# Colin SheppardUniversity of Wollongong | UOW · School of Chemistry

Colin Sheppard

MA, PhD, DSc

## About

725

Publications

267,546

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20,506

Citations

Introduction

Optics, microscopy, imaging

Additional affiliations

February 2016 - March 2016

January 2016 - January 2016

August 2015 - August 2015

Education

April 1984 - May 1986

September 1968 - May 1973

September 1965 - June 1968

## Publications

Publications (725)

Many books on polarization give tables of Mueller matrices. The coherency matrix has been found useful for interpretation of the Mueller matrix. Here we give a table of Mueller matrices M, coherency matrices C, and coherency matrix factors F for different polarization components and systems. F is not given for some complicated nondeterministic case...

Super-resolution microscopy is routinely used for fixed and thin samples, while its feasibility for imaging live and thick samples is still limited. In the case of stimulated emission depletion (STED) microscopy, the high-intensity illumination required to achieve effective sub-diffraction resolution can introduce photo-damage, thus reducing the co...

Depolarization has been found to be a useful contrast mechanism in biological and medical imaging. The Mueller matrix can be used to describe polarization effects of a depolarizing material. An historical review of relevant polarization algebra, measures of depolarization, and purity spaces is presented, and the connections with the eigenvalues of...

Measures of purity for partially polarized fields in three dimensions, and in particular, the separation into circularly and linearly polarized contributions, are reexamined, and a new degree of total linear polarization introduced. Explicit expressions for the characteristic decomposition in terms of coherency matrix elements are presented, includ...

Optical methods of super-resolution microscopy, such as confocal microscopy, structured illumination, nonlinear microscopy, and image scanning microscopy are reviewed. These methods avoid strong invasive interaction with a sample, allowing the observation of delicate biological samples. The meaning of resolution and the basic principles and differe...

Mueller matrix (MM) microscopy is an advanced imaging technique providing a full characterization of the optical polarization fingerprint of a sample. The Lu-Chipman (LC) decomposition, a method based on the modeling of elementary polarimetric arrangements and matrix inversions, is the gold standard to extract each polarimetric component separately...

Asian Journal of Physics
Vol. 30, No 7 (2021) 965-978
Available on: www.asianjournalofphysics.com
Electromagnetic focusing of linearly polarized, circularly polarized and radially polarized Gaussian beams by an aplanatic lens of high numerical aperture is considered. It is found that, unlike the paraxial case, for an objective with a high numerica...

Structured illumination microscopy and image scanning microscopy are two microscopical tech- niques, rapidly increasing in practical application, that can result in improvement in transverse spatial resolution, and/or improvement in axial imaging performance. The history and principles of these techniques are reviewed, and the imaging properties of...

In image scanning microscopy, the pinhole of a confocal microscope is replaced by a detector array. The point spread function for each detector element can be interpreted as the probability density function of the signal, the peak giving the most likely origin. This thus allows a form of maximum likelihood restoration, and compensation of aberratio...

Many of the most important resolution improvements in polarization-based techniques are based on the reduction of scattering effects. However, the determination of the coherency matrix elements from the experimental Mueller matrix can take advantage of scattering measurements to obtain additional information on the structural organization of a samp...

In confocal microscopy, the pinhole throws away valuable signal, limiting how small the pinhole can be, and therefore the attainable spatial resolution. In image scanning microscopy (ISM), most of the available light is detected by a detector array, and reassigned in the image to its most likely origin in the sample. The point spread function (PSF)...

If the pinhole in a confocal microscope is replaced by a detector array, each detector pixel simultaneously gives a confocal image. The resultant four-dimensional data set can be reconstructed to give improved resolution and signal to noise ratio.

Surface topography measuring interference microscopy is a three-dimensional (3D) imaging technique that provides quantitative analysis of industrial and biomedical specimens. Many different instrument modalities and configurations exist but they all share the same theoretical foundation. In this paper, we discuss a unified theoretical framework for...

Many of the most important resolution improvements in optical microscopy techniques are based on the reduction of scattering effects. The main benefit of polarimetry‐based imaging to this end is the discrimination between scattering phenomena originating from complex systems and the experimental noise. The determination of the coherency matrix elem...

Diffraction calculations are widely used in applications that require numerical simulation of optical wave propagation. Different numerical diffraction calculation methods have their own transform and sampling properties. In this study, we provide a unified analysis where five popular fast diffraction calculation methods are analyzed from the persp...

Image scanning microscopy is a technique of confocal microscopy in which the confocal pinhole is replaced by a detector array, and the image is reconstructed most straightforwardly by pixel reassignment. In the fluorescence mode, the detector array collects most of the fluorescent light, so the signal-to-noise ratio is much improved compared with c...

Calculation of the eigenvectors of two- and three-dimensional coherency matrices, and the four-dimensional coherency matrix associated with a Mueller matrix, is considered, especially for algebraic cases, in the light of recently published algorithms. The preferred approach is based on a combination of an evaluation of the charac- teristic polynomi...

