Timothy J. Holmes

Blind deconvolution of quantum-limited incoherent imagery: maximum-likelihood approach.

Previous research presented by the author and others into maximum-likelihood image restoration for incoherent imagery is extended to consider problems of blind deconvolution in which the impulse response of the system is assumed to be unknown. Potential applications that motivate this study are wide-field and confocal fluorescence microscopy, although applications in astronomy and infrared imaging are foreseen as well. The methodology incorporates the iterative expectation-maximization algorithm. Although the precise impulse response is assumed to be unknown, some prior knowledge about characteristics of the impulse response is used. In preliminary simulation studies that are presented, the circular symmetry and the band-limited nature of the impulse response are used as such. These simulations demonstrate the potential utility and present limitations of these methods.

Light Microscopic Images Reconstructed by Maximum Likelihood Deconvolution

The main purpose of this chapter is to introduce the reader to the methodology of maximum likelihood (ML)-based deblurring algorithms. It is aimed at the interdisciplinary scientist, who may not be concerned about the underlying mathematical foundations of the methodology but who needs to understand the main principles behind the algorithms used. Some mathematical principles are explained, but the interested reader may find more details in the numerous publications cited in Holmes (1989, 1992), Krishnamurthi et al (1992), and Shaw and Rawlins (1991). A sample image reconstruction is presented from each of three microscope modalities, including the wide-field epifluorescence (WFF) microscope, the confocal pinhole laser-scanned epifluorescence microscope (CLSM), and the transmitted light brightfleld (BF) microscope.

Cutaneous-evoked tinnitus. I. Phenomenology, psychophysics and functional imaging.

Complete and acute unilateral deafferentation of the auditory periphery (auditory and vestibular afferents) can induce changes in the central nervous system that may result in unique forms of tinnitus. These tinnitus perceptions can be controlled (turned on and off) or modulated (changed in pitch or loudness) by performing certain overt behaviors in other sensory/motor systems. Clinical reports from our laboratory and several other independent sources indicate that static change in eye gaze, from a neutral head-referenced position, is one such behavior that can evoke, modulate and/or suppress these phantom auditory events. This report deals with a new clinical entity and a form of tinnitus that can be evoked directly by cutaneous stimulation of the upper hand and fingertip regions. In 2 adults, cutaneous-evoked tinnitus was reported following neurosurgery for space-occupying lesions at the base of the skull and posterior craniofossa, where hearing and vestibular functions were lost completely and acutely in one ear (unilateral deafferentation) and facial nerve paralysis (unilateral deefferentation) was present either immediately following neurosurgery or had occurred as a delayed-onset event. Herein, we focus on the phenomenology of this discovery, provide perceptual correlates using contemporary psychophysical methods and document in one individual cutaneous-evoked tinnitus-related neural activity using functional magnetic resonance imaging. In a companion paper, neuroanatomical and physiological interactions between auditory and somatosensory systems, possible mechanistic accounts and relevant functional neuroimaging studies are reviewed.

Automated Three-Dimensional Tracing of Neurons in Confocal and Brightfield Images

Automated three-dimensional (3-D) image analysis methods are presented for tracing of dye-injected neurons imaged by fluorescence confocal microscopy and HRP-stained neurons imaged by transmitted-light brightfield microscopy. An improved algorithm for adaptive 3-D skeletonization of noisy images enables the tracing. This algorithm operates by performing connectivity testing over large N x N x N voxel neighborhoods exploiting the sparseness of the structures of interest, robust surface detection that improves upon classical vacant neighbor schemes, improved handling of process ends or tips based on shape collapse prevention, and thickness-adaptive thinning. The confocal image stacks were skeletonized directly. The brightfield stacks required 3-D deconvolution. The results of skeletonization were analyzed to extract a graph representation. Topological and metric analyses can be carried out using this representation. A semiautomatic method was developed for reconnection of dendritic fragments that are disconnected due to insufficient dye penetration, an imaging deficiency, or skeletonization errors.

Cutaneous-evoked tinnitus. II. Review of neuroanatomical, physiological and functional imaging studies

Cutaneous-evoked tinnitus is a clinical entity that has not been reported previously in the neurootological literature. Herein, a neuroscience framework that encompasses several distinct areas of research is used to conceptualize and help understand this phenomenon. We review normal neuroanatomical and physiological interactions between auditory and somatosensory systems in mammals. Also considered are mechanistic accounts of lesion-induced changes in the CNS following deafferentation/deefferentation of peripheral sensory or motor structures that may have a relationship to this phenomenon, as well as the role of functional imaging modalities in studying various phantom perceptions.

