Automated region of interest retrieval and classification using spectral analysis

Efficient use of whole slide imaging in pathology needs automated region of interest (ROI) retrieval and classification, through the use of image analysis and data sorting tools. One possible method for data sorting uses Spectral Analysis for Dimensionality Reduction. We present some interesting results in the field of histopathology and cytohematology

Towards a computer aided diagnosis system dedicated to virtual microscopy based on stereology sampling and diffusion maps

An original strategy is presented, combining stereological sampling methods based on test grids and data reduction methods based on diffusion maps, in order to build a knowledge image database with no bias introduced by a subjective choice of exploration areas. The practical application of the exposed methodology concerns virtual slides of breast tumors

Indexation automatique d'images numériques ( application aux images histopathologiques du cancer du sein et hématologiques de leucémies lympoïdes chroniques)

Dans un contexte où les économies de santé sont de plus en plus drastiques, où les spécialistes sont de moins en moins nombreux, alors que, grâce aux campagnes de dépistage, le nombre de cas à analyser est en constante augmentation, le travail des pathologistes devient de plus en plus difficile. En outre, les lésions précoces découvertes lors du dépistage sont souvent mal connues et/ou de très petite taille ce qui rend délicat le diagnostic histopathologique. Un problème similaire est rencontré en hématologie avec la pratique de plus en plus répandue des examens sanguins systématiques et la difficulté d'identification de cellules suspectes et d'évènements rares au sein d'un frottis sanguin. Il est par conséquent très important d apprécier dans quelle mesure la microscopie numérique et les outils d analyse automatique des images pourront dans l avenir aider ces spécialistes dans l accomplissement de leur tâche quotidienne. Le présent travail de thèse, mené dans cette optique, se fonde sur l'utilisation de lames virtuelles des préparations histologiques et cytologiques, acquises à basse ou à haute résolution. Il consiste à développer et à tester une série d'outils d'aide au diagnostic basés sur l indexation automatique des images. Cependant, l utilisation des lames virtuelles implique la manipulation d'une masse de données très importante, qui constitue un frein pour traiter, analyser et même visualiser les images de manière classique. Nous avons donc testé tout d abord la pertinence d'une analyse globale des images, puis d'une analyse locale de celles-ci, accompagnées d une réduction de dimension des données par diverses méthodes, dont l'analyse spectrale.Nous avons choisi de mettre en œuvre cette approche à propos de deux localisations dont l incidence constitue un problème de santé publique, les tumeurs mammaires et la leucémie lymphoïde chronique.In a context where health economies are increasingly curbed, where specialists are fewer and fewer, while, thanks to screening campaigns, the number of cases to analyze is constantly growing, the task of pathologists is more and more difficult. In addition, early lesions discovered during the screening are often poorly known and / or of very small size which makes the histopathological diagnosis difficult. A similar problem is encountered in hematology with the increasingly widespread practice of systematic blood tests and the difficulty of identifying suspicious cells and rare events in blood smears. It is therefore very important to assess how digital microscopy and automatic processing techniques will be able to help the specialists in their daily practice in the future. This present work is based on the use of virtual slides of histological and cytological preparations, acquired at low or high resolution. It aims at developing and testing several tools for computer assisted diagnosis based on automatic indexing of images. However, the use of virtual slides involves the manipulation of very large data and it is difficult to process, analyze or visualize these images in a classical way. The first objective of the study was to assess the relevance of a global analysis of images, then the contribution of their local analysis, with a dimensional reduction of data by various methods including spectral analysis. These methods have been applied to virtual slides of breast tumors and chronic lymphoid leukemia, two tumor locations whose incidence is a public health problem.CAEN-BU Sciences et STAPS (141182103) / SudocSudocFranceF

Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGS T , Able To Grow under Extreme Hydrostatic Pressures

We report the genome sequence of Thermococcus superprofundus strain CDGST, a new piezophilic and hyperthermophilic member of the order Thermococcales isolated from the world’s deepest hydrothermal vents, at the Mid-Cayman Rise. The genome is consistent with a heterotrophic, anaerobic, and piezophilic lifestyle

Precision Phenotyping of Nectar-Related Traits Using X-ray Micro Computed Tomography

Flower morphologies shape the accessibility to nectar and pollen, two major traits that determine plant–pollinator interactions and reproductive success. Melon is an economically important crop whose reproduction is completely pollinator-dependent and, as such, is a valuable model for studying crop-ecological functions. High-resolution imaging techniques, such as micro-computed tomography (micro-CT), have recently become popular for phenotyping in plant science. Here, we implemented micro-CT to study floral morphology and honey bees in the context of nectar-related traits without a sample preparation to improve the phenotyping precision and quality. We generated high-quality 3D models of melon male and female flowers and compared the geometric measures. Micro-CT allowed for a relatively easy and rapid generation of 3D volumetric data on nectar, nectary, flower, and honey bee body sizes. A comparative analysis of male and female flowers showed a strong positive correlation between the nectar gland volume and the volume of the secreted nectar. We modeled the nectar level inside the flower and reconstructed a 3D model of the accessibility by honey bees. By combining data on flower morphology, the honey bee size and nectar volume, this protocol can be used to assess the flower accessibility to pollinators in a high resolution, and can readily carry out genotypes comparative analysis to identify nectar-pollination-related traits

Visualization of each patch and its neighbourhood in order to exhibit the most similar patches

<p><b>Copyright information:</b></p><p>Taken from "Automated region of interest retrieval and classification using spectral analysis"</p><p>http://www.diagnosticpathology.org/content/3/S1/S17</p><p>Diagnostic Pathology 2008;3(Suppl 1):S17-S17.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2500116.</p><p></p

Result of breast VS segmentation by spectral analysis: (a) visualization of data sorting allowing segmentation of (b) the original image, (c) result of the segmentation

<p><b>Copyright information:</b></p><p>Taken from "Automated region of interest retrieval and classification using spectral analysis"</p><p>http://www.diagnosticpathology.org/content/3/S1/S17</p><p>Diagnostic Pathology 2008;3(Suppl 1):S17-S17.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2500116.</p><p></p