Graphical User Interface for Human Intervention in 2D-3D Registration of Medical Images

2013 ◽  
Author(s):  
Grant L. S. Marchelli ◽  
David R. Haynor ◽  
William R. Ledoux ◽  
Mark A. Ganter ◽  
Duane W. Storti
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
3D Imaging ◽  
Quality Measure ◽  
Reference Image ◽  
3D Registration ◽  
Data Set ◽  
Image Guided ◽  
2D And 3D

Image-guided medical therapies and image-guided biomechanical measurement systems often combine 2D and 3D imaging modalities. Determination of relations between the 2D and 3D imaging data is known as 2D-3D registration. Motivated by an ongoing project aimed at non-invasive, marker-free measurement of the kinematics of the bones in the foot during gait, we consider a registration approach that involves (1) computing projections of the 3D data set, (2) computing a quality measure to describe the agreement/discrepancy between the simulated projections and actual 2D images, and (3) optimization of the quality measure relative to the kinematic degrees of freedom to determine the optimal registration. For our particular project, the 3D imaging modality is CT scan, the 2D modality is bi-plane fluoroscopy, the computed projection is a digitally reconstructed radiograph (DRR), the quality measure is normalized cross-correlation (NCC) between a pair of DRRs and a pair of corresponding fluoroscope images, and the 2D imaging includes a sequence of several hundred stereo image pairs. We have recently released a software toolkit, DRRACC, that accelerates both the DRR and NCC computations via GPU-based parallel processing to enable more efficient automated determination of kinematic relations for optimal registration. While fully automated 2D-3D registration is desirable, there are situations (such as creating a reasonable starting configuration for optimization, re-starting after the optimizer fails to converge, and visual verification of registration relations) when it is desirable/necessary to have a human in the loop. In this paper, we present an OpenGL-based graphical user interface that employs the DRRACC toolkit to allow the user to manipulate the kinematics of individual objects (bones) segmented from the 3D imaging and to view the corresponding DRR and the associated correlation with a reference image in real time. We also present plots showing initial results for the dependence of the registration measure on pairs of kinematic parameters. The plots show well-defined peaks that support the hope for automated registration, but they also contain large relatively flat regions that may prove problematic for gradient-based optimizers and necessitate the sort of interface presented in this paper.

scholarly journals Highly Automated Dipole EStimation (HADES)

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
C. Campi ◽  
A. Pascarella ◽  
A. Sorrentino ◽  
M. Piana
Keyword(s):  
Inverse Problem ◽  
User Interface ◽  
Graphical User Interface ◽  
Particle Filtering ◽  
Synthetic Data ◽  
Nonlinear Relationship ◽  
Data Set ◽  
Automatic Estimation ◽  
Dipole Estimation ◽  
Dipolar Model

Automatic estimation of current dipoles from biomagnetic data is still a problematic task. This is due not only to the ill-posedness of the inverse problem but also to two intrinsic difficulties introduced by the dipolar model: the unknown number of sources and the nonlinear relationship between the source locations and the data. Recently, we have developed a new Bayesian approach, particle filtering, based on dynamical tracking of the dipole constellation. Contrary to many dipole-based methods, particle filtering does not assume stationarity of the source configuration: the number of dipoles and their positions are estimated and updated dynamically during the course of the MEG sequence. We have now developed a Matlab-based graphical user interface, which allows nonexpert users to do automatic dipole estimation from MEG data with particle filtering. In the present paper, we describe the main features of the software and show the analysis of both a synthetic data set and an experimental dataset.

scholarly journals Rapid Prototyping of Wireframe Scaffolded DNA Origami using ATHENA

2020 ◽  
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
William P. Bricker ◽  
Steve Jackson ◽  
Mark Bathe
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Materials Science ◽  
Dna Origami ◽  
Coarse Grained ◽  
Helix Bundle ◽  
Open Source Software Package ◽  
Algorithmic Approaches ◽  
High Degree ◽  
2D And 3D

ABSTRACTWireframe DNA origami assemblies can now be programmed automatically from the “top-down” using simple wireframe target geometries, or meshes, in 2D and 3D geometries using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (2HB or DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, stand-alone interface. Here, we present ATHENA, an open-source software package with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami in 2D or 3D using 2HB or 6HB edges. ATHENA enables external editing of sequences using the popular tool caDNAno, demonstrated here using asymmetric nanoscale positioning of gold nanoparticles, as well as atomic-level models for molecular dynamics, coarse-grained dynamics, or other computational chemistry simulation approaches. We anticipate ATHENA will significantly reduce the barrier for non-specialists to perform wireframe DNA origami sequence design and fabrication for custom applications in materials science, nanotechnology, therapeutics, and other areas.

