This Cottle_readme_20210511.txt file was generated on 20210511 by Brian Cottle Links to Publication Field updated 20211209 TK ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Spectral and image data for: Towards Cardiac Tissue Characterization Using Machine Learning and Light-Scattering Spectroscopy 2. Author Information Principal Investigator Contact Information Name: Robert Hitchcock Institution: University of Utah Address: 36 S Wasatch Drive, SMBB 4509, Salt Lake City, UT 84112 Email: r.hitchcock@utah.edu Associate or Co-investigator Contact Information Name: Frank Sachse Institution: University of Utah Address: The Nora Eccles Harrison CVRTI 95 S 2000 E, Room 204A, Salt Lake City, UT 84112-5000 Email: frank.sachse@utah.edu Alternate Contact Information Name: Nathan Knighton University of Utah Address: 201 Presidents' Cir, Salt Lake City, UT 84112 Email: nate.knighton@gmail.com Authors: Nate Knighton Email: nate.knighton@gmail.com Phone: 801-498-0455 Brian Cottle Email: brian.cottle@utah.edu Institution: University of Utah Address: The Nora Eccles Harrison CVRTI 95 S 2000 E, Room 204, Salt Lake City, UT 84112-5000 Sarthak Tiwari Email: u1254813@utah.edu Abhijit Mondal Email: Abhijit.Mondal@childrens.harvard.edu Institution: Boston Children's Hospital Department Number: 617-355-7932 Address: Department of Cardiac Surgery, 300 Longwood Avenue, Bader, 2nd Floor, Boston, Massachusetts 02115 Aditya Kaza Email: Aditya.Kaza@cardio.chboston.org Institution: Boston Children's Hospital Department Number: 617-355-7932 Address: Department of Cardiac Surgery, 300 Longwood Avenue, Bader, 2nd Floor, Boston, Massachusetts 02115 Frank Sachse: Email: frank.sachse@utah.edu Institution: University of Utah Address: The Nora Eccles Harrison CVRTI 95 S 2000 E, Room 204A, Salt Lake City, UT 84112-5000 Phone: 801-587-9514 Robert Hitchcock Email: r.hitchcock@utah.edu Institution: University of Utah Address: 36 S Wasatch Drive, SMBB 4509, Salt Lake City, UT 84112 Phone: 801-585-7741 3. Date of data collection (single date, range, approximate date) 20190101 to 20190208, 20200721 to 20200807 4. Geographic location of data collection (where was data collected?): Salt Lake City, UT 5. Information about funding sources that supported the collection of the data: National Institutes of Health National Institutes of Health (NIH)9000 Rockville Pike Bethesda, Maryland 20892; telephone 301-496-4000 Grant Number: R56 HL128813 Grant Number: R01 HL135077 Nora Eccles Treadwell Foundation 136 EAST SOUTH TEMPLE STE 2100 SALT LAKE CITY, UT 84111 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY NC - Allows others to use and share your data non-commercially and with attribution. 2. Links to publications that cite or use the data: Knighton, N., Cottle, B., Tiwari S., Mondal A., Kaza A., Sachse F., Hitchcock R., 2021. Toward Cardiac Tissue Characterization Using Machine Learning and Light-Scattering Spectroscopy, Journal of Biomedical Optics J. of Biomedical Optics, 26(11), 116001 (2021). https://doi.org/10.1117/1.JBO.26.11.116001 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? No If yes, list source(s): 6. Recommended citation for the data: Knighton, N., Cottle, B., Tiwari S., Mondal A., Kaza A., Sachse F., Hitchcock R., 2021. Spectral and image data for: Towards Cardiac Tissue Characterization Using Machine Learning and Light-Scattering Spectroscopy. The Hive: University of Utah Research Data Repository. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Folder/Filename: Images Short description: Contains images that follow the naming scheme of [HeartID]_[ImageWidth]_[ImageHeigh].png B. Folder/Filename: SpectraData Short description: Contains two files containing spectral data (R1Spectra.csv and R2Spectra.csv) and two files containing their associated wavelength data (R1Wavelengths.csv, R2Wavelengths.csv). 2. Relationship between files: Each entry in the spectral data files (R1Spectra.csv and R2Spectra.csv) is associated with an entry in the wavelengths files (R1Wavelengths.csv, R2Wavelengths.csv). See descriptions later in this readme file for how to determine which spectra are associated with which wavelengths. 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: (A more thorough methods can be found in the paper "Towards Cardiac Tissue Characterization Using Machine Learning and Light-Scattering Spectroscopy") A customized LSS setup was developed for application in cardiac tissue. Broad-spectrum light illuminated the tissue samples and was collected by a custom-built spectroscopy probe (Berkshire Photonics, Washington Depot, CT) connected to a pair of spectrometers. The probe utilized a central illumination fiber surrounded by 4 light collection fibers. A single fiber with a core diameter of 200 µm (FVP200220240, Molex, Phoenix, AZ) served as the illumination fiber. Each arm consisted of two collection fibers of 100 µm core diameter (FVP100110125, Molex). The two fibers, R1 and R2, were located at respective center-to-center distances of 210 µm and 345 µm from the illumination fiber. The light collection fibers formed two orthogonal arms adjacent to the centrally located illumination fiber. This arrangement was chosen for its small form factor and to mitigate the effects of optical anisotropy inherent to cardiac tissue. The LSS system was used to gather spectra from ovine ventricular tissue. All animal usage was approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Utah and Boston Children’s Hospital. We obtained an approximately 1 cm3 transmural tissue sample from the right ventricular free wall (RV) of formalin-fixed hearts from 18 animals with gestational ages ranging 4.3 to 56 months. Two additional samples from the left ventricular free wall and ventricular septum of the 2 youngest hearts brought the total sample size to 22. Samples were placed on a black foam pad and kept submerged in phosphate-buffered saline (PBS) before and during spectroscopy. Black open-cell foam prevented signal distortion caused by photons passing through the sample. Samples were examined using LSS to identify changes in ND. The LSS probe was positioned on the epicardial surface at multiple locations to gather 20 spectra for all samples. Spectral acquisition occurred at 5 Hz. Spectra from the tissue samples were recorded at full width at half maximum resolution of 0.6 nm in the wavelength range of 500-1100 nm. After acquisition, the raw spectra were saved for analysis. Tissue samples were stored in PBS for histology. After spectral measurements, tissue samples were sectioned within the probed region at the center of each sample. A vibratome (Leica Model VT1200S, Wetzlar, Germany) cut sections of 100 µm thickness perpendicular to the epicardial surface and parallel to the transmural plane of the heart wall. We chose this orientation so that light scattering structures were identified throughout the thickness of the ventricular wall. After sectioning, glycoconjugates of the extracellular matrix and glycoproteins of cell membranes were labeled using wheat germ agglutinin (WGA) conjugated to a fluorophore (WGA CF488A Conjugate, Biotium, Fremont, CA). Cell nuclei were stained with 1 µM 6-diamidino-2-phenylindole (DAPI, D3571, Life Technologies, Carlsbad, CA) according to a previously established protocol.25 All sections were washed in PBS and mounted on a glass slide with Fluoromount-G (#17984-25, Electron Microscopy Science, Hatfield, PA). A Leica SP8 confocal microscope with a 40x oil immersion lens (NA 1.3) was used to scan each section. Two-dimensional tile scans with a pixel size of 0.2 µm spanning 695 µm x 2467 µm were performed for the capture of cardiac tissue including the epicardium. DAPI was excited with a 405 nm laser and WGA CF488A Conjugate with a laser at 488 nm wavelength. 2. Methods for processing the data: Raw spectra from both the R1 and R2 fibers and their associated wavelength data were sorted according to the age of the animal from which the samples were taken. These data were then saved into four separate .csv files, namely R1Spectra.csv, R2Spectra.csv, R1Wavelengths.csv, and R2Wavelengths.csv. These files are included in the .zip folder titled "SpectralData.zip". Images were saved with the dimensions in the file name for ease of processing. These .png files are included in the .zip folder titled "Images.zip". 3. Instrument- or software-specific information needed to interpret the data: Software to load, view, or manipulate .csv files. MATLAB v2019a or newer or a Python environment v3.8 or newer recommended. 4. Standards and calibration information, if appropriate: None 5. Environmental/experimental conditions: None 6. Describe any quality-assurance procedures performed on the data: None 7. People involved with sample collection, processing, analysis and/or submission: N. Knighton, B. Cottle, S. Tiwari ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: R1Spectra.csv, R2Spectra.csv, R1Wavelengths.csv, R2Wavelengths.csv (within SpectralData.zip) ----------------------------------------- 1. Number of variables: Each spectrum is associated with a number, and a "count" value. The number is associated with a somewhat arbitrary ID that also is associated to a specific animal from which a sample was taken. 2. Number of cases/rows: 440 spectra samples 3. Variable List A. Name: Column 0 - Sample Number Description: An integer number associated with each spectrum taken. This number should be used to associated a spectrum with its corresponding wavelength values. A. Name: Column 1 - Heart ID Number Description: Sample number is an integer value associated with each heart. This number facilitates computations and sorting, and works more fluently with programming and data processing than the actual "Heart IDs", described below. Association with heart IDs: 0 = A3L (Heart A3, Left Ventricular Freewall sample) 1 = A3S (Heart A3, Ventricular Septum sample) 2 = A3 3 = A1L (Heart A1, Left Ventricular Freewall sample) 4 = A1S (Heart A1, Ventricular Septum Sample) 5 = A1 6 = 646 7 = 656 8 = 502 9 = 496 10 = 621 11 = 616 12 = 666 13 = 518 14 = 522 15 = 653 16 = 300 17 = 305 18 = 172 19 = 173 20 = Do1 21 = D02 B. Name: Column 2 - Nuclear Counts Description: The nuclear density count value associated with the sample. Association with heart ID Numbers: 0 = 4558 1 = 4923 2 = 6116 3 = 7198 4 = 3972 5 = 5391 6 = 2529 7 = 2849 8 = 2774 9 = 3182 10 = 2289 11 = 2946 12 = 3236 13 = 2480 14 = 2245 15 = 1638 16 = 1583 17 = 1607 18 = 1522 19 = 1606 20 = 1233 21 = 1251 C. Name: Column 3 through End of File - Spectral Values (R1Spectra.csv and R2Spectra.csv) or Wavelength Values (R1Wavelengths.csv and R2Wavelengths.csv) Description: The spectral values or their associated wavelengths measured. 4. Missing data codes: N/A 5. Specialized formats of other abbreviations used N/A