Publications

Automated HEp-2 mitotic cell recognition in IIF images is an important and yet scarcely explored step in the computer-aided diagnosis of autoimmune disorders. Such step is necessary to assess the goodness of the HEp-2 samples and helps the early diagnosis of the most difficult or ambiguous cases. In this work, we propose a completely unsupervised approach for HEp-2 mitotic cell recognition that overcomes the problem of mitotic/non-mitotic class imbalance due to the limited number of mitotic cells. Our technique automatically selects a limited set of candidate cells from the HEp-2 slide and then applies a clustering algorithm to identify the mitotic ones based on their texture. Finally, a second stage of clustering discriminates between positive and negative mitoses. Experiments on public IIF images demonstrate the performance of our technique compared to previous approaches.

We address the problem of automatic extraction of foreground objects from videos. The goal is to provide a method for unsupervised collection of samples which can be further used for object detection training without any human intervention. We use the well known Selective Search approach to produce an initial still-image based segmentation of the video frames. This initial set of proposals is pruned and temporally extended using optical flow and transductive learning. Specifically, we propose to use Dense Trajectories in order to robustly match and track candidate boxes over different frames. The obtained box tracks are used to collect samples for unsupervised training of track-specific detectors. Finally, the detectors are run on the videos to extract the final tubes. The combination of appearance-based static ”objectness” (Selective Search), motion information (Dense Trajectories) and transductive learning (detectors are forced to ”overfit” on the unsupervised data used for training) makes the proposed approach extremely robust. We outperform state-of-the-art systems by a large margin on common benchmarks used for tube proposal evaluation.

In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(D)J rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/.

The current state-of-the-art in video classification is based on Bag-of-Words using local visual descriptors. Most commonly these are histogram of oriented gradients (HOG), histogram of optical flow (HOF) and motion boundary histograms (MBH) descriptors. While such approach is very powerful for classification, it is also computationally expensive. This paper addresses the problem of computational efficiency. Specifically: (1) We propose several speed-ups for densely sampled HOG, HOF and MBH descriptors and release Matlab code; (2) We investigate the trade-off between accuracy and computational efficiency of descriptors in terms of frame sampling rate and type of Optical Flow method; (3) We investigate the trade-off between accuracy and computational efficiency for computing the feature vocabulary, using and comparing most of the commonly adopted vector quantization techniques: k-means, hierarchical k-means, Random Forests, Fisher Vectors and VLAD.

The interest in cultural cities is in constant growth, and so is the demand for new multimedia tools and applications that enrich their fruition. In this paper we propose an egocentric vision system to enhance tourists' cultural heritage experience. Exploiting a wearable board and a glass-mounted camera, the visitor can retrieve architectural details of the historical building he is observing and receive related multimedia contents. To obtain an effective retrieval procedure we propose a visual descriptor based on the covariance of local features. Differently than the common Bag of Words approaches our feature vector does not rely on a generated visual vocabulary, removing the dependence from a specific dataset and obtaining a reduction of the computational cost. 3D modeling is used to achieve a precise visitor's localization that allows browsing visible relevant details that the user may otherwise miss. Experimental results conducted on a publicly available cultural heritage dataset show that the proposed feature descriptor outperforms Bag of Words techniques.

Three-dimensional object recognition on range data and 3D point clouds is becoming more important nowadays. Since many real objects have a shape that could be approximated by simple primitives, robust pattern recognition can be used to search for primitive models. For example, the Hough transform is a well-known technique which is largely adopted in 2D image space. In this paper, we systematically analyze different probabilistic/randomized Hough transform algorithms for spherical object detection in dense point clouds. In particular, we study and compare four variants which are characterized by the number of points drawn together for surface computation into the parametric space and we formally discuss their models. We also propose a new method that combines the advantages of both single-point and multi-point approaches for a faster and more accurate detection. The methods are tested on synthetic and real datasets.

In this paper, we propose a general approach for automatic segmentation, color-based retrieval and classification of garments in fashion store databases, exploiting shape and color information. The garment segmentation is automatically initialized by learning geometric constraints and shape cues, then it is performed by modeling both skin and accessory colors with Gaussian Mixture Models. For color similarity retrieval and classification, to adapt the color description to the users’ perception and the company marketing directives, a color histogram with an optimized binning strategy, learned on the given color classes, is introduced and combined with HOG features for garment classification. Experiments validating the proposed strategy, and a free-to-use dataset publicly available for scientific purposes, are finally detailed.

Several papers addressed ellipse detection as a first step for several computer vision applications, but most of the proposed solutions are too slow to be applied in real time on large images or with limited hardware resources. This paper presents a novel algorithm for fast and effective ellipse detection and demonstrates its superior speed performance on large and challenging datasets. The proposed algorithm relies on an innovative selection strategy of arcs which are candidate to form ellipses and on the use of Hough transform to estimate parameters in a decomposed space. The final aim of this solution is to represent a building block for new generation of smart-phone applications which need fast and accurate ellipse detection also with limited computational resources. © 2014 Elsevier Ltd.

Metastatic spread to the liver is a frequent complication of colorectal cancer (CRC), occurring in almost half of the cases, for which personalized treatment strategies are highly desirable. To this aim, it has been proven that patient-derived mouse xenografts (PDX) of liver-metastatic CRC can be used to discover new therapeutic targets and determinants of drug resistance. To identify gene fusions in RNA-Seq data obtained from such PDX samples, we propose a novel pipeline that tackles the following issues: (i) discriminating human from murine RNA, to filter out transcripts contributed by the mouse stroma that supports the PDX; (ii) increasing sensitivity in case of suboptimal RNA-Seq coverage; (iii) prioritizing the detected chimeric transcripts by molecular features of the fusion and by functional relevance of the involved genes; (iv) providing appropriate sequence information for subsequent validation of the identified fusions. The pipeline, built on top of Chimerascan(R.Iyer, 2011) and deFuse(McPherson, 2011) aligner tools, was successfully applied to RNASeq data from 11 PDX samples. Among the 299 fusion genes identified by the aforementioned softwares, five were selected since passed all the filtering stages implemented into the proposed pipeline resulting as biologically relevant fusions. Three of them were experimentally confirmed.

The categorization of different staining patterns in HEp-2 cell slides by means of indirect immunofluorescence (IIF) is important for the differential diagnosis of autoimmune diseases. The clinical practice usually relies on the visual evaluation of the slides, which is time-consuming and subject to the specialist's experience. Thus, there is a growing demand for computer-aided solutions capable of automatically classifying HEp-2 staining patterns. In the attempt to identify the most suited strategy for this task, in this work we compare two approaches based on Support Vector Machines and Subclass Discriminant Analysis. These techniques classify the available samples, characterized through a limited set of optimal textural attributes that are identified with a feature selection scheme. Our experimental results show that both strategies have a good concordance with the diagnosis of the human specialist and show the better performance of the Subclass Discriminant Analysis (91% accuracy) compared to Support Vector Machines (87% accuracy).