Two-photon excitation (2PE) laser scanning microscopy is the imaging modality of choice when one desires to work with thick biological samples. However, its spatial resolution is poor, below confocal laser scanning microscopy. Here, we propose a straightforward implementation of 2PE image scanning microscopy (2PE-ISM) that, by leveraging our recent...

The historical development of multiphoton microscopy is described, starting with a review of two-photon absorption, and including two- and three-photon fluorescence microscopies, and second- and third-harmonic generation microscopies. The effects of pulse length on signal strength and breakdown are considered. Different contrast mechanisms, includi...

The Sinclair and Kennaugh matrices are widely used in the remote sensing discipline for signals detected in the backward direction. The connections between the Jones matrix and the Sinclair matrix, and
between the Mueller matrix and the Kennaugh matrix are explored. Different operations on the Jones matrix and their corresponding effects on the Mue...

Image scanning microscopy is a technique based on confocal microscopy, in which the confocal pinhole is replaced by a detector array, and the resulting image is reconstructed, usually by the process of pixel reassignment. The detector array collects most of the fluorescent light, so the signal-to-noise ratio is much improved compared with confocal...

Microscopy using a scanning approach is reviewed, with numerous references to previous work, as at 1987, before the confocal laser scanning microscope was widely available commercially. The advantages of microscope imaging using a scanning technique are described. The principles of confocal microscopy are introduced. Use of Bessel beam illumination...

We report a dual-contrast method of simultaneously measuring and visualizing the volumetric structural information in live biological samples in three-dimensional (3D) space. By introducing a direct way of deriving the 3D scattering potential of the object from the synthesized angular spectra, we obtain the quantitative subcellular morphology in re...

An important approach to interpretation of the Mueller matrix is based on the eigenvalues of the coherency matrix, given by the roots of a quartic characteristic equation. For the case of backscattering, one eigenvalue is zero from reciprocity arguments, and the characteristic equation reduces to a cubic. These two approaches (quartic and cubic) to...

Two-photon excitation (2PE) microscopy is the imaging modality of choice, when one desires to work with thick biological samples, possibly in-vivo. However, the resolution in two-photon microscopy is poor, below confocal microscopy, and the lack of an optical pinhole becomes apparent in complex samples as reduced quality of optical sectioning. Here...

Image scanning microscopy (ISM) can improve the effective spatial resolution of confocal microscopy to its theoretical limit. However, current implementations are not robust or versatile, and are incompatible with fluorescence lifetime imaging (FLIM). We describe an implementation of ISM based on a single-photon detector array that enables super-re...

The elements of the coherency matrix give the strength of the components of a Mueller matrix in the coherency basis. The Z-matrix (called the polarization-coupling matrix or state-generating matrix) represents a partial sum of the coherency expansion. For transmission through a deterministic medium, the coherency elements can be used directly as ge...

Explicit relationships between the defocused partially coherent cross-coefficient and phase space representations in the image plane are derived. Measurement of a phase space representation in the image plane in principle allows the complex image to be extracted. Implications for phase retrieval using the weak object transfer function or the transp...

Two photon microscopy (2PM) is one of the most widely used tools for in vivo deep tissue imaging. However, the spatial resolution and penetration depth are still limited due to the strong scattering background. Here we demonstrate a two‐photon focal modulation microscopy. By utilizing the modulation and demodulation techniques, background rejection...

For applications in optical systems it is often necessary to represent a circular aperture in a pixellated form. An objective parameter is introduced that is a measure of how well an approximate circle can be generated from a small array of square pixels. Both filled circles (disks) and rings are considered. Arrays with a width given by an even num...

Explicit expressions are presented for different phase-space representations (mutual intensity, Wigner distribution function, and ambiguity function) of the partially coherent image wave field in a microscope system. These are separated into system- and object-dependent parts. The partially coherent image in phase space can be described in terms of...

Image scanning microscopy (ISM) improves the spatial resolution of conventional confocal laser-scanning microscopy (CLSM), but current implementations reduce versatility and restrict its combination with fluorescence spectroscopy techniques, such as fluorescence lifetime. Here, we describe a natural design of ISM based on a fast single-photon detec...

We show that the coherency matrix associated with a general depolarizing Mueller matrix can be factorized into the product of a matrix, the coherency matrix factor, and its conjugate transpose. The coherency matrix factor contains all the information in the Mueller matrix, and directly shows useful properties in an illustrative fashion. Propagation...

For both fundamental study of biological processes and early diagnosis of diseases, information about nanoscale changes in tissue and cell structure is crucial. Nowadays almost all currently known nanoscopy methods rely upon the contrast created by fluorescent stains attached to the object or molecule of interest. This causes limitations due to the...

Two‐photon microscopy is the tool of choice for fluorescence imaging of deep tissues with high resolution, but can be limited in three‐dimensional acquisition speed and penetration depth. In this work, these issues are addressed by using an acoustic optofluidic lens capable of ultrafast beam shaping on a pixel basis. Driving the lens with different...

