Interactive Toolkit Research Articles

MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging \u2013 design, implementation and application on the example of DCE-MRI

BackgroundMany medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI)/computed tomography (CT), apparent diffusion coefficient calculations and intravoxel incoherent motion modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow.ResultsWe present a framework for medical image fitting tasks that is included in the Medical Imaging Interaction Toolkit MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth.ConclusionsProviding a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.

New tools for crop wild relative conservation planning

AbstractCrop wild relatives (CWR) are a vital source of traits for crop improvement – therefore, conserving CWR diversity is critical to ensure food, nutrition and economic security. Efficient CWR conservation planning is a critical first step to maintain this natural resource for future use. The development of National Strategic Action Plans (NSAPs) for the conservation and sustainable use of CWR is an effective means of conservation planning and also plays an important role in sensitizing policy makers and other stakeholders to the importance of CWR. Tools to guide and facilitate countries in CWR national conservation planning and NSAP development have been prepared, namely: an ‘Interactive Toolkit for CWR Conservation Planning’, a ‘Template for the Preparation of a NSAP for the Conservation and Sustainable Use of CWR’, a ‘Template for the Preparation of a Technical Background Document for a NSAP for the Conservation and Sustainable Use of CWR’, a ‘CWR Checklist and Inventory Data Template’ and an ‘Occurrence Data Collation Template’. In this short communication, we briefly explain what these tools are, how they were developed, how they can be used and where they can be found.

Feasibility of using Medical Imaging Interaction Toolkit in volumetric studies to accurate diagnosing of vascular emboli by Extended NURBS-based Cardiac-Torso phantom

Introduction: Important complications of venous thromboembolism (VTE) are a longer hospital stay, readmission, recurrence of the emboli, complications of anticoagulant therapy and death in a sever condition. In present study, the volume measurement accuracy of the medical imaging interaction toolkit (MITK) software on determining VTE in computed tomography images was evaluated. Methods: Several VTEs, ranged from 0.1 to 20 mm, were simulated in the arteries of a XCAT Phantom. Then, the MITK software was used for localization and volume measurement of the produced VTEs on the images of the simulated phantom. Results: The scatter plot and correlation coefficient were showed a high correlation between the calculated emboli volume measures by MITK software with those designed in the XCAT Phantom (r=0.98; p<0.001), The differences of the calculated measures and the simulated clots were mostly related to the clot volumes less than 0.1 ml (mainly due to the inability of the software to measure the range), which may be clinically ignored. However, a difference of about 0.01 ml for the clot volumes greater than 0.1 ml was in acceptable range. Conclusion: MITK software may be used for volume measurement studies in medical diagnosis, also for VTE accurate measurement to achieve a more accurate diagnosis and to eliminate the need to onsite diagnosis by the imaging system due to MITK capability on running in a personal computer.

Signed Real-Time Delay Multiply and Sum Beamforming for Multispectral Photoacoustic Imaging

Reconstruction of photoacoustic (PA) images acquired with clinical ultrasound transducers is usually performed using the Delay and Sum (DAS) beamforming algorithm. Recently, a variant of DAS, referred to as Delay Multiply and Sum (DMAS) beamforming has been shown to provide increased contrast, signal-to-noise ratio (SNR) and resolution in PA imaging. The main reasons for the use of DAS beamforming in photoacoustics are its simple implementation, real-time capability, and the linearity of the beamformed image to the PA signal. This is crucial for the identification of different chromophores in multispectral PA applications. In contrast, current DMAS implementations are not responsive to the full spectrum of sound frequencies from a photoacoustic source and have not been shown to provide a reconstruction linear to the PA signal. Furthermore, due to its increased computational complexity, DMAS has not been shown yet to work in real-time. Here, we present an open-source real-time variant of the DMAS algorithm, signed DMAS (sDMAS), that ensures linearity in the original PA signal response while providing the increased image quality of DMAS. We show the applicability of sDMAS for multispectral PA applications, in vitro and in vivo. The sDMAS and reference DAS algorithms were integrated in the open-source Medical Imaging Interaction Toolkit (MITK) and are available as real-time capable implementations.

