Journal: Ecology and Evolution

Article Title: Assessing the Impact of Environment on the Color of Painted Turtles ( Chrysemys picta ) in the Wild

doi: 10.1002/ece3.71702

Figure Lengend Snippet: Reflectance spectra of the carapace (A), plastron (B), and neck stripe (C) of the painted turtle. The dark line shows the mean spectrum across all individuals, and the shaded area shows the standard deviation.

Article Snippet: The spectrometer was calibrated using a Labsphere reflectance standard that reflects equally (99%) across the ultraviolet and visual spectrum (300–800 nm).

Techniques: Standard Deviation

Journal: Ecology and Evolution

Article Title: Assessing the Impact of Environment on the Color of Painted Turtles ( Chrysemys picta ) in the Wild

doi: 10.1002/ece3.71702

Figure Lengend Snippet: Plastron carotenoid chroma did not change with water clarity or any other fixed effects (A), though the shape of the spectra shifted slightly with water clarity (B). The regression line shows the estimate from the linear mixed effects model with population as a random effect and log‐transformed water clarity, plant density, their interaction, carapace length, and sex as fixed effects. Points are jittered along the x ‐axis for clarity. The mean reflectance spectrum is shown for each site, with the standard deviation shaded. The x ‐axis is from 300 to 750 nm and the y ‐axis is from 0% to 100% reflectance for all spectra.

Article Snippet: The spectrometer was calibrated using a Labsphere reflectance standard that reflects equally (99%) across the ultraviolet and visual spectrum (300–800 nm).

Techniques: Transformation Assay, Standard Deviation

Journal: Biomedical Optics Express

Article Title: Multi-parametric functional optical spectroscopy to monitor the metabolic and vascular changes in small head and neck tumors in vivo with radiation stress

doi: 10.1364/BOE.565339

Figure Lengend Snippet: ( A ) Representative SCC-61 and rSCC-61 tumors measured by our optical spectroscopy; ( B ) Tumor volumes of SCC-61 and rSCC-61 tumors on day 10 post cell injection; ( C ) Average diffuse reflectance spectra measured on all five in vivo SCC-61 tumors and five in vivo rSCC-61 tumors; ( D ) MC model extracted absorption coefficients of five in vivo SCC-61 tumors and five in vivo rSCC-61 tumors; ( E ) MC model extracted reduced scattering coefficients of five in vivo SCC-61 tumors and five in vivo rSCC-61 tumors. Tumor volume was estimated using the equation: volume = (Length x Width x Height)/2.

Article Snippet: All raw diffuse reflectance spectra were calibrated using a 20% reflectance standard (Spectralon, Labsphere) before quantitative analysis.

Techniques: Spectroscopy, Injection, In Vivo

Journal: Biomedical Optics Express

Article Title: Multi-parametric functional optical spectroscopy to monitor the metabolic and vascular changes in small head and neck tumors in vivo with radiation stress

doi: 10.1364/BOE.565339

Figure Lengend Snippet: Tumor volumes of SCC-61 (A) and rSCC-61 (E) tumors prior to and post RT. Average diffuse reflectance spectra measured on SCC-61 (B) and rSCC-61 tumors (F) , the MC model extracted absorption coefficients of SCC-61 (C) and rSCC-61 (G) tumors and the MC model extracted reduced scattering coefficients of SCC-61 (D) and rSCC-61 (H) tumors prior to and post radiation treatment. Tumor volume was estimated using the equation: volume = (Length x Width x Height) / 2. One animal from the SCC-61 group showed obvious tumor necrosis, therefore, the animal was euthanized before RT treatment per IACUC protocol.

Article Snippet: All raw diffuse reflectance spectra were calibrated using a 20% reflectance standard (Spectralon, Labsphere) before quantitative analysis.

Techniques:

Journal: Science Advances

Article Title: Machine reading and recovery of colors for hemoglobin-related bioassays and bioimaging

doi: 10.1126/sciadv.adt4831

Figure Lengend Snippet: ( A ) Detrimental color variations in digital photos of biological tissue captured under various white-light illumination conditions: light-emitting diodes (LEDs) with color temperature of 3000, 4300, and 5800 K, as well as fluorescent tube light. The colors under CIE illuminant E (equal energy radiator or spectrally uniform illumination) can be considered absolute. CIE illuminant E is achieved through spectral normalization using a diffuse (Lambertian) reflectance standard (see Materials and Methods). ( B ) Light conditions having distinct spectral profiles: fluorescent tube, incandescent light, white LED, and sunlight (fig. S1). ( C ) Representative photos of whole blood–mimicking samples in cuvettes at different hemoglobin (Hgb) concentrations, acquired under various light conditions. A conventional color chart (Macbeth ColorChecker or X-Rite ColorChecker) is juxtaposed with the samples. ( D ) Smartphone model–dependent RGB spectral response functions (also known as spectral sensitivity): Apple iPhone 12 Pro, Apple iPhone SE, Samsung Galaxy S21, and Samsung Galaxy A52 (fig. S2). ( E ) Representative photos captured using various smartphone models. ( F ) File formats with different bit depths (color depths) in the R, G, and B color channels: JPEG (8-bit depth), RAW (10-bit depth), and MP4 (8-bit depth). ( G ) Representative photo acquisition scenarios based on combinations of light conditions (B), smartphone models (D), and file formats (F). When multiple photos of the same sample are captured under varying conditions, accurate and precise color recovery ensures that recovered color values converge to the ground truth.

