The Time-SIFT method : detecting 3-D changes from archival photogrammetric analysis with almost exclusively image information

Archival aerial imagery is a source of worldwide very high resolution data for documenting paste 3-D changes. However, external information is required so that accurate 3-D models can be computed from archival aerial imagery. In this research, we propose and test a new method, termed Time-SIFT (Scale Invariant Feature Transform), which allows for computing coherent multi-temporal Digital Elevation Models (DEMs) with almost exclusively image information. This method is based on the invariance properties of the SIFT-like methods which are at the root of the Structure from Motion (SfM) algorithms. On a test site of 170 km2, we applied SfM algorithms to a unique image block with all the images of four different dates covering forty years. We compared this method to more classical methods based on the use of affordable additional data such as ground control points collected in recent orthophotos. We did extensive tests to determine which processing choices were most impacting on the final result. With these tests, we aimed at evaluating the potential of the proposed Time-SIFT method for the detection and mapping of 3-D changes. Our study showed that the Time-SIFT method was the prime criteria that allowed for computing informative DEMs of difference with almost exclusively image information and limited photogrammetric expertise and human intervention. Due to the fact that the proposed Time-SIFT method can be automatically applied with exclusively image information, our results pave the way to a systematic processing of the archival aerial imagery on very large spatio-temporal windows, and should hence greatly help the unlocking of archival aerial imagery for the documenting of past 3-D changes

The Time-SIFT method : detecting 3-D changes from archival photogrammetric analysis with almost exclusively image information

Archival aerial imagery is a source of worldwide very high resolution data for documenting paste 3-D changes. However, external information is required so that accurate 3-D models can be computed from archival aerial imagery. In this research, we propose and test a new method, termed Time-SIFT (Scale Invariant Feature Transform), which allows for computing coherent multi-temporal Digital Elevation Models (DEMs) with almost exclusively image information. This method is based on the invariance properties of the SIFT-like methods which are at the root of the Structure from Motion (SfM) algorithms. On a test site of 170 km2, we applied SfM algorithms to a unique image block with all the images of four different dates covering forty years. We compared this method to more classical methods based on the use of affordable additional data such as ground control points collected in recent orthophotos. We did extensive tests to determine which processing choices were most impacting on the final result. With these tests, we aimed at evaluating the potential of the proposed Time-SIFT method for the detection and mapping of 3-D changes. Our study showed that the Time-SIFT method was the prime criteria that allowed for computing informative DEMs of difference with almost exclusively image information and limited photogrammetric expertise and human intervention. Due to the fact that the proposed Time-SIFT method can be automatically applied with exclusively image information, our results pave the way to a systematic processing of the archival aerial imagery on very large spatio-temporal windows, and should hence greatly help the unlocking of archival aerial imagery for the documenting of past 3-D changes

In vitro characterization of the ability of Yersinia enterocolitica BT4 to colonize pigs and stainless steel surfaces

Yersiniosis is, after campylobacteriosis and salmonellosis, the third most frequently reported zoonosis in Europe. Humans become infected with Y. enterocolitica through the consumption of undercooked pork and raw food having been in contact with contaminated surfaces. Pigs, the main reservoir for human pathogenic strains, do not develop clinical signs. In France and worldwide, biotype 4 (BT4) is the biotype the most frequently isolated from both pigs and clinical yersiniosis. In this study, a collection of 26 pathogenic BT4 strains isolated from pig tonsils was used to investigate their ability to adhere and invade intestinal pig cells (IPEC-J2) and to adhere to abiotic surfaces (stainless steel coupons) using two in vitro tests. Regression analysis was performed between data sets obtained from IPECJ2 cells assays versus stainless steel assays. All BT4 strains were able to adhere and invade IPEC-J2 cells. However, the results showed heterogeneity between strains with respect to their ability to adhere to IPECJ2 cells, with a percentage of adhesion varying from 9% to more than 90%. The BT4 population displayed a more homogeneous ability to invade IPECJ2 cells with percentages varying from 10% to 26%. The BT4 strains displayed a great ability to adhere to the stainless steel surface, percentage of adhesion varying from 0.3% to 4.2%. No correlation was observed between IPEC-J2 cell adhesion, cell invasion and adhesion to the stainless steel surface (R² \u3c 0.02). In conclusion, these results reflect the ability of the different BT4 strains to colonize the intestinal tract of pigs and to contaminate the stainless steel surfaces of the food processing environment

