This readme file was generated on [2024-06-13] by [Victoria] ------------------- GENERAL INFORMATION ------------------- Title of Dataset: Data from: In vivo spectroscopy to concurrently characterize five metabolic and vascular endpoints relevant to aggressive breast cancer; Author Contact Information (Victoria D'Agostino, Duke University, vwd@duke.edu, ORCiD: 0000-0001-8267-5033) Principal Investigator: Nimmi Ramanujam Institution: Duke University Email: nimmi.ramanujam@duke.edu ORCID: 0000-0001-7319-8415 Date of data collection: 2022-2024 Geographic location of data collection: Durham, NC, USA Funding and grant numbers: Grant DGE 2139754 and Grant 1R01EB02818-01 -------------------- DATA & FILE OVERVIEW -------------------- File list: This data repository contains the following: - Data to re-create Figs 1 and 2 in a folder titled "Raw Data Figure 1 and 2". These values were collected via optical spectroscopy of scattering phantoms and extracted using an inverse Monte Carlo algorithm. These files are .mat files - Data to re-create Fig 3 in a folder titled "Raw Data Figure 3". These values were collected via optical spectroscopy of scattering phantoms and extracted using an inverse Monte Carlo algorithm.These files are .mat files - Values to recreate Fig 4 in a folder titled "Minimum Data Set Figure 4". These values were collected via optical spectroscopy of tissue mimicking phantoms, and extracted using an inverse Monte Carlo algorithm. Values are found in .txt files - Data to re-create Fig 5 in a folder titled "Raw Data Figure 5". These values were collected via optical spectroscopy of BALB/c mice, either of tumor- bearing or healthy mammary tissue and extracted using an inverse Monte Carlo algorithm. These files are .mat files - Values to recreate Fig 6 in a folder titled "Minimum Data Set Figure 6". These values were collected via optical spectroscopy of BALB/c mice, either of tumor- bearing or healthy mammary tissue, and extracted using an inverse Monte Carlo algorithm. This is a .xlsx file -------------------------- METHODOLOGICAL INFORMATION -------------------------- Description of methods used for collection/generation of data: Fluorescence spectroscopy -------------------------- DATA-SPECIFIC INFORMATION -------------------------- - Raw Data Figure 1 and 2: These values were collected via optical spectroscopy of scattering phantoms and extracted using an inverse Monte Carlo algorithm. These files are .mat files. - .mat files are STRUCT files with the following relevant -Optical Properties can be found in data.optical_properties - extracted_mua is the absorption coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is absorption coefficient (cm^-1) - extracted_mus_prime is the reduced scattering coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is reduced scattering coefficient (cm^-1) -Reflectance is the white light reflectance spectra - Measured is the raw, background subtracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) -Fluorescence is the fluorescence spectra - Measured is the raw, background subtracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Data to re-create Fig 3: These values were collected via optical spectroscopy of scattering phantoms and extracted using an inverse Monte Carlo algorithm.These files are .mat files - .mat files are STRUCT files with the following relevant -Optical Properties can be found in data.optical_properties - extracted_mua is the absorption coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is absorption coefficient (cm^-1) - extracted_mus_prime is the reduced scattering coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is reduced scattering coefficient (cm^-1) -Reflectance is the white light reflectance spectra - Measured is the raw, background subtracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) -Fluorescence is the fluorescence spectra - Measured is the raw, background subtracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Values to recreate Fig 4: These values were collected via optical spectroscopy of tissue mimicking phantoms, and extracted using an inverse Monte Carlo algorithm. Values are found in .txt files - 2-NBDG and Bodipy contain text files with 10 instances, each for a different phantom, with inverse Monte Carlo corrected fluorescence intensity corrected units (c.u.) - muA contains absorption coefficient (cm^-1) text files with 10 instances, each for a different phantom, with inverse Monte Carlo extracted absorption coefficient (cm^-1) - muS contains reduced scattering coefficient (cm^-1) text files with 10 instances, each for a different phantom, with inverse Monte Carlo extracted reduced scattering coefficient (cm^-1) - Data to re-create Fig 5: These values were collected via optical spectroscopy of BALB/c mice, either of tumor- bearing or healthy mammary tissue and extracted using an inverse Monte Carlo algorithm. These files are .mat files - .mat files are STRUCT files with the following relevant -Optical Properties can be found in data.optical_properties - extracted_mua is the absorption coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is absorption coefficient (cm^-1) - extracted_mus_prime is the reduced scattering coefficient spectrum - Column 1 is wavelengths (nm) - Column 2 is reduced scattering coefficient (cm^-1) -Reflectance is the white light reflectance spectra - Measured is the raw, background subtracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted reflectance spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) -Fluorescence is the fluorescence spectra - Measured is the raw, background subtracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Fit is the inverse Monte Carlo extracted fluorescence spectra - Column 1 is wavelengths (nm) - Column 2 is inverse Monte Carlo corrected (scaled) intensity corrected units (c.u.) - Values to recreate Fig 6 in a folder titled "Minimum Data Set Figure 6". These values were collected via optical spectroscopy of BALB/c mice, either of tumor- bearing or healthy mammary tissue, and extracted using an inverse Monte Carlo algorithm. This is a .xlsx file - These values are normalized values from inverse Monte Carlo results -TMRE60 is the 60 minute timepoints for TMRE fluorescence -NBDG60 is the 60 minute timepoints for 2-NBDG fluorescence -Bodipy is the 60 minute timepoints for Bodipy fluorescence -SO2 is the calculated oxygen saturation from background measurements -THB is the calculated total hemoglobin from background measurements ------------------------- USE and ACCESS INFORMATION -------------------------- Data License: http://creativecommons.org/publicdomain/zero/1.0/ To cite the data: D’Agostino, V. W., Deutsch, R. J., Kwan, M., Sunassee, E. D., Madonna, M. C., Palmer, G. M., Crouch, B. T., & Ramanujam, N. (2024). Data from: In vivo spectroscopy to concurrently characterize five metabolic and vascular endpoints relevant to aggressive breast cancer. Duke Research Data Repository. https://doi.org/10.7924/r4vx0k33z