Region-based representations of image and video: segmentation tools for multimedia services

This paper discusses region-based representations of image and video that are useful for multimedia services such as those supported by the MPEG-4 and MPEG-7 standards. Classical tools related to the generation of the region-based representations are discussed. After a description of the main processing steps and the corresponding choices in terms of feature spaces, decision spaces, and decision algorithms, the state of the art in segmentation is reviewed. Mainly tools useful in the context of the MPEG-4 and MPEG-7 standards are discussed. The review is structured around the strategies used by the algorithms (transition based or homogeneity based) and the decision spaces (spatial, spatio-temporal, and temporal). The second part of this paper proposes a partition tree representation of images and introduces a processing strategy that involves a similarity estimation step followed by a partition creation step. This strategy tries to find a compromise between what can be done in a systematic and universal way and what has to be application dependent. It is shown in particular how a single partition tree created with an extremely simple similarity feature can support a large number of segmentation applications: spatial segmentation, motion estimation, region-based coding, semantic object extraction, and region-based retrieval.Peer ReviewedPostprint (published version

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only few methods are publicly available. We introduce AxonDeepSeg, an open-source software that performs axon and myelin segmentation of microscopic images using deep learning. AxonDeepSeg features: (i) a convolutional neural network architecture; (ii) an easy training procedure to generate new models based on manually-labelled data and (iii) two ready-to-use models trained from scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Results show high pixel-wise accuracy across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and 84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed and morphological metrics are extracted and compared against the literature. AxonDeepSeg is freely available at https://github.com/neuropoly/axondeepsegComment: 14 pages, 7 figure

Fast connected component labeling algorithm: a non voxel-based approach

This paper presents a new approach to achieve connected component labeling on both binary images and volumes by using the Extreme Vertices Model (EVM), a representation model for orthogonal polyhedra, applied to digital images and volume datasets recently. In contrast with previous techniques, this method does not use a voxel-based approach but deals with the inner sections of the object.Postprint (published version

The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis

Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field

The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis.

Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field

Innovations in the Analysis of Chandra-ACIS Observations

As members of the instrument team for the Advanced CCD Imaging Spectrometer (ACIS) on NASA's Chandra X-ray Observatory and as Chandra General Observers, we have developed a wide variety of data analysis methods that we believe are useful to the Chandra community, and have constructed a significant body of publicly-available software (the ACIS Extract package) addressing important ACIS data and science analysis tasks. This paper seeks to describe these data analysis methods for two purposes: to document the data analysis work performed in our own science projects, and to help other ACIS observers judge whether these methods may be useful in their own projects (regardless of what tools and procedures they choose to implement those methods). The ACIS data analysis recommendations we offer here address much of the workflow in a typical ACIS project, including data preparation, point source detection via both wavelet decomposition and image reconstruction, masking point sources, identification of diffuse structures, event extraction for both point and diffuse sources, merging extractions from multiple observations, nonparametric broad-band photometry, analysis of low-count spectra, and automation of these tasks. Many of the innovations presented here arise from several, often interwoven, complications that are found in many Chandra projects: large numbers of point sources (hundreds to several thousand), faint point sources, misaligned multiple observations of an astronomical field, point source crowding, and scientifically relevant diffuse emission.Comment: Accepted by the ApJ, 2010 Mar 10 (\#343576) 39 pages, 16 figure

PINGS: the PPAK IFS Nearby Galaxies Survey

We present the PPAK Integral Field Spectroscopy (IFS) Nearby Galaxies Survey: PINGS, a 2-dimensional spectroscopic mosaicking of 17 nearby disk galaxies in the optical wavelength range. This project represents the first attempt to obtain continuous coverage spectra of the whole surface of a galaxy in the nearby universe. The final data set comprises more than 50000 individual spectra, covering in total an observed area of nearly 80 arcmin^2. In this paper we describe the main astrophysical issues to be addressed by the PINGS project, we present the galaxy sample and explain the observing strategy, the data reduction process and all uncertainties involved. Additionally, we give some scientific highlights extracted from the first analysis of the PINGS sample.Comment: Accepted for publication in MNRAS, 26 pages, 14 figures (some in low resolution), 3 table

The effects of spatial resolution on Integral Field Spectrograph surveys at different redshifts. The CALIFA perspective

Over the past decade, 3D optical spectroscopy has become the preferred tool for understanding the properties of galaxies and is now increasingly used to carry out galaxy surveys. Low redshift surveys include SAURON, DiskMass, ATLAS3D, PINGS and VENGA. At redshifts above 0.7, surveys such as MASSIV, SINS, GLACE, and IMAGES have targeted the most luminous galaxies to study mainly their kinematic properties. The on-going CALIFA survey ($z\sim0.02$) is the first of a series of upcoming Integral Field Spectroscopy (IFS) surveys with large samples representative of the entire population of galaxies. Others include SAMI and MaNGA at lower redshift and the upcoming KMOS surveys at higher redshift. Given the importance of spatial scales in IFS surveys, the study of the effects of spatial resolution on the recovered parameters becomes important. We explore the capability of the CALIFA survey and a hypothetical higher redshift survey to reproduce the properties of a sample of objects observed with better spatial resolution at lower redshift. Using a sample of PINGS galaxies, we simulate observations at different redshifts. We then study the behaviour of different parameters as the spatial resolution degrades with increasing redshift.Comment: 20 pages, 16 figures. Accepted for publication in A&

Calipso: Physics-based Image and Video Editing through CAD Model Proxies

We present Calipso, an interactive method for editing images and videos in a physically-coherent manner. Our main idea is to realize physics-based manipulations by running a full physics simulation on proxy geometries given by non-rigidly aligned CAD models. Running these simulations allows us to apply new, unseen forces to move or deform selected objects, change physical parameters such as mass or elasticity, or even add entire new objects that interact with the rest of the underlying scene. In Calipso, the user makes edits directly in 3D; these edits are processed by the simulation and then transfered to the target 2D content using shape-to-image correspondences in a photo-realistic rendering process. To align the CAD models, we introduce an efficient CAD-to-image alignment procedure that jointly minimizes for rigid and non-rigid alignment while preserving the high-level structure of the input shape. Moreover, the user can choose to exploit image flow to estimate scene motion, producing coherent physical behavior with ambient dynamics. We demonstrate Calipso's physics-based editing on a wide range of examples producing myriad physical behavior while preserving geometric and visual consistency.Comment: 11 page