Improved Image Guidance in TACE Procedures

Purpose of the work in this thesis is to improve the image guidance in TACE procedures. More specifically, we intend to develop and evaluate technology that permits dynamic roadmapping based on a 3D model of the liver vasculature

3D magnetic seed localization for augmented reality in surgery

Purpose: For tumor resection, surgeons need to localize the tumor. For this purpose, a magnetic seed can be inserted into the tumor by a radiologist and, during surgery, a magnetic detection probe informs the distance to the seed for localization. In this case, the surgeon still needs to mentally reconstruct the position of the tumor from the probe’s information. The purpose of this study is to develop and assess a method for 3D localization and visualization of the seed, facilitating the localization of the tumor. Methods: We propose a method for 3D localization of the magnetic seed by extending the magnetic detection probe with a tracking-based localization. We attach a position sensor (QR-code or optical marker) to the probe in order to track its 3D pose (respectively, using a head-mounted display with a camera or optical tracker). Following an acquisition protocol, the 3D probe tip and seed position are subsequently obtained by solving a system of equations based on the distances and the 3D probe poses. Results:The method was evaluated with an optical tracking system. An experimental setup using QR-code tracking (resp. using an optical marker) achieves an average of 1.6 mm (resp. 0.8 mm) 3D distance between the localized seed and the ground truth. Using a breast phantom setup, the average 3D distance is 4.7 mm with a QR-code and 2.1 mm with an optical marker. Conclusion: Tracking the magnetic detection probe allows 3D localization of a magnetic seed, which opens doors for augmented reality target visualization during surgery. Such an approach should enhance the perception of the localized region of interest during the intervention, especially for breast tumor resection where magnetic seeds can already be used in the protocol.</p

Continuous roadmapping in liver TACE procedures using 2D–3D catheter-based registration

PURPOSE: Fusion of pre/perioperative images and intra-operative images may add relevant information during image-guided procedures. In abdominal procedures, respiratory motion changes the position of organs, and thus accurate image guidance requires a continuous update of the spatial alignment of the (pre/perioperative) information with the organ position during the intervention. METHODS: In this paper, we propose a method to register in real time perioperative 3D rotational angiography images (3DRA) to intra-operative single-plane 2D fluoroscopic images for improved guidance in TACE interventions. The method uses the shape of 3D vessels extracted from the 3DRA and the 2D catheter shape extracted from fluoroscopy. First, the appropriate 3D vessel is selected from the complete vascular tree using a shape similarity metric. Subsequently, the catheter is registered to this vessel, and the 3DRA is visualized based on the registration results. The method is evaluated on simulated data and clinical data. RESULTS: The first selected vessel, ranked with the shape similarity metric, is used more than 39 % in the final registration and the second more than 21 %. The median of the closest corresponding points distance between 2D angiography vessels and projected 3D vessels is 4.7–5.4 mm when using the brute force optimizer and 5.2–6.6 mm when using the Powell optimizer. CONCLUSION: We present a catheter-based registration method to continuously fuse a 3DRA roadmap arterial tree onto 2D fluoroscopic images with an efficient shape similarity

Automated Detection of Cribriform Growth Patterns in Prostate Histology Images

Cribriform growth patterns in prostate carcinoma are associated with poor prognosis. We aimed to introduce a deep learning method to detect such patterns automatically. To do so, convolutional neural network was trained to detect cribriform growth patterns on 128 prostate needle biopsies. Ensemble learning taking into account other tumor growth patterns during training was used to cope with heterogeneous and limited tumor tissue occurrences. ROC and FROC analyses were applied to assess network performance regarding detection of biopsies harboring cribriform growth pattern. The ROC analysis yielded a mean area under the curve up to 0.81. FROC analysis demonstrated a sensitivity of 0.9 for regions larger than 0.0150 mm2 with on average 7.5 false positives. To benchmark method performance for intra-observer annotation variability, false positive and negative detections were re-evaluated by the pathologists. Pathologists considered 9% of the false positive regions as cribriform, and 11% as possibly cribriform; 44% of the false negative regions were not annotated as cribriform. As a final experiment, the network was also applied on a dataset of 60 biopsy regions annotated by 23 pathologists. With the cut-off reaching highest sensitivity, all images annotated as cribriform by at least 7/23 of the pathologists, were all detected as cribriform by the network and 9/60 of the images were detected as cribriform whereas no pathologist labelled them as such. In conclusion, the proposed deep learning method has high sensitivity for detecting cribriform growth patterns at the expense of a limited number of false positives. It can detect cribriform regions that are labelled as such by at least a minority of pathologists. Therefore, it could assist clinical decision making by suggesting suspicious regions.Comment: 15 pages, 6 figure