Adoption and effects of software engineering best practices in machine learning

Algorithms and the Foundations of Software technolog

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Géométrie 3D des lits de rivière par stéréophotogrammétrie à travers l'eau

soutenue en 2008 et publiée en 2009 du fait des délais de double publication dûs à la double tutelleEnvironmental questions are of a growing concern for public opinion as well as for national and international policies. A striking example is the one of the rivers : focusing multiple issues from which highly strategic ones (energy, irrigation), usage of their waters lead to a particularly fine compromise. In most commons approaches, state and function of this hydrosystem is described by measuring physical variable or by establishing relationships between variables of interest and physical parameters (hydraulical models, hydrobiological models). The aim of this thesis is hence to propose an answer to the problem of measuring river geometry by remote sensing. We first detail the specific context of river systems and establish a state-of-the-art of remote sensing methods, which shows a lack for light stereo-based methods. Then, we propose a full image acquisition and processing method allowing estimation of river immersed topography. This works involves the use of cheap and light hardware which makes it possible to be used flexibly. Classical stereorestitution methods have been adapted to the specific context of through-water photogrammetry. Finally, refraction correction methods integrating a priori knowledge (hydraulic and spatial consistency) have been developed. This method has been applied on a shallow, gravel-bed river and the accuracy and precision of immersed relief estimation is found to be compatible with requirements of hydrobiological models. We hence developed, tested, and validated an original method for estimating river 3D geometry which can supplement existing ones.Les considérations environnementales occupent une place croissante dans l'opinion publique ainsi que dans les politiques nationales et internationales. Le cas de la rivière en est un exemple particulièrement frappant : au centre d'enjeux multiples et pour certains hautement stratégiques (énergie, irrigation), elle est le théâtre d'un conflit d'usages donnant lieu à l'établissement de compromis particulièrement fins pour la gestion de la ressource. Dans les approches les plus courantes, la description de l'état et du fonctionnement d'un hydrosystème tel que celui de la rivière est effectuée par la mesure de variables physiques ou la mise en relation des variables d'intérêt avec les paramètres physiques quantifiables caractérisant le milieu (modèles hydrauliques, modèles hydrobiologiques). L'objectif de ce travail est donc de proposer une réponse à la question de la mesure de la géométrie de la rivière par télédétection. On s'attache tout d'abord à décrire le contexte particulier de la rivière mentionné plus haut puis à effectuer un état de l'art faisant ressortir une lacune pour la restitution du relief immergé par stéréo à travers l'eau avec des moyens légers. On propose ensuite une méthode complète d'acquisition d'images et de traitements permettant d'estimer le relief immergé de rivière. Le travail effectué repose sur la mise en oeuvre de moyens technologiques légers permettant une grande flexibilité pour l'acquisition des données. On se base sur les méthodes de stéréorestitution du relief, pour lesquelles on propose une adaptation au contexte spécifique de la photogrammétrie à travers l'eau. Enfin, on met en place des méthodes de correction des mesures brutes intégrant des contraintes a priori (cohérence hydraulique ; cohérence spatiale) pour la correction de l'effet de réfraction. L'application de la méthode développée en conditions opérationnelles sur une rivière peu profonde à fond de galets montre que la mesure du relief immergé par stéréophotogrammétrie est possible, et permet une représentation de la topographie du lit d'une qualité compatible avec les modèles hydrobiologiques (modèles habitat-poisson). On a ainsi développé, testé, validé et determiné les conditions d'application d'une méthode de mesure de la géométrie de la rivière par télédétection originale et complémentaire des technologies existantes

Time-SIFT module for Agisoft Metashape software

This module is designed to make it easier to use the Time-SIFT method on diachronic data sets from low-altitude (drone, kite, boom) or high-altitude (satellite, aircraft) airborne campaigns. PROCEDURE: The data must be separated in a folder called EPOCHS, with one campaign per folder (subfolders authorised) which brings together all the images from the same measurement date and the same sensor (RGB, IRC for example). Once loaded into Metashape (Run Script tab), a new menu bar appears summarising the various stages of Time-SIFT. For more information on the Time-SIFT method, please refer to : D. Feurer, F. Vinatier, Joining multi-epoch archival aerial images in a single SfM block allows 3-D change detection with almost exclusively image information, ISPRS Journal of Photogrammetry and Remote Sensing, Volume 146, 2018, Pages 495-506, ISSN 0924-2716, https://doi.org/10.1016/j.isprsjprs.2018.10.016. (http://www.sciencedirect.com/science/article/pii/S0924271618302946). The module presented is compatible with Agisoft Metashape (version 1.5 or higher

Time-SIFT module for Agisoft Metashape software

This module is designed to make it easier to use the Time-SIFT method on diachronic data sets from low-altitude (drone, kite, boom) or high-altitude (satellite, aircraft) airborne campaigns. PROCEDURE: The data must be separated in a folder called EPOCHS, with one campaign per folder (subfolders authorised) which brings together all the images from the same measurement date and the same sensor (RGB, IRC for example). Once loaded into Metashape (Run Script tab), a new menu bar appears summarising the various stages of Time-SIFT. For more information on the Time-SIFT method, please refer to : D. Feurer, F. Vinatier, Joining multi-epoch archival aerial images in a single SfM block allows 3-D change detection with almost exclusively image information, ISPRS Journal of Photogrammetry and Remote Sensing, Volume 146, 2018, Pages 495-506, ISSN 0924-2716, https://doi.org/10.1016/j.isprsjprs.2018.10.016. (http://www.sciencedirect.com/science/article/pii/S0924271618302946). The module presented is compatible with Agisoft Metashape (version 1.5 or higher