Optical phase contrast imaging of human retinal cells by changing the tissue refractive index

Purpose : Based on oblique partially coherent illumination of transparent samples, we developed a simple custom Optical Phase Imaging (OPI) microscope providing a label-free, semi-quantitative phase contrast imaging. The aim of this study was to explore this ex-vivo modality for retinal imaging and correlate it with standard clinical images and fluorescence microscopy. Methods : Multimodal macular imaging was performed on the flat-mounted retina of an eye presenting an epiretinal membrane with cystoid macular edema, enucleated for a peripheral melanoma. After glial fibrillary acidic protein (GFAP) - aquaporin (AQP)-4 – collagen (Col)-IV co-immuno-labeling and nuclei staining, the retina was cleared by index matching in a medium of refractive index (RI) 1.46 to decrease scattering for high-resolution deep-tissue ex vivo imaging. We performed a comparison of the clinical examinations obtained by Optical Coherence Tomography-Angiography and fluorescein angiography before enucleation, with the images obtained with confocal microscopy and OPI microscopy. Ex-vivo imaging of the retina mounted in a medium with a lower RI (1.40), close to the mean RI of Muller glial cell (MGC), was then repeated to better view the latter cells. Results : The retinal vessels were used as landmarks for correlating all imaging modalities. OPI microscopy allowed for different contrast imaging depending on the RI of the mounting medium. With the high RI medium (1.46), deep contrast imaging of nuclei and intraretinal cysts was obtained. The solution with a RI of 1.4 provided an improvement in the contrast of the retinal structures, from the inner layer (AQP4-positive MGC, epi-retinal membrane, nerve fibers surrounded by GFAP-positive astrocytes) to the photoreceptor segments. No AQP4 labeling was observed inside the cyst. AQP4-positive, GFAP-negative cells were visualized on the ColIV-labeled epi-retinal membrane, demonstrating that the membrane is made of retinal Muller glial cells. Conclusions : This morphological correlative imaging study demonstrated OPI on numerous cellular structures of a human retina by tuning the tissue RI. This label-free in-depth imaging modality offers a new research tool to study the cellular origin of retinal diseases.

Shot noise, refractive index tomography and aberrations estimation in digital holographic microscopy