scholarly journals Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

2021 ◽  
Vol 49 (18) ◽  
pp. 10265-10274
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
Molly F Parsons ◽  
William P Bricker ◽  
Torsten John ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Dna Origami ◽  
Coarse Grained ◽  
Top Down ◽  
Helix Bundle ◽  
Open Source Software Package ◽  
Algorithmic Approaches ◽  
High Degree ◽  
2D And 3D

Abstract Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

Fused magnetic resonance angiography and 2D fluoroscopic visualization for endovascular intracranial neuronavigation

2013 ◽  
Vol 118 (5) ◽  
pp. 1000-1002 ◽  
Author(s):  
Naci Kocer ◽  
Osman Kizilkilic ◽  
Drazenko Babic ◽  
Danny Ruijters ◽  
Civan Islak
Keyword(s):  
Image Guidance ◽  
Data Set ◽  
Image Guided ◽  
3D Angiography ◽  
Iodinated Contrast ◽  
Giant Cerebral Aneurysm ◽  
Fused Image ◽  
High Level ◽  
Guidance Technique ◽  
2D And 3D

Advanced transluminal neurovascular navigation is an indispensable image-guided method that allows for real-time navigation of endovascular material in critical neurovascular settings. Thus far, it has been primarily based on 2D and 3D angiography, burdening the patient with a relatively high level of iodinated contrast. However, in the patients with renal insufficiency, this method is no longer tolerable due to the contrast load. The authors present a novel image guidance technique based on periprocedural fluoroscopic images fused with a preinterventionally acquired MRI data set. The technique is illustrated in a case in which the fused image combination was used for endovascular treatment of a giant cerebral aneurysm.

scholarly journals TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

2021 ◽  
Vol 4 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Arne Beermann ◽  
Florian Leese
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Distribution Patterns ◽  
Assessment Tools ◽  
Biological Information ◽  
Distribution Data ◽  
Global Biodiversity Information Facility ◽  
Data Set ◽  
Wide Range ◽  
Dna Metabarcoding

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the need for easy-to-use, graphical user interface (GUI) software to analyze and visualize DNA metabarcoding data is growing. Here we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualization workflows. The input format of TTT is a so-called "TaXon table". This data format can easily be generated within TTT from two common file formats that can be obtained using various published DNA metabarcoding pipelines: a read table and a taxonomy table. TTT offers a wide range of processing, filtering and analysis modules. The user can analyze and visualize basic statistics, such as read proportion per taxon, as well as more sophisticated visualizations such as interactive Krona charts for taxonomic data exploration, or complex parallel category diagrams to assess species distribution patterns. Venn diagrams can be calculated to compare taxon overlap among replicates, samples, or analysis methods. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, rarefaction analyses, and principal coordinate or non-metric multidimensional scaling plots. The taxonomy of a data set can be validated via the Global Biodiversity Information Facility (GBIF) API to check for synonyms and spelling mistakes. Furthermore, geographical distribution data can be automatically downloaded from GBIF. Additionally, TTT offers a conversion tool for DNA metabarcoding data into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. Beyond that, TTT is able to produce fully interactive html-based graphics that can be analyzed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).

scholarly journals Transit Analysis Package: An IDL Graphical User Interface for Exoplanet Transit Photometry

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
J. Zachary Gazak ◽  
John A. Johnson ◽  
John Tonry ◽  
Diana Dragomir ◽  
Jason Eastman ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Likelihood Function ◽  
Light Curves ◽  
Parameter Uncertainties ◽  
Data Set ◽  
Specific Data ◽  
Software Release ◽  
Analysis Package ◽  
Good Agreement

We present an IDL graphical user-interface-driven software package designed for the analysis of exoplanet transit light curves. The Transit Analysis Package (TAP) software uses Markov Chain Monte Carlo (MCMC) techniques to fit light curves using the analytic model of Mandal and Agol (2002). The package incorporates a wavelet-based likelihood function developed by Carter and Winn (2009), which allows the MCMC to assess parameter uncertainties more robustly than classicχ2methods by parameterizing uncorrelated “white” and correlated “red” noise. The software is able to simultaneously analyze multiple transits observed in different conditions (instrument, filter, weather, etc.). The graphical interface allows for the simple execution and interpretation of Bayesian MCMC analysis tailored to a user’s specific data set and has been thoroughly tested on ground-based andKeplerphotometry. This paper describes the software release and provides applications to new and existing data. Reanalysis of ground-based observations of TrES-1b, WASP-4b, and WASP-10b (Winn et al., 2007, 2009; Johnson et al., 2009; resp.) and space-basedKepler4b–8b (Kipping and Bakos 2010) show good agreement between TAP and those publications. We also present new multi-filter light curves of WASP-10b and we find excellent agreement with previously published values for a smaller radius.

