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1. IDCube Lite: Free Interactive Discovery Cube software for multi and hyperspectral applications

   https://doi.org/10.1255/jsi.2021.a1  

   Mishra, Deependra ; Hurbon, Helena ; Wang, John ; Wang, Steven ; Du, Tommy ; Wu, Qian ; Kim, David ; Basir, Shiva ; Cao, Qian ; Zhang, Hairong ; et al ( May 2021 , Journal of Spectral Imaging)

   Multi- and hyperspectral imaging modalities encompass a growing number of spectral techniques that find many applications in geospatial, biomedical, machine vision and other fields. The rapidly increasing number of applications requires convenient easy-to-navigate software that can be used by new and experienced users to analyse data, and develop, apply and deploy novel algorithms. Herein, we present our platform, IDCube Lite, an Interactive Discovery Cube that performs essential operations in hyperspectral data analysis to realise the full potential of spectral imaging. The strength of the software lies in its interactive features that enable the users to optimise parameters and obtain visualmore »input for the user in a way not previously accessible with other software packages. The entire software can be operated without any prior programming skills allowing interactive sessions of raw and processed data. IDCube Lite, a free version of the software described in the paper, has many benefits compared to existing packages and offers structural flexibility to discover new, hidden features that allow users to integrate novel computational methods.« less
2. Excitation-scan mirror array system advancements to hyperspectral imaging applications

   https://doi.org/10.1117/12.2546485  

   Parker, Marina ; Browning, Craig M. ; Mayes, Sam A. ; Deal, Joshua ; Gunn Mayes, Samantha ; Rich, Thomas C. ; Leavesley, Silas J. ; Brown, Thomas G. ; Wilson, Tony ; Waller, Laura ( February 2020 , Proc. SPIE 11245, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVII)

   Hyperspectral imaging (HSI) technology has been applied in a range of fields for target detection and mixture analysis. While its original applications were in remote sensing, modern uses include agriculture, historical document authentications and medicine. HSI has shown great utility in fluorescence microscopy; however, acquisition speeds have been slow due to light losses associated with spectral filtering. We are currently developing a rapid hyperspectral imaging platform for 5-dimensional imaging (RHIP-5D), a confocal imaging system that will allow users to obtain simultaneous measurements of many fluorescent labels. We have previously reported on optical modeling performance of the system. This previous modelmore »investigated geometrical capability of designing a multifaceted mirror imaging system as an initial approach to sample light at many wavelengths. The design utilized light-emitting diodes (LEDs) and a multifaceted mirror array to combine light sources into a liquid light guide (LLG). The computational model was constructed using Monte Carlo optical ray software (TracePro, Lambda Research Corp.). Recent results presented here show transmission has increased up to 9% through parametric optimization of each component. Future work will involve system validation using a prototype engineered based on our optimized model. System requirements will be evaluated to determine if potential design changes are needed to improve the system. We will report on spectral resolution to demonstrate feasibility of the RHIP-5D as a promising solution for overcoming current HSI acquisition speed and sensitivity limitations.« less
3. Optimization of light transmission through an excitation-scan hyperspectral mirror array system

   https://doi.org/10.1117/12.2510555  

   Parker, Marina ; Browning, Craig ; Rich, Thomas C. ; Leavesley, Silas J. ; Farkas, Daniel L. ; Leary, James F. ; Tarnok, Attila ( March 2019 , Proc. SPIE 10881, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII, 108810O)

   Hyperspectral imaging has numerous applications in a range of fields for target detection. While its original applications were in remote sensing, new uses include analyzing food quality, agriculture and medicine, Hyperspectral imaging has shown utility in fluorescence microscopy for detecting signatures from many fluorescent molecules, but acquisition speeds have been slow due to the need to acquire many spectral bands and the light losses associated with spectral filtering. Therefore, a novel confocal microscope, the 5- Dimensional Rapid Hyperspectral Imaging Platform (RHIP-5D) was designed and is undergoing testing to overcome acquisition speed and sensitivity limitations. The current design utilizes light-emitting diodesmore »(LEDs) and a multifaceted mirror array to combine light sources into a liquid light guide. Initial tests demonstrated feasibility and we are now working on determining the ideal location of the liquid light guide, LEDs, lenses and mirror array to optimize optical transmission. A computational model was constructed using Monte Carlo optical ray tracing in TracePro software (Lambda Research Corp.). LED sources were simulated by importing irradiance properties from the manufacturers’ specifications. Optical properties of lenses were modeled using lens files available from the manufacturer. Analysis of the model includes geometry and parametric optimization, assessing lens power, mirror angles and location of optical elements. Initial results show an increase of transmission is possible by up to 20%. Future work will involve evaluating the position of the liquid light guide as well as analyzing lens configurations to further increase optical transmission.« less
4. Colorectal cancer detection by hyperspectral imaging using fluorescence excitation scanning