Blind deconvolution of fluorescence micrographs by maximum-likelihood estimation

We report some recent algorithmic refinements and the resulting simulated and real image reconstructions of fluorescence micrographs by using a blind-deconvolution algorithm based on maximum likelihood estimation. Blind-deconvolution methods encompass those that do not require either calibrated or theoretical predetermination of the point-spread function (PSF). Instead, a blind deconvolution reconstructs the PSF concurrently with deblurring of the image data. Two-dimensional computer simulations give some definitive evidence of the integrity of the reconstructions of both the fluorescence concentration and the PSF. A reconstructed image and a reconstructed PSF from a two-dimensional fluorescent data set show that the blind version of the algorithm produces images that are comparable with those previously produced by a precursory nonblind version of the algorithm. They furthermore show a remarkable similarity, albeit not perfectly identical, with a PSF measurement taken for the same data set, provided by Agard and colleagues. A reconstructed image of a three-dimensional confocal data set shows a substantial axial smear removal. There is currently an existing trade-off in using the blind deconvolution in that it converges at a slightly slower rate than the nonblind approach. Future research, of course, will address this present limitation.

Blind deconvolution of 3D transmitted light brightfield micrographs.

The blind deconvolution algorithm for 3D transmitted light brightfield (TLB) microscopy, published previously ( Holmes et al.Handbook of Biological Confocal Microscopy (1995), is summarized with example images. The main emphasis of this paper is to discuss more thoroughly the importance and usefulness of this method and to provide more detailed evidence, some being quantitative, of its necessity. Samples of horseradish peroxidase (HRP)‐stained pyramidal neurones were prepared and evaluated for the ability to see fine structures clearly, including the dendrites and spines. It is demonstrated that the appearance of fine spine structure, and means of identifying spine categories, is made possible by using blind deconvolution. A comparison of images of the same sample from reflected light confocal microscopy, which is the conventional light microscopic way of viewing the 3D structure of these HRP‐stained samples, shows that the blind deconvolution method is far superior for clearly showing the structure with less distortion and better resolution of the spines. The main significance of this research is that it is now possible to obtain clear images of 3D structure by light microscopy of absorbing stains. This is important because the TLB microscope is probably the most widely used modality in the life‐science laboratory, yet, until now, there has been no reliable means for it to provide visualization of 3D structure clearly. The main importance of the blind deconvolution approach is that it obviates the need to measure the point spread function of the optical system, so that it now becomes realistic to provide a 3D light microscopic deconvolution method that can be pervasively used by microscopists.

Developments with maximum likelihood X-ray computed tomography

An approach to the maximum-likelihood estimation of attenuation coefficients in transmission tomography is presented as an extension of earlier theoretical work by K. Lange and R. Carson (J. Comput. Assist. Tomography, vol.8, p.306-16, 1984). The reconstruction algorithm is based on the expectation-maximization (EM) algorithm. Several simplifying approximations are introduced which make the maximization step of the algorithm available. Computer simulations are presented using noise-free and Poisson randomized projections. The images obtained with the EM-type method are compared to those reconstructed with the EM method of Lange and Carson and with filtered backprojection. Preliminary results show that there are potential advantages in using the maximum likelihood approaches in situations where a high-contrast object, such as bone, is embedded in low-contrast soft tissue.

Expectation-maximization restoration of band-limited, truncated point-process intensities with application in microscopy

The problem posed in this paper is that of restoring a Poisson-point-process intensity that has been degraded by a band-limiting filter followed by a truncation of the signal. The approach is to derive a maximum-likelihood estimate from the count data of the degraded point process. The expectation-maximization algorithm is used to realize this estimate, while the derivation of this algorithm is an extension to previous developments by Shepp and Vardi [ IEEE Trans. Med. ImagingMI-2, 113 ( 1982)], Snyder et al. [ IEEE Trans. Nucl. Sci.NS-28, 3575 ( 1981)], and others used for positron-emission tomography. We also extend our own work reported earlier by considering the truncated signal, which is analogous to practical situations in both two- and three-dimensional microscopy in which the image of the specimen has been truncated. Computer simulations with one-dimensional and two-dimensional signals demonstrate such a reconstruction with reasonable success. The plausibility of doing such a reconstruction is explained in that for the noiseless case the transformation characterizing the degradation is invertible.

Iterative, constrained 3-D image reconstruction of transmitted light bright-field micrographs based on maximum likelihood estimation

We present several image reconstruction algorithms for generating three‐dimensional (3‐D) renderings of bright‐field micrographs that are founded on maximum likelihood estimation (MLE) theory. The basic principle of the algorithms is in estimating the values of the optical densities of the specimen. A computer simulation and initial experimental testing of a steepest ascent version of the algorithm is presented. The computer simulation demonstrates that the MLE algorithm has an advantage over previously used inverse filtering techniques in that it partially restores the zeroed Fourier components in the well‐known missing‐cone region. We present 3‐D reconstructions from real biological data to show the potential of the algorithm in practical applications.