Article Snippet: Using a white diffuse reflectance standard (SRT-99-050, Labsphere), the spectral intensity I ref (λ) reflected from the white reflectance standard under the identical imaging setting as the sample can be obtained I ref ( λ ) = L ( λ ) · C ( λ ) · D ( λ ) (2) Then, O (λ) is calculated by normalizing I m (λ) with respect to I ref (λ) O ( λ ) = I m ( λ ) I ref ( λ ) (3) CIE illuminant E, through spectral normalization, allows for the definition of the absolute colors of a sample, as the spectral intensity is not influenced by the physical illumination source or acquisition conditions.

Techniques:

Journal: Science Advances

Article Title: Machine reading and recovery of colors for hemoglobin-related bioassays and bioimaging

doi: 10.1126/sciadv.adt4831

Figure Lengend Snippet: ( A ) Macbeth ColorChecker containing 24 reference colors used for general photography. ( B ) Corresponding CIE xy chromaticity values under CIE illuminant E, measured using a spectrometer and a reflectance standard. The wide gamut of Macbeth ColorChecker overlaps with the sRGB color space. ( C ) Corresponding CIE LAB values under CIE illuminant E on the a * and b * axes. ( D ) Corresponding L* values as functions of a* and b* values. ( E and F ) Parametric spectral modeling of biological tissue (peripheral tissue and blood samples). Physiologically possible color variations are captured by 12,240 synthesized spectral data of peripheral tissue (E) and 10,000 synthesized spectral data of whole blood (F) (see Materials and Methods). ( G ) Blood Hgb gamut defined by three primary points of CIE xy chromaticity: ( x , y ) = (0.30, 0.31), (0.47, 0.42), and (0.63, 0.33). ( H ) Corresponding CIE LAB values on the a * and b * axes. ( I ) Corresponding L* values as functions of a* and b* values. ( J and K ) Importance of CIE XYZ Euclidean distance metric for machine readability and learning in color-based diagnostics, compared to Delta E values including CIE94 ( ∆ E 94 * ) and CIEDE2000 ( ∆ E 00 * ). Eleven representative colors are selected from the Hgb gamut, with equal CIE XYZ Euclidean distances between all pairs of adjacent colors. Delta E values incorporate human visual judgment and perception.

Article Snippet: Using a white diffuse reflectance standard (SRT-99-050, Labsphere), the spectral intensity I ref (λ) reflected from the white reflectance standard under the identical imaging setting as the sample can be obtained I ref ( λ ) = L ( λ ) · C ( λ ) · D ( λ ) (2) Then, O (λ) is calculated by normalizing I m (λ) with respect to I ref (λ) O ( λ ) = I m ( λ ) I ref ( λ ) (3) CIE illuminant E, through spectral normalization, allows for the definition of the absolute colors of a sample, as the spectral intensity is not influenced by the physical illumination source or acquisition conditions.

Techniques: Synthesized

Journal: Science Advances

Article Title: Machine reading and recovery of colors for hemoglobin-related bioassays and bioimaging

doi: 10.1126/sciadv.adt4831

Figure Lengend Snippet: ( A ) One-shot transduction learning of neural network–based color recovery with HemaChrome. The neural network is trained for each photo without relying on any preexisting training dataset. The training dataset consists of the color values of the reference colors in HemaChrome. Once trained on the specific photo, the network processes the RGB values acquired from the sample of interest in the photo to recover the corresponding CIE XYZ values. ( B ) HemaChrome chart with 116 reference colors for neural network–based color recovery. ( C ) Corresponding CIE xy chromaticity values under CIE illuminant E, measured using a spectrometer and a reflectance standard. ( D ) Corresponding CIE LAB values under CIE illuminant E on the a * and b * axes. ( E ) Corresponding L* values as functions of a* and b* values. ( F ) Representative photo of blood Hgb–mimicking samples to recover their absolute colors (under CIE illuminant E). ( G to J ) Average color differences between the ground truth and recovered CIE XYZ values for each test sample from photos captured across 36 diverse photo acquisition scenarios . The root mean square error (RMSE) (G), root mean square relative error (RMSRE) (H), average CIE94 ( ∆ E 94 * ) (I), and average CIEDE2000 ( ∆ E 00 * ) (J) are compared (eqs. S1, S2, S6, and S7). Among the three color correction methods, neural network color recovery using HemaChrome consistently returns minimal errors across all test samples.

Article Snippet: Using a white diffuse reflectance standard (SRT-99-050, Labsphere), the spectral intensity I ref (λ) reflected from the white reflectance standard under the identical imaging setting as the sample can be obtained I ref ( λ ) = L ( λ ) · C ( λ ) · D ( λ ) (2) Then, O (λ) is calculated by normalizing I m (λ) with respect to I ref (λ) O ( λ ) = I m ( λ ) I ref ( λ ) (3) CIE illuminant E, through spectral normalization, allows for the definition of the absolute colors of a sample, as the spectral intensity is not influenced by the physical illumination source or acquisition conditions.

Techniques: Transduction