DOI: 10.5281/zenodo.14889178
title: 240618_4DHSI_Bovine_Nerve

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 (Photo_Trotter.jpg). The trotter was kept in water before acquisition by us.

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 to avoid drying of the sample (Photo_SamplePrep.jpg)

Tissues in HSI images from top to bottom (see RGB_Nuance)





Ligament




Nerve




Nerve (same nerve bent, bottom segment has damaged part)



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 4 times and averaged. Respective data available in metadata files.

4D HSI

Nuance FX Imaging System (model: N-MSI-FX, CRi, Woburn, MA, USA) was used to acquire hyperspectral images.

Three sessions of autofluorescence imaging was carried out on the same sample, without changing the imaging field:





Excitation 300-400, 10 nm step, (data in Cubes_300_400_5)




Excitation 430-670, 10 nm step, (data in Cubes_430_670_10_Autoexposure)




Excitation 410-460, 10 nm step, (data in Cubes_410_460_10_FixedExposure)



Metadata

Imaging conditions per datacube in more detail are available in:





Metadata_300_400_5.csv




Metadata_430_670_10_Autoexposure.csv 




Metadata_410_460_10_FixedExposure.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 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 excitation light in microwatts (µW), measured approximately at the sample position.





light_fwhm_nm



Spectral width (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



Full width at half maximum (FWHM) of the emission wavelengths, 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 as it represents essentially a plastic petri dish