_around_incTheta_8.matHatchetfish raw camera angleFolder containing raw images of hatchetfish with angled incoming light and necessary text file used for plotting bar graph in 6a with barplot.m.angledng.zipHatchetfish raw camera verticalFolder containing raw camera images of hatchetfish under vertical illumination. Also includes text files containing data used in bar graph in figure 6a.hatchetfishdng.zipControl raw camera dngFolder containing raw images of control objects (aluminum, mirror, spectralon) for use in bar graph of figure 6a.verticalcontroldng.zipBar plot in Figure 6aFolder containing all files and data needed to plot figure 6a. Text data (pixel averages of the B channel from processed raw images) is obtained using hatchetfishpicanalysis.m.barplot.zipHatchetfish Image analysisMatlab file used to analze raw images of hatchetfish and control objects in different illuminations. Raw image files are contained in 3 folders: Hatchetfish raw camera angle, Hatchetfish raw camera vertical and Control raw camera dng.hatchetfishpicanalysis.mQuantifying Photophore GuideFiles needed to quantify light exiting downwelling photophores when entering through fish side.Photophorequant.zip