One-Vote Veto: Semi-Supervised Learning for Low-Shot Glaucoma Diagnosis.

Convolutional neural networks (CNNs) are a promising technique for automated glaucoma diagnosis from images of the fundus, and these images are routinely acquired as part of an ophthalmic exam. Nevertheless, CNNs typically require a large amount of well-labeled data for training, which may not be available in many biomedical image classification applications, especially when diseases are rare and where labeling by experts is costly. This article makes two contributions to address this issue: 1) It extends the conventional Siamese network and introduces a training method for low-shot learning when labeled data are limited and imbalanced, and 2) it introduces a novel semi-supervised learning strategy that uses additional unlabeled training data to achieve greater accuracy. Our proposed multi-task Siamese network (MTSN) can employ any backbone CNN, and we demonstrate with four backbone CNNs that its accuracy with limited training data approaches the accuracy of backbone CNNs trained with a dataset that is 50 times larger. We also introduce One-Vote Veto (OVV) self-training, a semi-supervised learning strategy that is designed specifically for MTSNs. By taking both self-predictions and contrastive predictions of the unlabeled training data into account, OVV self-training provides additional pseudo labels for fine-tuning a pre-trained MTSN. Using a large (imbalanced) dataset with 66,715 fundus photographs acquired over 15 years, extensive experimental results demonstrate the effectiveness of low-shot learning with MTSN and semi-supervised learning with OVV self-training. Three additional, smaller clinical datasets of fundus images acquired under different conditions (cameras, instruments, locations, populations) are used to demonstrate the generalizability of the proposed methods.

Photometric Stereo in a Scattering Medium.

Photometric stereo is widely used for 3D reconstruction. However, its use in scattering media such as water, biological tissue and fog has been limited until now, because of forward scattered light from both the source and object, as well as light scattered back from the medium (backscatter). Here we make three contributions to address the key modes of light propagation, under the common single scattering assumption for dilute media. First, we show through extensive simulations that single-scattered light from a source can be approximated by a point light source with a single direction. This alleviates the need to handle light source blur explicitly. Next, we model the blur due to scattering of light from the object. We measure the object point-spread function and introduce a simple deconvolution method. Finally, we show how imaging fluorescence emission where available, eliminates the backscatter component and increases the signal-to-noise ratio. Experimental results in a water tank, with different concentrations of scattering media added, show that deconvolution produces higher-quality 3D reconstructions than previous techniques, and that when combined with fluorescence, can produce results similar to that in clear water even for highly turbid media.

Detecting glaucoma progression from localized rates of retinal changes in parametric and nonparametric statistical framework with type I error control.

PURPOSE: We evaluated three new pixelwise rates of retinal height changes (PixR) strategies to reduce false-positive errors while detecting glaucomatous progression. METHODS: Diagnostic accuracy of nonparametric PixR-NP cluster test (CT), PixR-NP single threshold test (STT), and parametric PixR-P STT were compared to statistic image mapping (SIM) using the Heidelberg Retina Tomograph. We included 36 progressing eyes, 210 nonprogressing patient eyes, and 21 longitudinal normal eyes from the University of California, San Diego (UCSD) Diagnostic Innovations in Glaucoma Study. Multiple comparison problem due to simultaneous testing of retinal locations was addressed in PixR-NP CT by controlling family-wise error rate (FWER) and in STT methods by Lehmann-Romano's k-FWER. For STT methods, progression was defined as an observed progression rate (ratio of number of pixels with significant rate of decrease; i.e., red-pixels, to disk size) > 2.5%. Progression criterion for CT and SIM methods was presence of one or more significant (P < 1%) red-pixel clusters within disk. RESULTS: Specificity in normals: CT = 81% (90%), PixR-NP STT = 90%, PixR-P STT = 90%, SIM = 90%. Sensitivity in progressing eyes: CT = 86% (86%), PixR-NP STT = 75%, PixR-P STT = 81%, SIM = 39%. Specificity in nonprogressing patient eyes: CT = 49% (55%), PixR-NP STT = 56%, PixR-P STT = 50%, SIM = 79%. Progression detected by PixR in nonprogressing patient eyes was associated with early signs of visual field change that did not yet meet our definition of glaucomatous progression. CONCLUSIONS: The PixR provided higher sensitivity in progressing eyes and similar specificity in normals than SIM, suggesting that PixR strategies can improve our ability to detect glaucomatous progression. Longer follow-up is necessary to determine whether nonprogressing eyes identified as progressing by these methods will develop glaucomatous progression. (ClinicalTrials.gov number, NCT00221897).

Localizing parts of faces using a consensus of exemplars.

We present a novel approach to localizing parts in images of human faces. The approach combines the output of local detectors with a nonparametric set of global models for the part locations based on over 1,000 hand-labeled exemplar images. By assuming that the global models generate the part locations as hidden variables, we derive a Bayesian objective function. This function is optimized using a consensus of models for these hidden variables. The resulting localizer handles a much wider range of expression, pose, lighting, and occlusion than prior ones. We show excellent performance on real-world face datasets such as Labeled Faces in the Wild (LFW) and a new Labeled Face Parts in the Wild (LFPW) and show that our localizer achieves state-of-the-art performance on the less challenging BioID dataset.

Localized glaucomatous change detection within the proper orthogonal decomposition framework.