A methodology for water quantity and quality assessment for wetland development

1995 ◽  
Vol 31 (8) ◽  
pp. 293-300 ◽  
Author(s):  
Rolando G. Vadas ◽  
Luis A. Garcia ◽  
John W. Labadie
Keyword(s):  
User Interface ◽  
Quality Assessment ◽  
Graphical User Interface ◽  
Water Quantity ◽  
Climatic Data ◽  
Simulation And Optimization ◽  
Wetland Development ◽  
Wetland Complex ◽  
Water Quantity And Quality

A methodology is presented for water quantity and quality assessment for wetland development which enables planners to evaluate the results of restoring and managing a large wetland complex based on a set of criteria developed under multi-disciplinary guidelines. The methodology includes addressing temporal and spatial variability of climatic data for determination of wetland water requirements; determination of wetland evapotranspiration; determination of critical areas for wetland and agricultural development using GIS; modelling the water delivery ystem (quantity, quality, location, and timing) of a wetland complex using HEC-5 and WASP; and water management using the GAMS/MINOS optimization program. The methodology is applied through the use of a Decision Support System (DSS). The goal of the DSS is to provide tools for spatial and temporal simulation, evaluation and management of a wetland system. The user has access to a common analysis environment consisting of models and data within a Graphical User Interface (GUI). Simulation and optimization modules, combined with a graphical user interface, permit efficient and convenient study of various resource management scenarios.

scholarly journals CEPS: An Open Access MATLAB Graphical User Interface (GUI) for the Analysis of Complexity and Entropy in Physiological Signals

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 321
Author(s):  
David Mayor ◽  
Deepak Panday ◽  
Hari Kala Kandel ◽  
Tony Steffert ◽  
Duncan Banks
Keyword(s):  
User Interface ◽  
Open Access ◽  
Graphical User Interface ◽  
Linear Time ◽  
Physiological Signals ◽  
Physiological Data ◽  
Data Set ◽  
Convenience Sample ◽  
Paced Breathing ◽  
Entropy Measures

Background: We developed CEPS as an open access MATLAB® GUI (graphical user interface) for the analysis of Complexity and Entropy in Physiological Signals (CEPS), and demonstrate its use with an example data set that shows the effects of paced breathing (PB) on variability of heart, pulse and respiration rates. CEPS is also sufficiently adaptable to be used for other time series physiological data such as EEG (electroencephalography), postural sway or temperature measurements. Methods: Data were collected from a convenience sample of nine healthy adults in a pilot for a larger study investigating the effects on vagal tone of breathing paced at various different rates, part of a development programme for a home training stress reduction system. Results: The current version of CEPS focuses on those complexity and entropy measures that appear most frequently in the literature, together with some recently introduced entropy measures which may have advantages over those that are more established. Ten methods of estimating data complexity are currently included, and some 28 entropy measures. The GUI also includes a section for data pre-processing and standard ancillary methods to enable parameter estimation of embedding dimension m and time delay τ (‘tau’) where required. The software is freely available under version 3 of the GNU Lesser General Public License (LGPLv3) for non-commercial users. CEPS can be downloaded at https://bitbucket.org/deepak_panday/ceps/src/pipeline_v2/. In our illustration on PB, most complexity and entropy measures decreased significantly in response to breathing at 7 breaths per minute, differentiating more clearly than conventional linear, time- and frequency-domain measures between breathing states. In contrast, Higuchi fractal dimension increased during paced breathing. Conclusions: We have developed CEPS software as a physiological data visualiser able to integrate state of the art techniques. The interface is designed for clinical research and has a structure designed for integrating new tools. The aim is to strengthen collaboration between clinicians and the biomedical community, as demonstrated here by using CEPS to analyse various physiological responses to paced breathing.

scholarly journals FXD-CSD-GUI: a graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions

2019 ◽  
Vol 52 (6) ◽  
pp. 1437-1439
Author(s):  
Sigmund H. Neher ◽  
Helmut Klein ◽  
Werner F. Kuhs
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Crystal Size ◽  
Data Handling ◽  
Size Distributions ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
User Friendly

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

Determination of geometric accuracy of radiotherapy fields by port film and DRR using Matlab graphical user interface

2018 ◽  
Vol 57 (1) ◽  
pp. 259-269 ◽  
Author(s):  
Seyyed Mostafa Anjam ◽  
Nooshin Banaee ◽  
Hojjat Rahmani ◽  
Hassan Ali Nedaie
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Geometric Accuracy
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