Emergency preparedness through game playing

ABSTRACTThe lack of emergency preparedness in Mauritius has been the cause of many tragedies. Our approach to tackle this problem was by developing an emergency preparedness game layered and fused with a disaster warning and guidance system that emanates clarity to the unfathomable bearings of emergencies and natural disasters. The emergency preparedness game is based on a selection of diverse real life-threatening difficulties that entail different strategies aimed at bettering the survival instincts of users. It uses story-telling scenarios along with in-game footnotes that yield directives on how to brave fierce and unpredictable calamities. The game reinforces a sense of self-composedness and suppressing untimely fears of users in horrendous circumstances. With regard to the warning system, it unremittingly feeds users with notifications during emergencies, that encases shortest escape routes to lead them to safe locations via a fully functional GPS map. This application brings some novelties that are virtually non-existent in related applications. For instance, this application includes a warning and guidance system, a 3D scenario game to prepare its users for disasters, an interactive survival toolkit selection, an SMS rescue feature and a mass notification system via the web.

Mobilizing Rural Communities to Prevent Childhood Obesity: A Tool Kit

The tool kit Mobilizing Rural Communities to Prevent Childhood Obesity is the product of a seven-state multidisciplinary research project focused on enhancing obesity prevention efforts by integrating community coaching into the work of rural community coalitions. The interactive tool kit is available at no cost both in print form and online, and it consists of five tutorials that present best practices and lessons learned throughout the research project. Extension professionals working within health promotion coalitions may wish to use or promote the tool kit. Coalition members can complete the activities contained in the tool kit individually or as a group.

Mobilizing Rural Communities to Prevent Childhood Obesity: A Tool Kit

The tool kit Mobilizing Rural Communities to Prevent Childhood Obesity is the product of a seven-state multidisciplinary research project focused on enhancing obesity prevention efforts by integrating community coaching into the work of rural community coalitions. The interactive tool kit is available at no cost both in print form and online, and it consists of five tutorials that present best practices and lessons learned throughout the research project. Extension professionals working within health promotion coalitions may wish to use or promote the tool kit. Coalition members can complete the activities contained in the tool kit individually or as a group.

DrawROI: An interactive toolkit to extract phenological time series data from digital repeat photography

drawROI: An interactive toolkit to extract phenological time series data from digital repeat photography

Development of “down the road”: An interactive toolkit about driving cessation for dementia caregivers

ABSTRACTConcerns about safe driving practices in individuals with dementia often fall to caregivers, who are frequently faced with the difficult task of initiating the conversation about driving and driving cessation with their loved ones. This is a topic that can be a very emotional and sensitive for older adults. Several print-based resources are currently available to caregivers; however, emerging research suggests that disseminating information through applied theater, a genre of theater typically based on research that addresses a social issue, may be more effective in changing attitudes than these traditional print-based methods. Applied theater touches upon the emotional complexities involved in decision-making about driving, deepening a viewer’s experience with the content. This work used research obtained from focus groups and individual interviews with 17 (eight informal and nine formal) dementia caregivers as a foundation for the development of a toolkit called Down the Road, which consists of an applied theater production about driving safety called No Particular Place to Go (in DVD-format), an accompanying viewer guidebook, and supplemental information cards. The content of Down the Road centers around eight main themes identified by dementia caregivers, including (1) the importance of driving, (2) the assessment process, (3) information about refresher courses and driving schools, (4) risk factors and warning signs, (5) starting the conversation, (6) dealing with resistance, (7) the need for support, and (8) alternative transportation options. Down the Road incorporates the expressed needs of dementia caregivers to translate knowledge into an effective, research-based toolkit that can provide caregivers with an interactive resource for use individually or in facilitated groups.

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000Hz and a latency of 2.81ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

Pilot test of an interactive education toolkit on drug use

Pilot test of an interactive education toolkit on drug use

Plume Tracker: Interactive mapping of volcanic sulfur dioxide emissions with high-performance radiative transfer modeling