PURPOSE: To detect localized glaucomatous structural changes using proper orthogonal decomposition (POD) framework with false-positive control that minimizes confirmatory follow-ups, and to compare the results to topographic change analysis (TCA). METHODS: We included 167 participants (246 eyes) with ≥4 Heidelberg Retina Tomograph (HRT)-II exams from the Diagnostic Innovations in Glaucoma Study; 36 eyes progressed by stereo-photographs or visual fields. All other patient eyes (n = 210) were non-progressing. Specificities were evaluated using 21 normal eyes. Significance of change at each HRT superpixel between each follow-up and its nearest baseline (obtained using POD) was estimated using mixed-effects ANOVA. Locations with significant reduction in retinal height (red pixels) were determined using Bonferroni, Lehmann-Romano k-family-wise error rate (k-FWER), and Benjamini-Hochberg false discovery rate (FDR) type I error control procedures. Observed positive rate (OPR) in each follow-up was calculated as a ratio of number of red pixels within disk to disk size. Progression by POD was defined as one or more follow-ups with OPR greater than the anticipated false-positive rate. TCA was evaluated using the recently proposed liberal, moderate, and conservative progression criteria. RESULTS: Sensitivity in progressors, specificity in normals, and specificity in non-progressors, respectively, were POD-Bonferroni = 100%, 0%, and 0%; POD k-FWER = 78%, 86%, and 43%; POD-FDR = 78%, 86%, and 43%; POD k-FWER with retinal height change ≥50 µm = 61%, 95%, and 60%; TCA-liberal = 86%, 62%, and 21%; TCA-moderate = 53%, 100%, and 70%; and TCA-conservative = 17%, 100%, and 84%. CONCLUSIONS: With a stronger control of type I errors, k-FWER in POD framework minimized confirmatory follow-ups while providing diagnostic accuracy comparable to TCA. Thus, POD with k-FWER shows promise to reduce the number of confirmatory follow-ups required for clinical care and studies evaluating new glaucoma treatments. (ClinicalTrials.gov number, NCT00221897.).

Robust structure and motion from outlines of smooth curved surfaces.

This paper addresses the problem of estimating the motion of a camera as it observes the outline (or apparent contour) of a solid bounded by a smooth surface in successive image frames. In this context, the surface points that project onto the outline of an object depend on the viewpoint and the only true correspondences between two outlines of the same object are the projections of frontier points where the viewing rays intersect in the tangent plane of the surface. In turn, the epipolar geometry is easily estimated once these correspondences have been identified. Given the apparent contours detected in an image sequence, a robust procedure based on RANSAC and a voting strategy is proposed to simultaneously estimate the camera configurations and a consistent set of frontier point projections by enforcing the redundancy of multiview epipolar geometry. The proposed approach is, in principle, applicable to orthographic, weak-perspective, and affine projection models. Experiments with nine real image sequences are presented for the orthographic projection case, including a quantitative comparison with the ground-truth data for the six data sets for which the latter information is available. Sample visual hulls have been computed from all image sequences for qualitative evaluation.

ACE: automated CTF estimation.

We present a completely automated algorithm for estimating the parameters of the contrast transfer function (CTF) of a transmission electron microscope. The primary contribution of this paper is the determination of the astigmatism prior to the estimation of the CTF parameters. The CTF parameter estimation is then reduced to a 1D problem using elliptical averaging. We have also implemented an automated method to calculate lower and upper cutoff frequencies to eliminate regions of the power spectrum which perturb the estimation of the CTF parameters. The algorithm comprises three optimization subproblems, two of which are proven to be convex. Results of the CTF estimation method are presented for images of carbon support films as well as for images of single particles embedded in ice and suspended over holes in the support film. A MATLAB implementation of the algorithm, called ACE, is freely available.

Acquiring linear subspaces for face recognition under variable lighting.

Previous work has demonstrated that the image variation of many objects (human faces in particular) under variable lighting can be effectively modeled by low-dimensional linear spaces, even when there are multiple light sources and shadowing. Basis images spanning this space are usually obtained in one of three ways: A large set of images of the object under different lighting conditions is acquired, and principal component analysis (PCA) is used to estimate a subspace. Alternatively, synthetic images are rendered from a 3D model (perhaps reconstructed from images) under point sources and, again, PCA is used to estimate a subspace. Finally, images rendered from a 3D model under diffuse lighting based on spherical harmonics are directly used as basis images. In this paper, we show how to arrange physical lighting so that the acquired images of each object can be directly used as the basis vectors of a low-dimensional linear space and that this subspace is close to those acquired by the other methods. More specifically, there exist configurations of k point light source directions, with k typically ranging from 5 to 9, such that, by taking k images of an object under these single sources, the resulting subspace is an effective representation for recognition under a wide range of lighting conditions. Since the subspace is generated directly from real images, potentially complex and/or brittle intermediate steps such as 3D reconstruction can be completely avoided; nor is it necessary to acquire large numbers of training images or to physically construct complex diffuse (harmonic) light fields. We validate the use of subspaces constructed in this fashion within the context of face recognition.

Automatic particle selection: results of a comparative study.

Manual selection of single particles in images acquired using cryo-electron microscopy (cryoEM) will become a significant bottleneck when datasets of a hundred thousand or even a million particles are required for structure determination at near atomic resolution. Algorithm development of fully automated particle selection is thus an important research objective in the cryoEM field. A number of research groups are making promising new advances in this area. Evaluation of algorithms using a standard set of cryoEM images is an essential aspect of this algorithm development. With this goal in mind, a particle selection "bakeoff" was included in the program of the Multidisciplinary Workshop on Automatic Particle Selection for cryoEM. Twelve groups participated by submitting the results of testing their own algorithms on a common dataset. The dataset consisted of 82 defocus pairs of high-magnification micrographs, containing keyhole limpet hemocyanin particles, acquired using cryoEM. The results of the bakeoff are presented in this paper along with a summary of the discussion from the workshop. It was agreed that establishing benchmark particles and using bakeoffs to evaluate algorithms are useful in promoting algorithm development for fully automated particle selection, and that the infrastructure set up to support the bakeoff should be maintained and extended to include larger and more varied datasets, and more criteria for future evaluations.