Florian Charrière

The present thesis develops some specific aspects of digital holographic microscopy (DHM), namely the effect of shot noise on the phase image accuracy, the use of DHM in micro-tomography and in aberrations evaluation of a microscope objective (MO). DHM is an imaging technique, allowing to measure quantitatively the wavefront transmitted through or reflected by a specimen seen through a MO. A hologram, composed by the interference of the wave coming from the object with a reference wave, is recorded with a camera and then numerically processed to extract both amplitude and phase information. Thanks to its interferometric nature, DHM provides phase images, corresponding to a nanometric accuracy along the optical axis of the microscope, revealing extremely detailed information about the specimen surface in reflection configuration or its internal structure in transmission configuration. DHM has proven its efficiency on numerous applications fields going from cells biology to MEMS-MOEMS devices. In a first part, the use of DHM as metrological tools in the field of micro-optics testing is demonstrated. DHM measurement principle is compared with techniques employed in Twyman-Green, Mach-Zehnder, and white-light interferometers. Refractive microlenses are characterized with reflection DHM and the data are confronted with data obtained with standard interferometers. Specific features of DHM such as digital focussing, measurement of shape differences with respect to a perfect model, surface roughness measurements, and evaluation of a lens optical performance are discussed. The capability to image nonspherical lenses without modification of the optical setup, a key advantage of DHM against conventional interferometers, is demonstrated on a cylindrical mircrolens and a square lenses array. A second part treats the effect of shot noise in DHM. DHM is a single shot imaging technique, and its short hologram acquisition time (down to microseconds) offers a reduced sensitivity to vibrations. Real time observation is achievable, thanks to present performances of personal computers and digital camera. Fast dynamic imaging at low-light level involves few photons, requiring proper settings of the system (integration time and gain of the camera; power of the light source) to minimize the influence of shot noise on the hologram when the highest phase accuracy is aimed. With simulated and experimental data, a systematic analysis of the fundamental shot noise influence on phase accuracy in DHM is presented. Different configurations of the reference wave and the object wave intensities are also discussed, illustrating the detection limit and the coherent amplification of the object wave. In a third part, DHM has for the first time been applied to perform optical diffraction tomography of biological specimens: a pollen grain and living amoebas. Quantitative 2D phase images are acquired for regularly-spaced angular positions of the specimen covering a total angle of π, allowing to build 3D quantitative refractive index distributions by an inverse Radon transform. A precision of 0.01 for the refractive index estimation and a spatial resolution in the micron range are shown. For the amoebas, morphometric measurements are extracted from the tomographic reconstructions. The fourth part presents a DHM technique to determine the integral refractive index and morphology of cells. As the refractive index is a function of the cell dry mass, depending on the intra-cellular concentration and the organelles arrangement, the optical phase shift induced by the specimen on the transmitted wave can be regarded as a powerful endogenous contrast agent. The dual-wavelengths technique proposed in this thesis exploits the dispersion of the perfusion medium to obtain a set of equations, allowing decoupling the contributions of the refractive index and the cellular thickness to the total phase signal. The two wavelengths are chosen in the vicinity of the absorption peak of a dye added to the perfusion medium, where the absorption is accompanied by a strong variation of the refractive index as a function of the wavelength. The technique is demonstrated on yeasts. The last part exposes two methods capable of measuring the complex 3D amplitude point spread function (APSF) of an optical imaging system. The first approach consists in evaluating in amplitude and phase the image of a single emitting point, a 60 nm diameter tip of a Scanning Near Field Optical Microscopy (SNOM) fiber, with an original digital holographic setup. A single hologram giving access to the transverse APSF, the 3D APSF is obtained by performing an axial scan of the SNOM fiber. The method is demonstrated on an 20x 0.4 NA MO. For a 100x 1.3 NA MO, measurements performed with the new setup are compared with the prediction of an analytical aberrations model. The second method allows measuring the APSF of a MO with a single holographic acquisition of its pupil wavefront. The aberration function is extracted from this pupil measurement and then inserted in a scalar model of diffraction allowing to calculate the distribution of the complex wavefront propagated around the focal point. The results are compared with a direct measurement of the APSF achieved with the first proposed approach.

EPFL2007

Cellular dynamics explored with digital holographic microscopy

Benjamin Rappaz

Obtaining high resolution 3D quantitative images is critical for elucidating the relationship between cell dynamics and physiological or pathological processes. However the feasibility of such cellular dynamic studies is limited by the resolution of the 3D images, the required acquisition time and the degree of invasiveness of the currently available imaging techniques as well as their limitation to provide quantitative information. Digital Holographic Microscopy (DHM) is an optical imaging technique developed to meet most of these requirements to accurately explore cell dynamics. In short, DHM allows to quantitatively measure the wavefront transmitted through a specimen and magnified by a microscope objective. A hologram, which contains the whole information of the transmitted wavefront, is formed by the interference of the wave coming from the object with a reference wave, and recorded with a camera. The hologram reconstruction process, based on the electromagnetic wave propagation theory, permits to numerically process the hologram in order to extract both amplitude and phase information. This process allows to obtain an exact replica of the wave diffracted or transmitted by the observed specimen. Thanks to its interferometric nature, DHM yields phase images with a nanometric sensitivity along the optical axis of the microscope, revealing extremely detailed minute information about the cell morphology and internal structure, as well as cellular micromovements in the nanometer range. So far, DHM has proven its efficiency on numerous fields in material sciences. This thesis presents some technical developments achieved with DHM and extends the applications of this technique to life sciences in general and cellular structure and dynamics in particular. The quantitative phase images generated by DHM represent an endogenous contrast signal which contains dual information about both the cell morphology and the refractive index (RI), which is essentially related to the intracellular (protein) content. The first part of this thesis (chapter 2) presents two different approaches to separately extract these two contributions and obtain an independent measurement of both the cell morphology and RI, thus providing an interpretation of the phase signal which is more readily exploitable and more relevant for cell biologists. The RI is a function of the dry mass, thus the phase signal variation in time can be related to biomass production and provides a direct interpretation of the phase signal. In section 3.1 this relation is exploited to study the dry mass production during the cell cycle of fission yeast. The decoupling procedure presented in section 2.1 allows to measure the thickness and RI of cells. In section 3.2, we use this decoupling procedure to measure the Mean Corpuscular Volume (MCV) and RI of red blood cells. These measurements are also compared to those obtained by other techniques. In addition, as far as red blood cell are concerned, the RI can be related to the Mean Corpuscular Hemoglobin Content (MCHC). The MCV, RI and MCHC are important clinical parameters that can be non-invasively and instantly measured with DHM. The membrane of red cells presents a flickering at a nanometric scale which can reflect their metabolic state, related to ATP content. Due to the technical difficulty to measure this flickering, it has been difficult to investigate the origin of these fluctuations. DHM, thanks to its nanometric and microsecond sensitivity, allows to monitor these Cell Membrane Fluctuations (CMF). In section 3.3 DHM is used to measure CMF of healthy and metabolically-impaired red blood cells. The last section of this thesis (section 3.4) assesses how DHM can quantitatively monitor minute cell morphological and optical changes induced by agonist-mediated activation of specific membrane receptors. This is illustrated by tracking the phase signal variations during excitotoxic activation of neurons by the neurotransmitter glutamate.

