The Experts below are selected from a list of 27372 Experts worldwide ranked by ideXlab platform
Timothy H Lucas - One of the best experts on this subject based on the ideXlab platform.
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an open source automated platform for three dimensional visualization of subdural electrodes using ct mri coregistration
Epilepsia, 2014Co-Authors: Allan Azarion, Allison Pearce, Veena T Krish, Joost B Wagenaar, Weixuan Chen, Yuanjie Zheng, Hongzhi Wang, Timothy H LucasAbstract:Summary Objective Visualizing implanted subdural electrodes in three-dimensional (3D) space can greatly aid in planning, executing, and validating resection in epilepsy surgery. Coregistration software is available, but cost, complexity, insufficient accuracy, or validation limit adoption. We present a fully automated open-source Application, based on a novel method using postimplant computerized tomography (CT) and postimplant magnetic resonance (MR) images, for accurately visualizing intracranial electrodes in 3D space. Methods CT-MR rigid brain coregistration, MR nonrigid registration, and prior-based segmentation were carried out on seven patients. Postimplant CT, postimplant MR, and an external labeled atlas were then aligned in the same space. The coregistration algorithm was validated by manually marking identical anatomic landmarks on the postimplant CT and postimplant MR images. Following coregistration, distances between the center of the landmark masks on the postimplant MR and the coregistered CT images were calculated for all subjects. Algorithms were implemented in open-source software and translated into a “drag and drop” Desktop Application for Apple Mac OS X. Results Despite postoperative brain deformation, the method was able to automatically align intrasubject multimodal images and segment cortical subregions, so that all electrodes could be visualized on the parcellated brain. Manual marking of anatomic landmarks validated the coregistration algorithm with a mean misalignment distance of 2.87 mm (standard deviation 0.58 mm)between the landmarks. Software was easily used by operators without prior image processing experience. Significance We demonstrate an easy to use, novel platform for accurately visualizing subdural electrodes in 3D space on a parcellated brain. We rigorously validated this method using quantitative measures. The method is unique because it involves no preprocessing, is fully automated, and freely available worldwide. A Desktop Application, as well as the source code, are both available for download on the International Epilepsy Electrophysiology Portal (https://www.ieeg.org) for use and interactive refinement.
L. Valenti - One of the best experts on this subject based on the ideXlab platform.
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myVCF: a Desktop Application for high-throughput mutations data management
'Oxford University Press (OUP)', 2017Co-Authors: A. Pietrelli, L. ValentiAbstract:Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants. We developed myVCF, a standalone, easy-to-use Desktop Application, which is based on a browser interface and is suitable for Windows, Mac and UNIX systems. myVCF is an efficient platform that is able to manage multiple sequencing projects created from VCF files within the system; stores genetic variants and samples genotypes from an annotated VCF files into a SQLite database; implements a flexible search engine for data exploration, allowing to query for chromosomal region, gene, single variant or dbSNP ID. Besides, myVCF generates a summary statistics report about mutations distribution across samples and across the genome/exome by aggregating the information within the VCF file. In summary, the myVCF platform allows end-users without strong programming and bioinformatics skills to explore, query, visualize and export mutations data in a simple and straightforward way
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myvcf a Desktop Application for high throughput mutations data management
Bioinformatics, 2017Co-Authors: A. Pietrelli, L. ValentiAbstract:Summary Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants. We developed myVCF, a standalone, easy-to-use Desktop Application, which is based on a browser interface and is suitable for Windows, Mac and UNIX systems. myVCF is an efficient platform that is able to manage multiple sequencing projects created from VCF files within the system; stores genetic variants and samples genotypes from an annotated VCF files into a SQLite database; implements a flexible search engine for data exploration, allowing to query for chromosomal region, gene, single variant or dbSNP ID. Besides, myVCF generates a summary statistics report about mutations distribution across samples and across the genome/exome by aggregating the information within the VCF file. In summary, the myVCF platform allows end-users without strong programming and bioinformatics skills to explore, query, visualize and export mutations data in a simple and straightforward way. Availability and implementation https://apietrelli.github.io/myVCF/. Contact pietrelli@ingm.org. Supplementary information Supplementary data are available at Bioinformatics online.
Jarny Choi - One of the best experts on this subject based on the ideXlab platform.
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guide a Desktop Application for analysing gene expression data
BMC Genomics, 2013Co-Authors: Jarny ChoiAbstract:Multiplecompeting bioinformatics tools exist for next-generation sequencing data analysis. Many of these tools are available as R/Bioconductor modules, and it can be challenging for the bench biologist without any programming background to quickly analyse genomics data. Here, we present an Application that is designed to be simple to use, while leveraging the power of R as the analysis engine behind the scenes. Genome Informatics Data Explorer (Guide) is a Desktop Application designed for the bench biologist to analyse RNA-seq and microarray gene expression data. It requires a text file of summarised read counts or expression values as input data, and performs differential expression analyses at both the gene and pathway level. It uses well-established R/Bioconductor packages such as limma for its analyses, without requiring the user to have specific knowledge of the underlying R functions. Results are presented in figures or interactive tables which integrate useful data from multiple sources such as gene annotation and orthologue data. Advanced options include the ability to edit R commands to customise the analysis pipeline. Guide is a Desktop Application designed to query gene expression data in a user-friendly way while automatically communicating with R. Its customisation options make it possible to use different bioinformatics tools available through R/Bioconductor for its analyses, while keeping the core usage simple. Guide is written in the cross-platform framework of Qt, and is freely available for use from http://guide.wehi.edu.au .
