Erora opisena optical and tomography data and associated MATLAB scripts
Data files
Aug 02, 2024 version files 3.78 GB
-
13_immersion.mat
18.61 MB
-
14_immersion.mat
15.49 MB
-
145_immersion.mat
13.49 MB
-
15_immersion.mat
13.12 MB
-
air.mat
29.45 MB
-
area_thickness_models.mat
205.71 KB
-
blackfoil_oil.mat
13.53 MB
-
dark_10x_HSM.mat
93.56 MB
-
dark_20x_1_HSM.mat
94.27 MB
-
dark_50x_1_HSM.mat
63.82 MB
-
dark_50x_SEM.mat
96.57 MB
-
mirror_10x_HSM.mat
324.69 MB
-
mirror_20x_1_HSM.mat
299.88 MB
-
mirror_50x_1_HSM.mat
247.07 MB
-
mirror_50x_SEM.mat
340.03 MB
-
mirror_standard.mat
119.60 MB
-
opisena1_sample1_10x_MSP.mat
14.76 KB
-
opisena1_sample1_20x_MSP.mat
14.67 KB
-
opisena1_sample1_50x_MSP.mat
14.65 KB
-
README.md
3.19 KB
-
scales_10x_HSM.mat
126.22 MB
-
scales_20x_1_HSM.mat
136.05 MB
-
scales_50x_1_HSM.mat
143.91 MB
-
scales_50x_SEM.mat
182.15 MB
-
ZEISS_810Ultra_Erlangen_Butterfly4_LFOV_bottom_Reconstruction.tif
806.47 MB
-
ZEISS_810Ultra_Erlangen_Butterfly4_LFOV_top_Reconstruction.tif
602.70 MB
Abstract
Biophotonic nanostructures in butterfly wing scales remain fascinating examples of biological functional materials, with intriguing open questions regarding formation and evolutionary function. One particularly interesting butterfly species, Erora opisena (Lycaenidae: Theclinae), develops wing scales that contain three-dimensional photonic crystals that closely resemble a single gyroid geometry. Unlike most other gyroid-forming butterflies, E. opisena develops discrete gyroid crystallites with a pronounced size gradient hinting at a developmental sequence frozen in time. Here, we present a novel application of a hyperspectral (wavelength-resolved) microscopy technique to investigate the ultrastructural organisation of these gyroid crystallites in dry, adult wing scales. We show that reflectance corresponds to crystallite size, where larger crystallites reflect green wavelengths more intensely; this relationship could be used to infer size from the optical signal. We further successfully resolve the red-shifted reflectance signal from wing scales immersed in refractive index liquids with varying refractive index, including values similar to water or cytosol. Such photonic crystals with lower refractive index contrast may be similar to the hypothesized nanostructural forms in the developing butterfly scales. The ability to resolve these fainter signals hints at the potential of this facile light microscopy method for in vivo analysis of nanostructure formation in developing butterflies.
https://doi.org/10.5061/dryad.w0vt4b912
This data set contains reflectance data of single-wing scales measured using hyperspectral microscopy and microspectrophotometry as well as two tomography data sets of a single-wing scale.
Description of the data and file structure
Reflectance data measured using hyperspectral microscopy presented in Figure 2 is calculated using the dark data, the sample data, and the reference data which are all included in MATLAB files each containing one variable that is a three-dimensional matrix where each page is an image taken under a specific wavelength of light.
Dark data is contained within the following files:
dark_10x_HSM.mat
dark_20x_1_HSM.mat
dark_50x_1_HSM.mat
Sample data is contained within the following files:
scales_10x_HSM.mat
scales_20x_1_HSM.mat
scales_50x_1_HSM.mat
Reference data is contained within the following files:
mirror_10x_HSM.mat
mirror_20x_1_HSM.mat
mirror_50x_1_HSM.mat
Microspectrophotometry data presented in Figure 2 is contained within the files:
opisena1_sample1_10x_MSP.mat
opisena1_sample1_20x_MSP.mat
opisena1_sample1_50x_MSP.mat
Reflectance data presented in Figure 3 is calculated using the dark data (dark_50x_SEM.mat), the sample data (scales_50x_SEM.mat), and the reference data (mirror_50x_SEM.mat). Each file contains a single variable that is a three-dimensional matrix where each page is an image taken under a specific wavelength of light. Optical model data is contained within the file named area_thickness_models.mat. This file contains a MATLAB structure containing all the data presented in the grey shading of Figure 3G.
Reflectance data presented in Figure 4 was measured under differing immersion conditions. All conditions used the same reference and dark measurements contained within the files: mirror_standard.mat (reference), and blackfoil_oil.mat (dark). For scales measured in air, the sample data is within the file air.mat. Sample data for the following immersion conditions are contained within the file names in brackets: 1.3 (13_immersion.mat), 1.4 (14_immersion.mat), 1.45 (145_immersion.mat), and 1.5 (15_immersion.mat).
X-ray tomography data from a single scale has been stitched together using the data contained within the files:
ZEISS_810Ultra_Erlangen_Butterfly4_LFOV_top_Reconstruction.tif ZEISS_810Ultra_Erlangen_Butterfly4_LFOV_bottom_Reconstruction.tif
Visualizations of this tomography data were previously published in science.org/doi/10.1126/sciadv.1603119.
Code/Software
The MATLAB code included here is a custom-made application that controls the liquid crystal filter and monochromatic camera via a serial interface. The software files include kurios.m, hyperspectral_image_acquisition.mlapp, and calibration_app.mlapp. The two .mlapp files are MATLAB app files that can be opened in MATLAB and generate a user interface that allows the user to control different parameters of the Kurios liquid crystal filter. The kurios.m file defines the serial and communication ports for the Kurios liquid crystal filter.
These data sets were collected using hyperspectral microscopy, microspectrophotometry and x-ray tomography.
For hyperspectral microscopy, illumination was provided by a Zeiss Axioscope 5 microscope collimated white LED source or a halogen light source (OSL2, Thorlabs) that was passed through a collimating lens (OSL2COL, Thorlabs) and a shortpass filter (FESH0750, Thorlabs). The collimated light was passed through a tunable bandpass filter (Kurios, Thorlabs Inc.), and a quartz depolariser to counteract any polarisation effect of the liquid crystal filter (DPU-25, Thorlabs; a schematic diagram is shown in Figure 1A). The tunable bandpass filter was controlled over the serial interface by custom software written in MATLAB 2023a (The MathWorks Inc., USA). The bandwidth was set to medium, delivering a restricted spectrum of light with a full width at half-maximum (FWHM) of approximately 18 nm (Figure 1B). Samples were illuminated with wavelengths between 430–720 nm in 10 nm steps. For each illumination wavelength, an image was captured with a 20 MP monochromatic camera with pixel size 2.4 μm (BFS-U3-200S6M-C, Teledyne FLIR) mounted to the camera port of the microscope. Because the illumination intensities were not equal across all wavelengths (Figure 1B), a calibration run was initially conducted on a reference aluminium mirror (PF10-03-F01, Thorlabs) and the exposure times and gain values of the camera were adjusted such that the average pixel intensity of each image was approximately equal. This ensured that pixels were neither overexposed nor under-exposed for any one wavelength. Subsequently, the sample was measured using the calibrated exposure and gain values and the reflectance at each wavelength was calculated by averaging the pixels in the area of interest, subtracting the dark background from the sample data, and then dividing the sample data by the reference mirror to obtain relative reflectance.