   https://doi.org/10.1117/12.2290696  

   Leavesley, Silas J. ; Deal, Joshua ; Martin, Will A. ; Lall, Malvika ; Lopez, Carmen ; Rich, Thomas C. ; Boudreaux, Carole W. ; Rider, Paul F. ; Hill, Shante ( February 2018 , Proc. SPIE 10489, Optical Biopsy XVI: Toward Real- Time Spectroscopic Imaging and Diagnosis, 104890K)

   Hyperspectral imaging technologies have shown great promise for biomedical applications. These techniques have been especially useful for detection of molecular events and characterization of cell, tissue, and biomaterial composition. Unfortunately, hyperspectral imaging technologies have been slow to translate to clinical devices – likely due to increased cost and complexity of the technology as well as long acquisition times often required to sample a spectral image. We have demonstrated that hyperspectral imaging approaches which scan the fluorescence excitation spectrum can provide increased signal strength and faster imaging, compared to traditional emission-scanning approaches. We have also demonstrated that excitation-scanning approaches may bemore »able to detect spectral differences between colonic adenomas and adenocarcinomas and normal mucosa in flash-frozen tissues. Here, we report feasibility results from using excitation-scanning hyperspectral imaging to screen pairs of fresh tumoral and nontumoral colorectal tissues. Tissues were imaged using a novel hyperspectral imaging fluorescence excitation scanning microscope, sampling a wavelength range of 360-550 nm, at 5 nm increments. Image data were corrected to achieve a NIST-traceable flat spectral response. Image data were then analyzed using a range of supervised and unsupervised classification approaches within ENVI software (Harris Geospatial Solutions). Supervised classification resulted in >99% accuracy for single-patient image data, but only 64% accuracy for multi-patient classification (n=9 to date), with the drop in accuracy due to increased false-positive detection rates. Hence, initial data indicate that this approach may be a viable detection approach, but that larger patient sample sizes need to be evaluated and the effects of inter-patient variability studied.« less
5. Geometric super-resolution on push-broom hyperspectral imaging for plasma optical emission spectroscopy

   https://doi.org/10.1039/C8JA00235E  

   Shi, Songyue ; Gong, Xiaoxia ; Mu, Yan ; Finch, Kevin ; Gamez, Gerardo ( January 2018 , Journal of Analytical Atomic Spectrometry)

   Push-broom hyperspectral imaging (Pb-HSI) is a powerful technique for obtaining the spectral information along with the spatial information simultaneously for various applications, from remote sensing to chemical imaging. Spatial resolution improvement is beneficial in many instances; however, typical solutions suffer from the limitation of geometric extent, lowered light throughput, or reduced field-of-view (FOV). Sub-pixel shifting (SPS) acquires higher-resolution images, compared to typical imaging approaches, from the deconvolution of low-resolution images acquired with a higher sampling rate. Furthermore, SPS is particularly suited for Pb-HSI due to its scanning nature. In this study, an SPS approach is developed and implemented on amore »Pb-HSI system for plasma optical emission spectroscopy. The preliminary results showed that a periodic deconvolution error was generated in the final SPS Pb-HSI images. The periodic error was traced back to random noise present in the raw/convoluted SPS data and its frequency displays an inverse relationship with the number of sub-pixel samples acquired. Computer modelled data allows studying the effect of varying the relative standard deviation (RSD) in the raw/convoluted SPS data on the final reconstructed SPS images and optimization of noise filtering. The optimized SPS Pb-HSI technique was used to acquire the line-of-sight integrated optical emission maps from an atmospheric pressure micro-capillary dielectric barrier discharge (μDBD). The selected plasma species of interest (He, I, N 2 , N 2 + , and O) yield some insight into the underlying mechanisms. The SPS Pb-HSI technique developed here will allow implementing geometric super-resolution in many applications, for example, it will be used for extracting radially resolved information from Abel's inversion protocols, where improved fitting is expected due to the increase in resolution/data points.« less