This Readme.txt file was generated on May 25, 2022 by MICHAELA TAYLOR-WILLIAMS

-------------------
GENERAL INFORMATION
-------------------

Title of Dataset: Multispectral imaging of nailfold capillaries using LED illumination

Author Information

	Principal Investigator: Sarah E. Bohndiek, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom, seb53@cam.ac.uk;
	Associate or Co-investigator: Michaela Taylor-Williams, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom, mrt50@cam.ac.uk
	Associate or Co-investigator: Steve Mead, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom, sfm36@cam.ac.uk

Date of data collection: June 2020 to April 2022

Geographic location of data collection: Cambridge, Cambridgeshire, United Kingdom 

Information about funding sources or sponsorship that supported the collection of the data:

This work was funded by Cancer Research UK under grant numbers C9545/A29580 and EPSRC EP/R003599/1. Michaela Taylor-Williams is funded by the Sir John Monash Foundation and Cambridge Trust, Steve Mead is funded by the EPSRC Centre for Doctoral Training in Connected Electronic and Photonic Systems (EP/S022139/1). (EStJS). LH is funded by a studentship from the National Physical Laboratory. LH acknowledges funding from the MedAccel program of the National Physical Laboratory financed by the Department for Business, Energy and Industrial Strategy's Industrial Strategy Challenge Fund. CW acknowledges the financial support of the Wellcome Trust (Interdisciplinary Fellowship) and Wolfson College, Cambridge.

--------------------------
SHARING/ACCESS INFORMATION
-------------------------- 

Licenses/restrictions placed on the data, or limitations of reuse:
CC BY

Recommended citation for the data:

Citation for and links to publications that cite or use the data:
Taylor-Williams et al. Multispectral imaging of nail fold capillaries using LED illumination. J Biomed Opt.

--------------------
DATA & FILE OVERVIEW
--------------------
Figure 1:
LED_modelling_Prhal_spectrum.m performs the calculations of the output Differences_in_abs for FWHM of Gaussians 5, 10, 15, 20, 25, 30, 35, 40 nm; the first column is the wavelength, while the second is the change in reflectance.

Figure 3:
(a) and (b) are in the ‘Measured’ folder.
(c) Is from ‘Illumination_remodelled_figs.m’ and the resultant Figure 2
(d) Made using Fiji (Image J) from (a).

Figure 4:
(a) and (b) are in the ‘Measured’ folder.
(c) Is from ‘Illumination_remodelled_figs.m’ and the resultant Figure 1.

Figure 5:
(a) Norm_stack_cropped.tif contains the six images in a single tif stack. Original raw data files can be provided on request to the corresponding PI.
(b) Run ‘Boxplot.m’

Figure 6:
(e) Summary SNR.xlsx
(f & g) In the ‘Individual Capillaries’ folder
(h) Schematic made in Adobe Illustrator
Supp. Figure 2: 
Data format is consistent for 3 LEDs and is the files ‘Cyan 505nm zero-adjusted run1.csv’, ‘Green 572nm zero-adjusted run1.csv’, ‘Amber 590nm zero-adjusted run1.csv’ for the Cyan, Green, and Amber LED respectively. 
Lines 1-12 Include Measurement settings
Lines 16-1816 
Column 1: Sample number
Column 2: Day (MM/dd/yyyy)
Column 3: Time of day (hh:mm:ss)
Column 4: Irradiance (W/cm^2)

Supp. Figure 4:
File: 20201222_LED_Spectral_data.mat
Table Column 1: Wavelength (nm)
Table Column 2: Cyan irradiance (W/cm^2)
Table Column 3: Green irradiance (W/cm^2)
Table Column 4: Amber irradiance (W/cm^2)

Supp. Figure 5: 
(a) NA figure diagram
(b) Run ‘Plot_variance_against_mean_values_Basler_rev1.m’ which loads ‘cyanLEDdara15x7.mat. Column 2 is mu(y) - mu(y.dark); and, column 4 omega(y) - omega(y.dark).
(c) Run ‘Plot_mean_values_against_photon_flux_Basler_rev1.m’ which loads ‘cyanLEDdara15x7.mat. Column 1 is the camera's exposure time, which is later converted to photons per pixel, and, column 2 is the signal measured on the sensor. 
(d) Run ‘Plot_SNR_against_phton_flux_cyan_Basler.m’ which loads ‘cyanLEDdara15x7.mat. Column 1 is the camera's exposure time, which is later converted to photons per pixel, and, column 7 is the SNR.

Supp. Figure 6: 
'Halogen_analysis.mat’ Variables:
wavelengths: wavelengths (nm) of spectral measurements 
halogen: 1x13 Cell array including 10 spectral measurements at each of the 13 halogen settings, the wavelengths of the spectral measurements correspond to the variable wavelengths
average: the average spectra of the halogen at each of the 13 settings
halogen_std: the standard deviation spectra of the halogen at each of the 13 settings
total_power_val: the sum of the average spectra to calculate normalised irradiance, and associated standard deviation
‘Linearity_measurements_Grasshopper_folder_w_errors.m’: Calculates the mean and standard deviation of the sensor’s response from five images collected, these are in the variable stats which are then plotted against the total_power_val for the figure.

Supp. Figure 7:
(a) and (f) are the same as shown in Figures 3 and 4. 
(b-d) and (g-i) are made in Light Tools
(e) and (j) are made using ‘Illumination_remodelled_figs.m’ and are the output in Figures 4 and 5.

--------------------------
METHODOLOGICAL INFORMATION
--------------------------

Please refer to the main publication for more details on data acquisition.

Methods for processing the data:
Data has been analysed using MATLAB R2020a, Microsoft Excel, and LightTools. 

People involved with sample collection, processing, analysis and/or submission: 
Study concept and design: MT-W, SM, CW, SEB; Modeling: MT-W, TWS; System design and fabrication: MT-W, SM; Acquisition of data: MT-W, SM, LH; Analysis of data: MT-W, SM, SEB; Writing the manuscript: All authors.