Regional Center of Excellence at the Orbeli Institute of Physiology

Part of EU Open Research Repository
Published February 19, 2025 | Version v1
Dataset Open

240701_4DHSI_Bovine_Nerve

Authors/Creators

  • 1. ROR icon L. A. Orbeli Institute of Physiology NAS RA
  • 2. ROR icon George Washington University

Contributors

  • 1. ROR icon American University of Armenia
  • 2. ROR icon L. A. Orbeli Institute of Physiology NAS RA

Description

A 4D hyperspectral imaging (HSI) dataset capturing autofluorescence of bovine nerve and ligament tissues. Imaging was performed under multiple excitation conditions, representing the fourth dimension. Ground truth masks are included for tissue segmentation analysis.

Materials & Methods

Sample Preparation

Nerve and ligament were isolated from a bovine trotter acquired at the local market. The trotter was kept in water before acquisition by us, but was stored in the freezer before the experiment date.

For imaging, the nerve and ligament were put in a 90 mm plastic petri dish, attached to the bottom using a tape, and covered with 30 mL medical-grade normal saline (0.9%) to avoid drying of the sample (see in Photos)

Tissues in HSI images*, from top to bottom:

  • Nerve

  • Ligament

* The original dataset included three pieces of tissues, one of which identity was uncertain, so we cropped it and included only two tissues.

Sample Excitation/Illumination for HSI

For illuminating the sample:

  • Instrument: Tunable Light Source (model: TLS130B-300X, Newport Corporation)

  • Fiber Bundle Focusing Assembly was used to obtain higher intensities (model: 77776, Newport Corporation)

  • Simple concave mirror was used to direct light from the instrument to the sample

Light source optical power was measured at each wavelength using Optical Power Meter (model: 1936-R, Newport Corporation) with a Photodiode Sensor (model: 918D-UV-OD3R, Newport Corporation). Measurement was repeated 5 times and averaged. Respective data are available in metadata file(s).

4D HSI

Nuance FX Imaging System (Model: N-MSI-FX, CRi, Woburn, MA, USA) was used to acquire HSI data with parameters described in:

  • Metadata.csv 

Metadata Variables

Variable

Description

cube_name

Identifier or filename of the hyperspectral image cube, often including sample or acquisition details.

excitation_nm

Central wavelength (in nm) of the excitation/illumination light used for fluorescence or reflectance imaging.

emission_start_nm

Shortest wavelength (in nm) captured in the emission spectrum, defining the lower detection limit.

emission_end_nm

Longest wavelength (in nm) captured in the emission spectrum, defining the upper detection limit.

step_nm

Spectral resolution or step size (in nm) between consecutive bands in the hyperspectral image.

exposure_time_ms

Duration (in milliseconds) for which the sensor is exposed to light per spectral band.

acquisition_timestamp

Timestamp of the imaging process.

notes

Free-text field for additional comments, observations, or metadata.

light_source

Type and/or model of the illumination source (e.g., laser, LED, halogen lamp).

light_power_uW

Power of the illumination/excitation light in microwatts (µW), measured approximately at the sample position.

light_fwhm_nm

Spectral width (FWHM in nm) of the excitation light source.

emission_wavelengths_nm

List or array of specific wavelengths (in nm) at which emission signals are recorded.

emission_fwhm_nm

List or array of full width at half maxima (FWHM in nm) for each emission wavelength, indicating spectral resolution.

sensor_gain

Amplification factor applied to the sensor signal.

custom_field

User-defined or placeholder column for additional metadata.

Ground Truth Masks

Masks generated manually and semi-manually are available to serve as a ground truth reference for tissues in the HSI images.

  • Mask_Manual.png

  • Mask_SemiManual.png

Pixel labels in masks:

  • Background: 0

  • Ligament: 100

  • Nerve: 200

Background has some fluorescence - it represents essentially a plastic petri dish

Files

Cubes.zip

Files (219.7 MB)

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Additional details

Funding

European Commission
NAR-SAR-IPH - Regional Center of Excellence at the Orbeli Institute of Physiology 101087403

Dates

Created
2024-07-01