We describe the development of Plume Tracker, an interactive toolkit for the analysis of multispectral thermal infrared observations of volcanic plumes and clouds. Plume Tracker is the successor to MAP_SO2, and together these flexible and comprehensive tools have enabled investigators to map sulfur dioxide (SO2) emissions from a number of volcanoes with TIR data from a variety of airborne and satellite instruments. Our objective for the development of Plume Tracker was to improve the computational performance of the retrieval procedures while retaining the accuracy of the retrievals. We have achieved a 300× improvement in the benchmark performance of the retrieval procedures through the introduction of innovative data binning and signal reconstruction strategies, and improved the accuracy of the retrievals with a new method for evaluating the misfit between model and observed radiance spectra. We evaluated the accuracy of Plume Tracker retrievals with case studies based on MODIS and AIRS data acquired over Sarychev Peak Volcano, and ASTER data acquired over Kilauea and Turrialba Volcanoes. In the Sarychev Peak study, the AIRS-based estimate of total SO2 mass was 40% lower than the MODIS-based estimate. This result was consistent with a 45% reduction in the AIRS-based estimate of plume area relative to the corresponding MODIS-based estimate. In addition, we found that our AIRS-based estimate agreed with an independent estimate, based on a competing retrieval technique, within a margin of ±20%. In the Kilauea study, the ASTER-based concentration estimates from 21 May 2012 were within ±50% of concurrent ground-level concentration measurements. In the Turrialba study, the ASTER-based concentration estimates on 21 January 2012 were in exact agreement with SO2 concentrations measured at plume altitude on 1 February 2012.

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).

Affective Quantification of Color Gestalt: Modeling of Affective Factors for Combinative Color Design

Integrated combination of multiple colors as it is, color gestalt invariably troubles researchers as they seek to understand and analyze the complex constructions of affective factors. The author proposes a set of quantification methods for measuring color-affective factors of harmony, preference and structural composition. He also describes quantified models and interactive toolkits he built for both experimental purposes and user study. The author proposes a holistic method for understanding color combination that stands in contrast to conventional methods. Through this method, perception of color gestalt becomes computable and analyzable, inviting further research on interactive color computing and parametric design.

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies.

BackgroundA central question for disease studies and crop improvements is how genetics variants drive phenotypes. Genome Wide Association Study (GWAS) provides a powerful tool for characterizing the genotype-phenotype relationships in complex traits and diseases. Epistasis (gene-gene interaction), including high-order interaction among more than two genes, often plays important roles in complex traits and diseases, but current GWAS analysis usually just focuses on additive effects of single nucleotide polymorphisms (SNPs). The lack of effective computational modelling of high-order functional interactions often leads to significant under-utilization of GWAS data.ResultsWe have developed a novel Bayesian computational method with a Markov Chain Monte Carlo (MCMC) search, and implemented the method as a Bayesian High-order Interaction Toolkit (BHIT) for detecting epistatic interactions among SNPs. BHIT first builds a Bayesian model on both continuous data and discrete data, which is capable of detecting high-order interactions in SNPs related to case—control or quantitative phenotypes. We also developed a pipeline that enables users to apply BHIT on different species in different use cases.ConclusionsUsing both simulation data and soybean nutritional seed composition studies on oil content and protein content, BHIT effectively detected some high-order interactions associated with phenotypes, and it outperformed a number of other available tools. BHIT is freely available for academic users at http://digbio.missouri.edu/BHIT/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2217-6) contains supplementary material, which is available to authorized users.

Quantifying the human–building interaction: Considering the active, adaptive occupant in building performance simulation

This paper introduces a Human and Building Interaction Toolkit (HABIT) for simulating the thermally adaptive behaviors and comfort of office occupants alongside building energy consumption. The toolkit uses the Building Controls Virtual Test Bed (BCVTB) to co-simulate a field-tested, agent-based behavior model with an EnergyPlus medium office model. The usefulness of the toolkit is demonstrated through a series of zone and building-level case study simulations that examine the wisdom of pairing local heating and cooling options with strategic thermostat set point offsets, judging from the energy, Indoor Environmental Quality (IEQ), and cost perspectives.Results generally suggest that trading efficient local heating/cooling options for whole space conditioning has both energy and comfort benefits, saving up to 28% of monthly HVAC energy while improving the acceptability of thermal conditions in a Philadelphia climate. Nevertheless, cost analysis shows that the fuel source of conserved energy must be considered – particularly in the case of personal heater use, which adds to electric plug loads and associated utility and CO2 emissions cost penalties. Moreover, costs from even small changes in simulated occupant productivity tend to overwhelm energy costs, suggesting the need to improve the accuracy and precision of available productivity models across multiple seasons and climates.