We demonstrate a fast, switchable achromatic phase shifter operating on the geometric phase principle, using ferroelectric liquid crystal technology for rapid 3D biological imaging in a full field optical coherence tomography.

The effect of combining the image scanning microscopy (ISM) technique with two-photon fluorescence microscopy is analyzed. The effective spatial frequency cutoff can be doubled, as compared with conventional two-photon fluorescence microscopy, and the magnitude of the optical transfer function near the cutoff of conventional two-photon microscopy i...

Three-dimensional imaging at high-spatiotemporal resolutions and over large penetration depths is key for unmasking the dynamics and structural organization of complex biological systems. However, the need to axially shift the focus, with consequent limitations in imaging speed, and signal degradation at large depths due to scattering effects, make...

Many books on polarization give tables of Mueller matrices. The coherency matrix has been found useful for interpretetion of the Mueller matrix. Here we give a table of Mueller matrices M, coherency matrices C, and coherency matrix factors F for different polarization components and systems. F is not given for some complicated nondeterministic case...

An error in our paper [J. Opt. Soc. Am. A33, 741 (2016)JOAOD60740-323210.1364/JOSAA.33.000741] is pointed out.

The use of an array of detectors can help overcoming the traditional limitation of confocal microscopy: the compromise between signal and theoretical resolution. Each element independently records a view of the sample and the final image can be reconstructed by pixel reassignment or by inverse filtering (e.g. deconvolution). In this work, we used a...

Here we report a method for visualization of volumetric structural information of live biological samples with no exogenous contrast agents. The process is made possible through a technique that involves generation, synthesis and analysis of three-dimensional (3D) Fourier components of light diffracted by the sample. This leads to the direct recove...

Image scanning microscopy (ISM) is a variation of confocal microscopy in which the confocal pinhole is replaced by a detector array. 1,2 The simplest way to reconstruct the image is using the principle of pixel reassignment, where the signal from each detector element is reassigned to an effective imaging point, different from the illumination poin...

Diffraction of light limits the spatial resolution of far-field conventional fluorescence to roughly 200 nm. Confocal laser scanning microscopy allows for a resolution enhancement of √2, while super resolution techniques such as stimulated emission depletion (STED) microscopy reach theoretically unlimited resolution. However, the effective resoluti...

The extraction of the elementary polarization properties of a uniform medium from a deterministic Mueller matrix has been considered by several researchers. The relationship between a parameterization of the deterministic Mueller matrix that we described recently and the elementary polarization properties for a uniform medium is investigated. The e...

Many papers have claimed the attainment of super-resolution, i.e. resolution beyond that achieved classically, by measurement of the profile of a feature in the image. We argue that measurement of the contrast of the image of a dark bar on a bright background does not give a measure of resolution, but of detection sensitivity. The width of a bar th...

A deterministic Mueller matrix (Mueller–Jones matrix) contains seven independent parameters. By writing the so-called coherence vector in parametric form, the Mueller matrix can also be written in parametric form, where the matrix elements automatically satisfy the known relationships between each other. Three of these parameters are also related t...

The optical transfer function (OTF) is widely used to compare the performance of different optical systems. Conventionally, the OTF is normalized to unity for zero spatial frequency, but in some cases it is better to consider the unnormalized OTF, which gives the absolute value of the image signal. Examples are in confocal microscopy and image scan...

If light is focused or collected with a high numerical aperture lens, as may occur in imaging and optical encryption applications, polarization should be considered in three dimensions (3D). The matrix algebra of polarization behavior in 3D is discussed. It is useful to convert between the Mueller matrix and two different Hermitian matrices, repres...

An arbitrary Mueller matrix can be decomposed into a sum of up to four deterministic Mueller–Jones matrices, with strengths given by the eigenvalues of an associated Hermitian matrix. A geometrical representation of the eigenvalues in terms of the matrix invariants, using a barycentric (quaternary) plot, is presented. Different polarization purity...

This Notebook generates the matrices for 3D polarization in the paper ”Three-dimensional polarization algebra”, by Colin J.R.Sheppard, Marco Castello and Alberto Diaspro.

Concentration of light is limited by a fundamental physical principle, which ensures that étendue, the product of area and solid angle, can never decrease in an optical system. In microscopy, many superresolving methods, which can overcome the classical resolution limit, have recently emerged. We propose, and demonstrate experimentally, that it is...

We propose and demonstrate a novel subtraction microscopy algorithm, exploiting fluorescence
emission difference or switching laser mode and their derivatives for image enhancement. The key
novelty of the proposed approach lies in the weighted subtraction coefficient, adjusted pixel-by-pixel
with respect to the intensity distributions of initial...

This Notebook generates the transformation matrices for 2D polarization in the paper ”Expressions for parallel decomposition of the Müller matrix”, by Colin J.R.Sheppard, Marco Castello and Alberto Diaspro, J. Opt. Soc. Am. A (2016). The transformation matrices convert between the Müller matrix M, the Müller matrix in the standard (Cartesian) basis...