Combined hyperspectral imaging of macroscopic and microscopic samples for tissue optical and structural properties evaluation

Stergar, Jošt (author), Milanič, Matija (mentor)

The goal of the work presented in this thesis was to compare spectroscopic properties of tissues on the macro scale with their underlying microscopic structural properties. Three main objectives that dictate the organization of this thesis were identified. (I) To develop and characterize two hyperspectral imaging systems that can im- age on two different length scales (macro- to mezo-scopic and microscopic imaging systems). (II) To develop and characterize tissue phantoms that can be used for system characterization and as a testing ground for physical models. (III) To use both systems in a clinical study and search for relationships between microscopic tissue structure and their optical properties. Basics of light-tissue interaction are presented in the first chapter. A brief overview of scattering and absorption interaction of light with the tissue is pre- sented through the radiative transfer equation (RTE). A special emphasis is given to the treatment of light scattering according to Mie theory. Since solving RTE is a difficult task, few algorithms that extract optical properties from measured spectra are presented. In the second chapter, development and characterization of the two hyperspectral systems are presented. Mezzo- to macro-scopic imaging system based on imaging spectrograph is presented first, followed by a hyperspectral microscopy system build around a laboratory microscope and a custom developed monochromator. In the third chapter, research regarding tissue phantoms is presented. After presenting the recipe for phantoms, phantom components and their structure are analyzed in depth. Using the knowledge about the phantom properties, both spec- troscopic and structural, effects of their microscopic structure are explored using Mie scattering. Theoretic and macroscopic imaging results are compared to hyper- spectral microscopy. In the fourth chapter, hyperspectral imaging is used in a pre-clinical study of peritonitis in mouse models. Abdominal walls are imaged using the macroscopic system and tissue properties (blood volume fraction, oxygenation, scattering) are evaluated. Based on these properties, biomarkers that show statistical significance in separating diseased and healthy subjects are identified. All the biomarkers are verified and compared to histology. From macroscopic images, blood vasculature structure is extracted and another set of biomarkers is obtained. Based on hyper- spectral microscopic, Fourier-space biomarkers that characterize tissue structure are devised and correlated to macroscopic optical properties. To conclude, two hyperspectral systems were developed and successfully used in a pre-clinical environment. Tissue phantoms were developed and effects of the scat- tering component properties on measurable reflectance spectra were explored. In a pre-clinical study, biomarkers were obtained from both hyperspectral modalities and results compared between both length scales.

• Language: English
• Keywords: Spectroscopy, hyperspectral imaging, microscopy, biomedical optics, light scattering, Monte Carlo transport, tissue phantoms, peritonitis, biomarkers
• Work type: Doctoral dissertation
• Typology: 2.08 - Doctoral Dissertation
• Organization: FMF - Faculty of Mathematics and Physics
• Year: 2021
• PID: 20.500.12556/RUL-131664
• COBISS.SI-ID: 79143939
• Publication date in RUL: 01.10.2021

Secondary language

• Language: Slovenian
• Title: Združeno hiperspektralno slikanje makroskopskih in mikroskopskih vzorcev za ocenjevanje optičnih in strukturnih lastnosti tkiv

Abstract

Cilj doktorskega dela je primerjava spektroskopskih lastnosti tkiv na makroskopski skali z njihovo mikroskopsko strukturo. V sklopu dela smo identificirali tri poglavitne cilje. (I) Razviti in karakterizirati dva hiperspektralna sistema, ki skupaj pokrijeta makro- in mezo-skopsko področje slikanja ter mikroskopijo. (II) Razviti in karak- terizirati tkivne fantome, ki bodo služili za karakterizacijo sistemov in kot podlaga za preverjanje fizikalnih modelov. (III) Uporabiti oba sistema v klinični študiji in iskati povezave med spektroskopskimi lastnostmi tkiv in njihovo strukturo. V prvem poglavju predstavimo osnovno teorijo interakcije med svetlobo in tkivi. Predstavimo sipanje svetlobe in njeno absorbcijo, pri čemer izhajamo iz enačbe sevalnega prenosa. Poseben poudarek posvetimo obravnavi sipanja v skladu z Mie- vo teorijo sipanja. Ker je izračun interakcije med svetlobo in tkivom računsko trd oreh, predstavimo nekaj algoritmov, ki lahko iz spektroskopskih podatkov izluščijo lastnosti tkiva. V drugem poglavju predstavimo razvoj in karakterizacijo obeh hiperspektralnih sistemov. Razvoj mezo- do makro-skopskega sistema je osnovan na uporabi slikov- nega spektrografa, medtem ko je razvoj hiperspektralne mikroskopije osnovan na integraciji laboratorijskega mikroskopa z lastno razvitim monokromatorjem. V tretjem poglavju predstavimo izdelavo in karakterizacijo tkivnih fantomov. Po obravnavi recepture za pripravo fantomov se lotimo natančnega preučevanja optičnih in strukturnih lastnosti, tako celotnih fantomov, kot njihovih osnovnih gradnikov. Z uporabo spoznanj o lastnostih fantomov analiziramo spektroskopske podatke, pri čemer uporabimo Mie-vo teorijo sipanja za opis sipalnih lastnosti. Makroskopske in teoretične rezultate primerjamo z rezultati mikroskopske hiperspektralne analize. V četrtem poglavju uporabimo hiperspektralno slikanje v pred-klinični študiji peritonitisa na mišjih modelih. Trebušne stene slikamo z makroskopskim sistemom in na podlagi hiperspektralnih podatkov izluščimo lastnosti tkiv (prostorski delež krvi, oksigenacija, sipalne lastnosti). Iz njih izračunamo značilke, ki lahko statistično značilno določijo, ali je preiskovan subjekt obolel ali zdrav. Vse značilke primerjamo s histološkimi preiskavami. Iz makroskopskih slik izluščimo tudi strukturo žilja iz katere izračunamo dodaten set značilk. Na podlagi hiperspektralne mikroskopije iz- računamo reprezentacijo slike v Fourier-ovem prostoru, ki jo uporabimo za določanje nove značilke strukture vzorcev, ki korelira z makroskopskimi optičnimi lastnostmi. V sklopu dela sta bila razvita in karakterizirana dva hiperspektralna sistema, ki smo ju uspešno uporabili v pred-klinični študiji. Razvili smo trdne tkivne fantome in njihove optične lastnosti z uporabo Mie-ve teorije sipanja povezali z mikroskopskimi strukturnimi lastnostmi. V pred-klinični študiji peritonitisa smo določili značilke na obeh velikostnih skalah in jih v iskanju povezav primerjali.

• Keywords: Spektroskopija, hiperspektralno slikanje, mikroskopija, biomedi- cinska optika, sipanje svetlobe, Monte Carlo transport, tkivni fantomi, peritonitis, značilke