Digital pathology represents one of the major evolutions in modern medicine. Pathological examinations constitute the gold standard in many medical protocols, and also play a critical and legal role in the diagnosis process. In the conventional cancer diagnosis, pathologists analyze biopsies to make diagnostic and prognostic assessments, mainly based on the cell morphology and architecture distribution. Recently, computerized methods have been rapidly evolving in the area of digital pathology, with growing applications related to nuclei detection, segmentation, and classification. In cancer research, these approaches have played, and will continue to play a key (often bottleneck) role in minimizing human intervention, consolidating pertinent second opinions, and providing traceable clinical information. Pathological studies have been conducted for numerous cancer detection and grading applications, including brain, breast, cervix, lung, and prostate cancer grading. Our study presents, discusses, and extracts the major trends from an exhaustive overview of various nuclei detection, segmentation, feature computation, and classification techniques used in histopathology imagery, specifically in hematoxylin-eosin and immunohistochemical staining protocols. This study also enables us to measure the challenges that remain, in order to reach robust analysis of whole slide images, essential high content imaging with diagnostic biomarkers and prognosis support in digital pathology.

The computation of good image descriptors is key to the instance retrieval problem and has been the object of much recent interest from the multimedia research community. With deep learning becoming the dominant approach in computer vision, the use of representations extracted from Convolutional Neural Nets (CNNs) is quickly gaining ground on Fisher Vectors (FVs) as favoured state-of-the-art global image descriptors for image instance retrieval. While the good performance of CNNs for image classification are unambiguously recognised, which of the two has the upper hand in the image retrieval context is not entirely clear yet.In this work, we propose a comprehensive study that systematically evaluates FVs and CNNs for image retrieval. The first part compares the performances of FVs and CNNs on multiple publicly available data sets. We investigate a number of details specific to each method. For FVs, we compare sparse descriptors based on interest point detectors with dense single-scale and multi-scale variants. For CNNs, we focus on understanding the impact of depth, architecture and training data on retrieval results. Our study shows that no descriptor is systematically better than the other and that performance gains can usually be obtained by using both types together. The second part of the study focuses on the impact of geometrical transformations such as rotations and scale changes. FVs based on interest point detectors are intrinsically resilient to such transformations while CNNs do not have a built-in mechanism to ensure such invariance. We show that performance of CNNs can quickly degrade in presence of rotations while they are far less affected by changes in scale. We then propose a number of ways to incorporate the required invariances in the CNN pipeline.Overall, our work is intended as a reference guide offering practically useful and simply implementable guidelines to anyone looking for state-of-the-art global descriptors best suited to their specific image instance retrieval problem. * V. Chandrasekhar, J. Lin and O. Morère contributed equally to this work.

Histopathological examination is a powerful method for the prognosis of critical diseases. But, despite significant advances in high-speed and high-resolution scanning devices or in virtual exploration capabilities, the clinical analysis of Whole Slide Images (WSI) largely remains the work of human experts. We propose an innovative platform in which multi-scale computer vision algorithms perform fast analysis of a histopathological WSI. It relies on specific high and generic low resolution image analysis algorithms embedded in a multi-scale framework to rapidly identify the high power fields of interest used by the pathologist to assess a global grading. GPU technologies as well speed up the global time-efficiency of the system. In a sense, sparse coding and sampling is the keystone of our approach. In terms of validation, we are designing a computer-aided breast biopsy analysis application based on histopathology images and designed in collaboration with a pathology department. The current ground truth slides correspond to about 36,000 high magnification (40X) high power fields. The time processing to achieve automatic WSI analysis is on a par with the pathologist's performance (about ten minutes a WSI), which constitutes by itself a major contribution of the proposed methodology.