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0–5 cm) and deeper (7.5–20 cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20 cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes

Contacts et acculturations en Méditerranée occidentale

La question des contacts entre les différents peuples qui bordent les rives de la Méditerranée nord occidentale est l’un des sujets phares de la recherche archéologique de ces trente dernières années. Que l’on parle d’époque archaïque et classique ou de Protohistoire et d’âge du Fer, les échanges et les processus d’acculturation de ces peuples qui entrèrent alors en contact les uns avec les autres : Grecs, Celtes, Phéniciens, Ibères, Ligures, Étrusques, ont retenu l’attention des chercheurs travaillant sur l’expansion grecque dans ces régions, sur les trafics commerciaux, sur les échanges culturels. L’œuvre de Michel Bats (Directeur de recherche honoraire du CNRS) traverse toutes ces thématiques : la présence des Phocéens et des Étrusques dans le bassin occidental de la Méditerranée, l’acculturation et les identités ethno-culturelles, les recherches sur la céramique et ses usages dans une perspective anthropologique, l’appropriation de l’écriture par les sociétés protohistoriques. Ses collègues et amis, en organisant ce colloque et en participant à ces actes, entendent lui témoigner leur amitié et leur dette intellectuelle. Ce volume réunit des articles des meilleurs spécialistes, actuels de la question - des chercheurs de toute la Méditerranée - autour des quatre grands thèmes que nous venons d’évoquer afin tout à la fois de dresser un bilan et de définir de nouvelles perspectives. Cet ouvrage présente donc aussi bien des synthèses - sur la présence grecque en Espagne, sur l’origine de l’écriture, sur les pratiques funéraires, sur les identités culturelles et ethniques - que des découvertes récentes concernant la thématique des contacts et de l’acculturation en Méditerranée nord occidentale : l’agglomération du Premier âge du Fer de La Cougourlude (Lattes, Hérault) fouillée durant l’été 2010 ; le sanctuaire hellénistique de Cumes et les fouilles récentes de Fratte en Italie ; les ateliers de potiers de Rosas en Espagne ; les dernières découvertes d’Olbia de Provence

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

3D magnetic seed localization for augmented reality in surgery

Purpose: For tumor resection, surgeons need to localize the tumor. For this purpose, a magnetic seed can be inserted into the tumor by a radiologist and, during surgery, a magnetic detection probe informs the distance to the seed for localization. In this case, the surgeon still needs to mentally reconstruct the position of the tumor from the probe’s information. The purpose of this study is to develop and assess a method for 3D localization and visualization of the seed, facilitating the localization of the tumor. Methods: We propose a method for 3D localization of the magnetic seed by extending the magnetic detection probe with a tracking-based localization. We attach a position sensor (QR-code or optical marker) to the probe in order to track its 3D pose (respectively, using a head-mounted display with a camera or optical tracker). Following an acquisition protocol, the 3D probe tip and seed position are subsequently obtained by solving a system of equations based on the distances and the 3D probe poses. Results:The method was evaluated with an optical tracking system. An experimental setup using QR-code tracking (resp. using an optical marker) achieves an average of 1.6 mm (resp. 0.8 mm) 3D distance between the localized seed and the ground truth. Using a breast phantom setup, the average 3D distance is 4.7 mm with a QR-code and 2.1 mm with an optical marker. Conclusion: Tracking the magnetic detection probe allows 3D localization of a magnetic seed, which opens doors for augmented reality target visualization during surgery. Such an approach should enhance the perception of the localized region of interest during the intervention, especially for breast tumor resection where magnetic seeds can already be used in the protocol.</p