Skin Optics Analysis based on ISSA Data
Junhui He and Tina Lasisi
2025-12-18
Last updated: 2025-12-18
Checks: 5 2
Knit directory: SkinOptics/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 9956d2d | Junhui He | 2025-12-17 | Build site. |
| Rmd | a6f7dc4 | Junhui He | 2025-12-17 | update JID_SkinOptics.Rmd |
| html | 32c3e8f | Junhui He | 2025-12-11 | Rebuild site to apply navbar layout |
| html | b2cbe44 | Junhui He | 2025-12-11 | Build site. |
| Rmd | df71367 | Junhui He | 2025-12-11 | modify face site |
| html | d98f12d | Junhui He | 2025-12-11 | Build site. |
| Rmd | 2fc3d03 | Junhui He | 2025-12-11 | add correlation analysis |
| html | 81580b5 | Junhui He | 2025-12-11 | build workflowr |
| Rmd | e11deee | Junhui He | 2025-12-11 | calculate EI |
| html | e11deee | Junhui He | 2025-12-11 | calculate EI |
| Rmd | 53d4f9c | Junhui He | 2025-12-11 | create SkinOptics |
| html | 53d4f9c | Junhui He | 2025-12-11 | create SkinOptics |
Clarifications
Melanin index (MI) is calculated from skin reflectance at 680 nm, where \(R_{680}\) is the measured reflectance percentage (0-100):
- \[MI = -100 \times \log_{10}(R_{680} / 100)\]
- This is equivalent to the standard formula \(MI = 100 \times \log_{10}(1/R)\), where \(R\) is reflectance as a decimal (0-1)
- Internally, this is computed by first calculating absorbance (\(A_{680} = -\log_{10}(R_{680} / 100)\)), then multiplying by 100
Erythema index (EI) is calculated as: \[EI = 100 \times \log_{10}\left(\frac{R_{680}}{(R_{550} + R_{560})/2}\right)\] where \(R_{550}\), \(R_{560}\), and \(R_{680}\) are the reflectance percentages at 550 nm, 560 nm, and 680 nm, respectively.
EI variability is measured by the standard deviation of EIs within a sliding window of MI values. The window size is set to 20 MI units, and the step size is 1 MI unit.
- For each center MI value in the sequence, all EI values corresponding to MI values within the window (center MI \(\pm\) 10) are collected, and their standard deviation is computed.
- The center MI values range from the 1st to the 99th percentile of observed MI values.
FACE site refers to Forehead or Cheek, while PALM site refers to the Palm of the hand.
Representative FACE MI:
- For each subject, the FACE MI is given by the Forehead MI if the Forehead MI is available; otherwise, it is the Cheek MI.
- For subjects with multiple measurements at the same FACE site, we randomly select one measurement.
- Each subject has only one representative FACE reflectance spectra.
First derivatives of skin spectra are estimated using local polynomial regression with bandwidth selected by the dpill function, scaled by a factor of 0.7.
Eumelanin classes are defined based on melanin index ranges as follows:
- Low: \(MI < 25\)
- Intermediate low: \(25 \leq MI < 50\)
- Intermediate: \(50 \leq MI < 75\)
- Intermediate high: \(75 \leq MI < 100\)
- High: \(MI \geq 100\)
The pdf files generated in this analysis are saved in the “output” directory.
Visualizations
Face readings before deduplication: 4603 Unique individuals with Face readings: 2102 Face readings after deduplication: 2102 Palm readings before deduplication: 776 Unique individuals with Palm readings: 776 Palm readings after deduplication: 776 Distribution of melanin index by site
Final data summary:Face: n = 2101 | Unique individuals: 2101 Palm: n = 776 | Unique individuals: 776 Combined: n = 2877 
Unique subjects per site across representative face melanin index bins (Heatmap)
| Version | Author | Date |
|---|---|---|
| 53d4f9c | Junhui He | 2025-12-11 |
| Eumelanin class | Number of subjects |
|---|---|
| Low | 77 |
| Intermediate low | 1800 |
| Intermediate | 191 |
| Intermediate high | 30 |
| High | 3 |
| Eumelanin class | Number of subjects |
|---|---|
| Low | 127 |
| Intermediate low | 621 |
| Intermediate | 27 |
| Intermediate high | 1 |
Reflectance by eumelanin classes
First derivatives of reflectance by eumelanin classes
Face reflectance derivatives by face eumelanin class
Palm reflectance derivatives by palm eumelanin class
Palm reflectance derivatives by face eumelanin class
| Version | Author | Date |
|---|---|---|
| b2cbe44 | Junhui He | 2025-12-11 |
Composite figure: Face reflectance and derivatives by eumelanin class
First derivatives of absorbance by eumelanin classes
Face absorbance derivatives by face eumelanin class
Palm absorbance derivatives by palm eumelanin class
Palm absorbance derivatives by face eumelanin class
| Version | Author | Date |
|---|---|---|
| b2cbe44 | Junhui He | 2025-12-11 |
Correlation between reflectance derivative sd and melanin index
- Regression analysis
Call:
lm(formula = sd_ref ~ log_mi + I(log_mi^2), data = sd_face)
Residuals:
Min 1Q Median 3Q Max
-0.069033 -0.014140 -0.001695 0.011080 0.100513
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1.558619 0.066400 23.47 <2e-16 ***
log_mi -0.681307 0.035862 -19.00 <2e-16 ***
I(log_mi^2) 0.076171 0.004826 15.78 <2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.02264 on 2098 degrees of freedom
Multiple R-squared: 0.6497, Adjusted R-squared: 0.6494
F-statistic: 1946 on 2 and 2098 DF, p-value: < 2.2e-16
Call:
lm(formula = sd_ref ~ log_mi, data = sd_palm)
Residuals:
Min 1Q Median 3Q Max
-0.066053 -0.016370 0.000337 0.015371 0.071971
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.560165 0.013160 42.56 <2e-16 ***
log_mi -0.120567 0.003789 -31.82 <2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.0238 on 774 degrees of freedom
Multiple R-squared: 0.5668, Adjusted R-squared: 0.5662
F-statistic: 1013 on 1 and 774 DF, p-value: < 2.2e-16
Correlation between absorbance derivative sd and melanin index
Correlation between erythema index and melanin index by site
| Version | Author | Date |
|---|---|---|
| 9956d2d | Junhui He | 2025-12-17 |
Correlation between erythema index variability and melanin index by site
- EI variability is measured by the standard deviation of EIs within a
sliding window of MI values. The window size is set to 20 MI units, and
the step size is 1 MI unit.
- For each center MI value in the sequence, all EI values corresponding to MI values within the window (center MI ± 10) are collected, and their standard deviation is computed.
- The center MI values range from the 1st to the 99th percentile of observed MI values.
| Version | Author | Date |
|---|---|---|
| 9956d2d | Junhui He | 2025-12-17 |
R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Tahoe 26.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggpubr_0.6.0 here_1.0.1 KernSmooth_2.23-26 openxlsx_4.2.8.1
[5] scales_1.4.0 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[9] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.2.1 ggplot2_4.0.1 tidyverse_2.0.0 knitr_1.50
loaded via a namespace (and not attached):
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[49] backports_1.5.0 timechange_0.3.0 rmarkdown_2.29 ggsignif_0.6.4
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