EPFL2008

Optical microscopy for imaging through scattering media

Xin Yang

Optical microscopy has been widely used in the life sciences and biological research for several decades. It possesses many advantages over x-ray radiography, computed tomography, ultrasound imaging and magnetic resonance imaging, in terms of being low cost, high resolution, harmless and capable of multiple contrast mechanism, etc. However, the weakness of optical microscopy is the inability to perform deep tissue imaging. Owing to the short wavelength of optical waves, it experiences much more scattering than longer waves in inhomogeneous materials such as biological tissues. Scattering scrambles the wavefront and limits the penetration depth of optical microscopy to only hundreds of microns. We explore in this thesis, novel optical approaches to image through scattering media. There are two main categories of the state of art techniques: imaging with ballistic photons, which requires separation of ballistic photons from the sneak or multiple scattered ones; and imaging with scattered photons, which relies on manipulation of the scattered photons according to the specific scattering properties. We primarily focus on the second category in this thesis. Taking advantage of the reversibility of light, phase conjugation has a long history in aberration compensation. A deterministic wave is incident on a scattering medium and results in a random scattered field. If we record the full information of the scattered field (amplitude and phase) and generate a phase conjugated replica of it, the phase conjugated wave can follow the same path and reconstruct the original deterministic wave after passing back through the scattering medium. In this work, phase conjugation is achieved using digital method, called digital phase conjugation. The scattered field is recorded through digital holography, and a spatial light modulator is applied to construct the phase conjugated wave. Second harmonic radiation imaging probes are used as the original light source, rendering the generation of a focus behind the scattering medium. The memory effect, which indicates the correlation between speckles with different incident angles, is exploited to move the focus around and obtain three-dimensional scanning microscopy behind scattering medium. Speckle scanning microscopy is the second method demonstrated in this thesis for imaging through turbid media. In contrast to digital phase conjugation, which requires access from both sides of the scatterers to measure the scattered field, in speckle scanning microscopy, excitation and collection can be achieved from the same side. The specific scattering events are not taken into account, instead, the statistic property of the scatterers plays a major role. This technique makes full use of two facts: 1. The statistically averaged autocorrelation of speckle fields approaches a delta function; 2. When a speckle pattern scans across a fluorescence object, the collected fluorescence intensity is proportional to the convolution of the speckle field and the object. Linking these two facts with delicate calculation, we can eventually minimize the influence of the speckle, and reconstruct two-dimensional images of objects behind turbid medium. Encouraged by the success of two-dimensional speckle scanning microscopy, we investigate more advanced possibilities by simulation, including three-dimensional speckle scanning and reference based speckle scanning techniques. [...]

EPFL2014