We propose an automated algorithm for classifying diagnostic categories of otitis media (middle ear inflammation); acute otitis media, otitis media with effusion and no effusion. Acute otitis media represents a bacterial superinfection of the middle ear fluid and otitis media with effusion a sterile effusion that tends to subside spontaneously. Diagnosing children with acute otitis media is hard, leading to overprescription of antibiotics that are beneficial only for children with acute otitis media, prompting a need for an accurate and automated algorithm. To that end, we design a feature set understood by both otoscopists and engineers based on the actual visual cues used by otoscopists; we term this otitis media vocabulary. We also design a process to combine the vocabulary terms based on the decision process used by otoscopists; we term this otitis media grammar. The algorithm achieves 84% classification accuracy, in the range or outperforming clinicians who did not receive special training, as well as state-of-the-art classifiers.

Plant development is orchestrated by transcription factors whose expression has become observable in living plants through the use of fluorescence microscopy. However, the exact quantification of expression levels is still not solved and most analysis is only performed through visual inspection. With the objective of automating the quantification of cell nuclei fluorescence we present a new approach to detect cell nuclei in 3D fluorescence confocal microscopy, based on the use of the sliding band convergence filter (SBF). The SBF filter detects cell nuclei and estimate their shape with high accuracy in each 2D image plane. For 3D detection, individual 2D shapes are joined into 3D estimates and then corrected based on the analysis of the fluorescence profile. The final nuclei detection's precision/recall are of 0.779/0.803 respectively, and the average Dice's coefficient of 0.773.

Microscopy cell image analysis is a fundamental tool for biological research. In particular, multivariate fluorescence microscopy is used to observe different aspects of cells in cultures. It is still common practice to perform analysis tasks by visual inspection of individual cells which is time consuming, exhausting and prone to induce subjective bias. This makes automatic cell image analysis essential for large scale, objective studies of cell cultures. Traditionally the task of automatic cell analysis is approached through the use of image segmentation methods for extraction of cells' locations and shapes. Image segmentation, although fundamental, is neither an easy task in computer vision nor is it robust to image quality changes. This makes image segmentation for cell detection semi-automated requiring frequent tuning of parameters. We introduce a new approach for cell detection and shape estimation in multivariate images based on the sliding band filter (SBF). This filter's design makes it adequate to detect overall convex shapes and as such it performs well for cell detection. Furthermore, the parameters involved are intuitive as they are directly related to the expected cell size. Using the SBF filter we detect cells' nucleus and cytoplasm location and shapes. Based on the assumption that each cell has the same approximate shape center in both nuclei and cytoplasm fluorescence channels, we guide cytoplasm shape estimation by the nuclear detections improving performance and reducing errors. Then we validate cell detection by gathering evidence from nuclei and cytoplasm channels. Additionally, we include overlap correction and shape regularization steps which further improve the estimated cell shapes. The approach is evaluated using two datasets with different types of data: a 20 images benchmark set of simulated cell culture images, containing 1000 simulated cells; a 16 images Drosophila melanogaster Kc167 dataset containing 1255 cells, stained for DNA and actin. Both image datasets present a difficult problem due to the high variability of cell shapes and frequent cluster overlap between cells. On the Drosophila dataset our approach achieved a precision/recall of 95%/69% and 82%/90% for nuclei and cytoplasm detection respectively and an overall accuracy of 76%.

The study of cancer cell invasion under the effect of different conditions is fundamental for the understanding of the cancer invasion mechanism and to test possible therapies for its regulation. To simulate invasion across tissue basement membrane, biologists established in vitro assays with cancer cells invading extracellular matrix components. However, analysis of such assays is manual, being timeconsuming and error-prone, which motivates an objective and automated analysis tool. Towards automating such analysis we present a methodology to detect cells in 3D matrix cell assays and correctly estimate their invasion, measured by the depth of the penetration in the gel. Detection is based on the sliding band filter, by evaluating the gradient convergence and not intensity. As such it can detect low contrast cells which otherwise would be lost. For cell depth estimation we present a focus estimator based on the convergence gradients magnitude. The final cell detections precision and recall are of 0.896 and 0.910 respectively, and the average error in the cells position estimate is of 0.41µm, 0.37µm and 3.7µm in the x, y and z directions, respectively.

In vivo observation of cells in the Arabidopsis thaliana root, by time-lapse confocal microscopy, is central to biology research. The research herein described is based on large amount of image data, which must be analyzed to determine the location and state of individual cells. Automating the process of cell tracking is an important step to create tools which will facilitate the analysis of cellspsila evolution through time. Here we introduce a confocal tracking system designed in two stages. At the image acquisition stage, we track the area under analysis based on point-to-point correspondences and motion estimation. After image acquisition, we compute cell-to-cell correspondences through time. The final result is a temporal structured information about each cell.

This paper presents a novel approach for visual scene modeling and classification, investigating the combined use of text modeling methods and local invariant features. Our work attempts to elucidate (1) whether a text-like bag-of-visterms representation (histogram of quantized local visual features) is suitable for scene (rather than object) classification, (2) whether some analogies between discrete scene representations and text documents exist, and (3) whether unsupervised, latent space models can be used both as feature extractors for the classification task and to discover patterns of visual co-occurrence. Using several data sets, we validate our approach, presenting and discussing experiments on each of these issues. We first show, with extensive experiments on binary and multi-class scene classification tasks using a 9,500-image data set, that the bag-of-visterms representation consistently outperforms classical scene classification approaches. In other data sets we show that our approach competes with or outperforms other recent, more complex, methods. We also show that Probabilistic Latent Semantic Analysis (PLSA) generates a compact scene representation, discriminative for accurate classification, and more robust than the bag-of-visterms representation when less labeled training data is available. Finally, through aspect-based image ranking experiments, we show the ability of PLSA to automatically extract visually meaningful scene patterns, making such representation useful for browsing image collections.

We present a new approach to model visual scenes in image collections, based on local invariant features and probabilistic latent space models. Our formulation provides answers to three open questions:(l) whether the invariant local features are suitable for scene (rather than object) classification; (2) whether unsupennsed latent space models can be used for feature extraction in the classification task; and (3) whether the latent space formulation can discover visual co-occurrence patterns, motivating novel approaches for image organization and segmentation. Using a 9500-image dataset, our approach is validated on each of these issues. First, we show with extensive experiments on binary and multi-class scene classification tasks, that a bag-of-visterm representation, derived from local invariant descriptors, consistently outperforms state-of-the-art approaches. Second, we show that probabilistic latent semantic analysis (PLSA) generates a compact scene representation, discriminative for accurate classification, and significantly more robust when less training data are available. Third, we have exploited the ability of PLSA to automatically extract visually meaningful aspects, to propose new algorithms for aspect-based image ranking and context-sensitive image segmentation.