VisDock: A Toolkit for Cross-Cutting Interactions in Visualization

Standard user applications provide a range of cross-cutting interaction techniques that are common to virtually all such tools: selection, filtering, navigation, layer management, and cut-and-paste. We present VisDock, a JavaScript mixin library that provides a core set of these cross-cutting interaction techniques for visualization, including selection (lasso, paths, shape selection, etc), layer management (visibility, transparency, set operations, etc), navigation (pan, zoom, overview, magnifying lenses, etc), and annotation (point-based, region-based, data-space based, etc). To showcase the utility of the library, we have released it as Open Source and integrated it with a large number of existing web-based visualizations. Furthermore, we have evaluated VisDock using qualitative studies with both developers utilizing the toolkit to build new web-based visualizations, as well as with end-users utilizing it to explore movie ratings data. Results from these studies highlight the usability and effectiveness of the toolkit from both developer and end-user perspectives.

Dose Matters: An Approach to Strengthening Community Health Strategies to Achieve Greater Impact

Dose Matters describes the concept of “population dose”—an approach to strengthening and evaluating the impact of complex multisector, multilevel, place-based initiatives. This discussion paper reports on what is promising about the approach while recognizing the measurement and other challenges that still lie ahead. The concept emerged from ongoing evaluations of Kaiser Permanente’s Community Health Initiative investments, conducted by the Center for Community Health and Evaluation (CCHE) at the Group Health Research Institute in collaboration with partners at the University of California. Following an overview of the Community Health Initiative, this report describes the concept in more detail and explains how it can be used to estimate the population-level impact of a set of related interventions. The estimated impact or dose of an intervention is the product of reach (the number of people touched by the intervention) and strength (the effect size or impact on each person reached). The dose concept can also be used in planning and implementation to yield greater impact. We hope that Dose Matters will introduce the concept of population dose in enough detail that a broad audience of community health researchers, evaluators, practitioners, and planners will be both prepared and eager to apply these analyses and approaches to their own work. Additional guidance is available in the form of an interactive toolkit developed by CCHE and Kaiser Permanente (see the Related Resources box). Together, Dose Matters and the toolkit will describe in detail the uses of dose for both evaluators and researchers, who will use the quantitative calculations, and community-based organizations and funders, who will apply the overall concept to strengthen every phase of improving community health outcomes, from planning to implementation to evaluation.

Интерактивный графический инструментарий глобального вычислительного эксперимента в службе морских оперативных прогнозов

Эффективность и полнота численного моделирования в океанологии и гидрометеорологии всецело обусловливаются алгоритмическими особенностями построения интерактивного вычислительного эксперимента в масштабах Мирового океана с адаптивным покрытием закрытых морей и прибрежных акваторий уточненными математическими моделями, с возможностью программного распараллеливания уточняющих расчетов вблизи конкретных — защищаемых участков морского побережья. Важной составляющей исследований представляются методы непрерывной графической визуализации в ходе вычислений, в том числе осуществляемой в параллельных процессах с общей оперативной памятью или по контрольным точкам на внешних носителях. Результаты вычислительных экспериментов используются в описании гидродинамических процессов вблизи побережья, учет которых важен в организации морских служб контроля и прогноза опасных морских явлений.

An analytic measure of perceptual factors for color composition

AbstractColor images are usually observed as integrated objects, or called color gestalt. That is why color effect of image is not only affected by the color components themselves, but also determined remarkably by the image constructive frame, which holds the colors. Although, previous researchers have already explored this issue, the conclusions are usually descriptive principles that one should keep in mind for color designing. Precise quantification for image composition of color gestalt is still an ignored field in color research domain. As the use of computer‐aided design (CAD) increases in the color design field, more quantifiable measures for constructive feature factors that affect color gestalt are needed. In this article, we introduce a three‐dimensional model of image composition that can both quantify the effect of color gestalt and rebuild image composition to acquire certain color effect for color combination. This method pioneers a new perspective of appreciating the influence of image construction on color combination effect, and a new way of researching color by affective computing or Kansei engineering technology. To test the feasibility of the scale model by a usage study, an interactive toolkit was also built. Practice has confirmed that this method is a technical meaning in application technically meaningful approach, and will spur further research on color composition. © 2015 Wiley Periodicals, Inc. Col Res Appl, 41, 165–174, 2016