Allan Azarion - One of the best experts on this subject based on the ideXlab platform.
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an open source automated platform for three dimensional visualization of subdural electrodes using ct mri coregistration
Epilepsia, 2014Co-Authors: Allan Azarion, Allison Pearce, Veena T Krish, Joost B Wagenaar, Weixuan Chen, Yuanjie Zheng, Hongzhi Wang, Timothy H LucasAbstract:Summary Objective Visualizing implanted subdural electrodes in three-dimensional (3D) space can greatly aid in planning, executing, and validating resection in epilepsy surgery. Coregistration software is available, but cost, complexity, insufficient accuracy, or validation limit adoption. We present a fully automated open-source Application, based on a novel method using postimplant computerized tomography (CT) and postimplant magnetic resonance (MR) images, for accurately visualizing intracranial electrodes in 3D space. Methods CT-MR rigid brain coregistration, MR nonrigid registration, and prior-based segmentation were carried out on seven patients. Postimplant CT, postimplant MR, and an external labeled atlas were then aligned in the same space. The coregistration algorithm was validated by manually marking identical anatomic landmarks on the postimplant CT and postimplant MR images. Following coregistration, distances between the center of the landmark masks on the postimplant MR and the coregistered CT images were calculated for all subjects. Algorithms were implemented in open-source software and translated into a “drag and drop” Desktop Application for Apple Mac OS X. Results Despite postoperative brain deformation, the method was able to automatically align intrasubject multimodal images and segment cortical subregions, so that all electrodes could be visualized on the parcellated brain. Manual marking of anatomic landmarks validated the coregistration algorithm with a mean misalignment distance of 2.87 mm (standard deviation 0.58 mm)between the landmarks. Software was easily used by operators without prior image processing experience. Significance We demonstrate an easy to use, novel platform for accurately visualizing subdural electrodes in 3D space on a parcellated brain. We rigorously validated this method using quantitative measures. The method is unique because it involves no preprocessing, is fully automated, and freely available worldwide. A Desktop Application, as well as the source code, are both available for download on the International Epilepsy Electrophysiology Portal (https://www.ieeg.org) for use and interactive refinement.
Lia Duarte - One of the best experts on this subject based on the ideXlab platform.
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distributed temperature measurement in a self burning coal waste pile through a gis open source Desktop Application
ISPRS international journal of geo-information, 2017Co-Authors: Lia Duarte, Joana Ribeiro, Ana Claudia Teodoro, J A Goncalves, Deolinda Flores, Alexia Lopezgil, Alejandro Dominguezlopez, Xabier Angulovinuesa, Sonia Martinlopez, Miguel GonzalezherraezAbstract:Geographical Information Systems (GIS) are often used to assess and monitor the environmental impacts caused by mining activities. The aim of this work was to develop a new Application to produce dynamic maps for monitoring the temperature variations in a self-burning coal waste pile, under a GIS open source environment—GIS-ECOAL (freely available). The performance of the Application was evaluated with distributed temperature measurements gathered in the S. Pedro da Cova (Portugal) coal waste pile. In order to obtain the temperature data, an optical fiber cable was disposed over the affected area of the pile, with 42 location stakes acting as precisely-located control points for the temperature measurement. A monthly data set from July (15 min of interval) was fed into the Application and a video composed by several layouts with temperature measurements was created allowing for recognizing two main areas with higher temperatures. The field observations also allow the identification of these zones; however, the identification of an area with higher temperatures in the top of the studied area was only possible through the visualization of the images created by this Application. The generated videos make possible the dynamic and continuous visualization of the combustion process in the monitored area.
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assessing soil erosion risk using rusle through a gis open source Desktop and web Application
Environmental Monitoring and Assessment, 2016Co-Authors: Lia Duarte, Ana Claudia Teodoro, J A Goncalves, Daniel Cristian Ferreira Soares, Mario CunhaAbstract:Soil erosion is a serious environmental problem. An estimation of the expected soil loss by water-caused erosion can be calculated considering the Revised Universal Soil Loss Equation (RUSLE). Geographical Information Systems (GIS) provide different tools to create categorical maps of soil erosion risk which help to study the risk assessment of soil loss. The objective of this study was to develop a GIS open source Application (in QGIS), using the RUSLE methodology for estimating erosion rate at the watershed scale (Desktop Application) and provide the same Application via web access (web Application). The Applications developed allow one to generate all the maps necessary to evaluate the soil erosion risk. Several libraries and algorithms from SEXTANTE were used to develop these Applications. These Applications were tested in Montalegre municipality (Portugal). The maps involved in RUSLE method—soil erosivity factor, soil erodibility factor, topographic factor, cover management factor, and support practices—were created. The estimated mean value of the soil loss obtained was 220 ton km−2 year−1 ranged from 0.27 to 1283 ton km−2 year−1. The results indicated that most of the study area (80 %) is characterized by very low soil erosion level (<321 ton km−2 year−1) and in 4 % of the studied area the soil erosion was higher than 962 ton km−2 year−1. It was also concluded that areas with high slope values and bare soil are related with high level of erosion and the higher the P and C values, the higher the soil erosion percentage. The RUSLE web and the Desktop Application are freely available.