Whole slide image registration for the study of tumor heterogeneity

Consecutive thin sections of tissue samples make it possible to study local variation in e.g. protein expression and tumor heterogeneity by staining for a new protein in each section. In order to compare and correlate patterns of different proteins, the images have to be registered with high accuracy. The problem we want to solve is registration of gigapixel whole slide images (WSI). This presents 3 challenges: (i) Images are very large; (ii) Thin sections result in artifacts that make global affine registration prone to very large local errors; (iii) Local affine registration is required to preserve correct tissue morphology (local size, shape and texture). In our approach we compare WSI registration based on automatic and manual feature selection on either the full image or natural sub-regions (as opposed to square tiles). Working with natural sub-regions, in an interactive tool makes it possible to exclude regions containing scientifically irrelevant information. We also present a new way to visualize local registration quality by a Registration Confidence Map (RCM). With this method, intra-tumor heterogeneity and charateristics of the tumor microenvironment can be observed and quantified.Comment: MICCAI2018 - Computational Pathology and Ophthalmic Medical Image Analysis - COMPA

A Novel Optical/digital Processing System for Pattern Recognition

This paper describes two processing algorithms that can be implemented optically: the Radon transform and angular correlation. These two algorithms can be combined in one optical processor to extract all the basic geometric and amplitude features from objects embedded in video imagery. We show that the internal amplitude structure of objects is recovered by the Radon transform, which is a well-known result, but, in addition, we show simulation results that calculate angular correlation, a simple but unique algorithm that extracts object boundaries from suitably threshold images from which length, width, area, aspect ratio, and orientation can be derived. In addition to circumventing scale and rotation distortions, these simulations indicate that the features derived from the angular correlation algorithm are relatively insensitive to tracking shifts and image noise. Some optical architecture concepts, including one based on micro-optical lenslet arrays, have been developed to implement these algorithms. Simulation test and evaluation using simple synthetic object data will be described, including results of a study that uses object boundaries (derivable from angular correlation) to classify simple objects using a neural network

A Computer Aided Detection system for mammographic images implemented on a GRID infrastructure

The use of an automatic system for the analysis of mammographic images has proven to be very useful to radiologists in the investigation of breast cancer, especially in the framework of mammographic-screening programs. A breast neoplasia is often marked by the presence of microcalcification clusters and massive lesions in the mammogram: hence the need for tools able to recognize such lesions at an early stage. In the framework of the GPCALMA (GRID Platform for Computer Assisted Library for MAmmography) project, the co-working of italian physicists and radiologists built a large distributed database of digitized mammographic images (about 5500 images corresponding to 1650 patients) and developed a CAD (Computer Aided Detection) system, able to make an automatic search of massive lesions and microcalcification clusters. The CAD is implemented in the GPCALMA integrated station, which can be used also for digitization, as archive and to perform statistical analyses. Some GPCALMA integrated stations have already been implemented and are currently on clinical trial in some italian hospitals. The emerging GRID technology can been used to connect the GPCALMA integrated stations operating in different medical centers. The GRID approach will support an effective tele- and co-working between radiologists, cancer specialists and epidemiology experts by allowing remote image analysis and interactive online diagnosis.Comment: 5 pages, 5 figures, to appear in the Proceedings of the 13th IEEE-NPSS Real Time Conference 2003, Montreal, Canada, May 18-23 200

Multilayer Complex Network Descriptors for Color-Texture Characterization

A new method based on complex networks is proposed for color-texture analysis. The proposal consists on modeling the image as a multilayer complex network where each color channel is a layer, and each pixel (in each color channel) is represented as a network vertex. The network dynamic evolution is accessed using a set of modeling parameters (radii and thresholds), and new characterization techniques are introduced to capt information regarding within and between color channel spatial interaction. An automatic and adaptive approach for threshold selection is also proposed. We conduct classification experiments on 5 well-known datasets: Vistex, Usptex, Outex13, CURet and MBT. Results among various literature methods are compared, including deep convolutional neural networks with pre-trained architectures. The proposed method presented the highest overall performance over the 5 datasets, with 97.7 of mean accuracy against 97.0 achieved by the ResNet convolutional neural network with 50 layers.Comment: 20 pages, 7 figures and 4 table

Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance