MITK Diffusion Imaging

2012 ◽  
Vol 51 (05) ◽  
pp. 441-448 ◽  
Author(s):  
P. F. Neher ◽  
I. Reicht ◽  
T. van Bruggen ◽  
C. Goch ◽  
M. Reisert ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
High Performance ◽  
Diffusion Imaging ◽  
Software Tool ◽  
Brain Anatomy ◽  
Sustainable Evaluation ◽  
Imaging Research ◽  
Interactive Data

SummaryBackground: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets.Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field.Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITKDI, are demonstrated using in-vivo datasets.Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use in stallable application.Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.

scholarly journals Karawun: assisting evaluation of advances in multimodal imaging for neurosurgical planning and intraoperative neuronavigation

2021 ◽  
Author(s):  
Richard Beare ◽  
Bonnie Alexander ◽  
Aaron Warren ◽  
Michael Kean ◽  
Marc Seal ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Image Guidance ◽  
Image Data ◽  
Software Tool ◽  
Neurosurgical Planning ◽  
Wide Range ◽  
Imaging Research ◽  
The Impact ◽  
Integrate Research

AbstractSubmitted to Magnetic Resonance in MedicinePurposeTo introduce a tool allowing neurosurgeons to evaluate the results of research tractography workflows for presurgical planning and intraoperative image-guidance, using standard neurosurgical navigation platforms.Theory and MethodsImproving communication between neurosurgeons and researchers developing new image acquisition and processing methods is critical for rapid translation of research to surgical practice. Presenting research outputs within existing clinical workflows is one approach that can assist such interdisciplinary communication. Neurosurgical navigation platforms can display and manipulate a wide range of medical image data and associated delineations and thus allow clinicians to evaluate the impact of new imaging research on their work. Currently, it is extremely difficult to integrate research-based image processing outputs into standard neurosurgical navigation platforms.ResultsIn this note we introduce Karawun, an open-source software tool for converting outputs from research imaging pipelines, especially diffusion MRI tractography reconstructions using advanced methodologies currently unavailable on commercial navigation platforms, into forms that can be imported into the Brainlab neurosurgical navigation platform (Brainlab AG, Munich, Germany). The externally created tractography images and delineations can be viewed and manipulated as if they were created by Brainlab. We illustrate how two surgical workups, created using open-source tools and different processing choices can be presented to the neurosurgeon who can evaluate the impact of the differences between the two workups on surgical decisions.ConclusionKarawun allows researchers developing novel imaging methodologies to display their results in environments that are familiar to clinical end-users, especially neurosurgeons, thus assisting translation of research into clinical practice.

scholarly journals CaImAn an open source tool for scalable calcium imaging data analysis

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrea Giovannucci ◽  
Johannes Friedrich ◽  
Pat Gunn ◽  
Jérémie Kalfon ◽  
Brandon L Brown ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Calcium Imaging ◽  
High Performance ◽  
Human Performance ◽  
Streaming Data ◽  
Imaging Data ◽  
Two Photon ◽  
Real Time Analysis

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

scholarly journals Minimizing the Computational Effort to Optimize Solar Concentrators with the Open-Source Tools SunPATH and Tonatiuh++

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4412
Author(s):  
Manuel J. Blanco ◽  
Victor Grigoriev ◽  
Kypros Milidonis ◽  
George Tsouloupas ◽  
Miguel Larrañeta ◽  
...  
Keyword(s):  
Open Source ◽  
Time Domain ◽  
High Performance ◽  
Software Tool ◽  
Spatial Domain ◽  
Computational Effort ◽  
Test Case ◽  
Optical Efficiency ◽  
The Time Domain

Integrals that are of interest in the analysis, design, and optimization of concentrating solar thermal systems (CST), such as the annual optical efficiency of the light collection and concentration (LCC) subsystem, can be accurately computed or estimated in two distinct ways: on the time domain and on the spatial domain. This article explores these two ways, using a case study that is highly representative of the commercial CST systems being deployed worldwide. In the time domain, the computation of these integrals are explored using 1-min, 10-min, and 1-h solar DNI input data and using The Cyprus Institute (CyI)’s High-Performance Computing (HPC) system and an open-source ray tracer, Tonatiuh++, being actively developed at CyI. In the spatial domain, the computation of these integrals is explored using SunPATH, another open-source software tool being actively developed at CyI, in tandem with Tonatiuh++. The comparison between the time and spatial domain approach clearly indicate that the spatial domain approach using SunPATH is dramatically more computationally efficient than the time domain approach. According to the results obtained, at least for the case study analyzed in this article, to compute the annual energy delivered by the LCC subsystem with a relative error less than 0.1%, it is enough to provide SunPATH with 1-h DNI data as input, request from SunPATH the sun position and weights of just 30 points in the celestial sphere, and run Tonatiuh++ to simulate these 30 points using 15 million rays per run. As the test case is highly representative, it is expected that this approach will yield similar results for most CST systems of interest.

scholarly journals Characterization of Metabolites of Leonurine (SCM-198) in Rats after Oral Administration by Liquid Chromatography/Tandem Mass Spectrometry and NMR Spectrometry

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Qing Zhu ◽  
Jinlian Zhang ◽  
Ping Yang ◽  
Bo Tan ◽  
Xinhua Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
High Performance ◽  
Therapeutic Potential ◽  
Software Tool ◽  
Gradient Elution ◽  
Tandem Mass ◽  
Two Phase

Leonurine, a major bioactive component fromHerba Leonuri, shows therapeutic potential for cardiovascular disease and stroke prevention in some preclinical experiments. The aim of this study is to characterize metabolites of leonurine in rats using high performance liquid chromatography coupled with tandem mass spectrometry (HPLC/MS/MS). The chromatographic separation was performed on an Agilent ZORBAX SB-C18 column using a gradient elution with acetonitrile/ammonium acetate buffer (10 mM, pH 4.0) solvent system. An information dependent acquisition (IDA) method was developed for screening and identifying metabolites of leonurine under positive ion mode. Compared with control, the interesting compound in the extracted ion chromatogram (XIC) of thein vivosamples was chosen and further identified by analyzing their retention times, changes in observed mass (Δm/z), and spectral patterns of product ion utilizing advanced software tool. For the first time, a total of three metabolites were identified, including two phase II metabolites generated by glucuronidation (M1) and sulfation (M2) and one phase I metabolite formed by O-demethylation (M3). Finally, the lead metabolite M1 was isolated from urine and its structure was characterized as leonurine-10-O-β-D-glucuronide by NMR spectroscopy (1H,13C, HMBC, and HSQC).

scholarly journals Visual Pathway Study Using In Vivo Diffusion Tensor Imaging Tractography to Complement Classic Anatomy

2011 ◽  
Vol 70 (suppl_1) ◽  
pp. ons145-ons156 ◽  
Author(s):  
Wentao Wu ◽  
Laura Rigolo ◽  
Lauren J. O'Donnell ◽  
Isaiah Norton ◽  
Sargent Shriver ◽  
...  
Keyword(s):  
Diffusion Tensor Imaging ◽  
Diffusion Tensor ◽  
Diffusion Imaging ◽  
Visual Pathways ◽  
Brain Anatomy ◽  
3 Dimensional ◽  
Complementary Method ◽  
The Individual ◽  
Diffusion Tensor Imaging Tractography

Abstract BACKGROUND: Knowledge of the individual course of the optic radiations (ORs) is important to avoid postoperative visual deficits. Cadaveric studies of the visual pathways are limited because it has not been possible to separate the OR from neighboring tracts accurately and results may not apply to individual patients. Diffusion tensor imaging studies may be able to demonstrate the relationships between the OR and neighboring fibers in vivo in individual subjects. OBJECTIVE: To use diffusion tensor imaging tractography to study the OR and the Meyer loop (ML) anatomy in vivo. METHODS: Ten healthy subjects underwent magnetic resonance imaging with diffusion imaging at 3 T. With the use of a fiducial-based diffusion tensor imaging tractography tool (Slicer 3.3), seeds were placed near the lateral geniculate nucleus to reconstruct individual visual pathways and neighboring tracts. Projections of the ORs onto 3-dimensional brain models were shown individually to quantify relationships to key landmarks. RESULTS: Two patterns of visual pathways were found. The OR ran more commonly deep in the whole superior and middle temporal gyri and superior temporal sulcus. The OR was closely surrounded in all cases by an inferior longitudinal fascicle and a parieto/occipito/temporo-pontine fascicle. The mean left and right distances between the tip of the OR and temporal pole were 39.8 ± 3.8 and 40.6 ± 5.7 mm, respectively. CONCLUSION: Diffusion tensor imaging tractography provides a practical complementary method to study the OR and the Meyer loop anatomy in vivo with reference to individual 3-dimensional brain anatomy.

scholarly journals CalmAn: An open source tool for scalable Calcium Imaging data Analysis

2018 ◽  
Author(s):  
Andrea Giovannucci ◽  
Johannes Friedrich ◽  
Pat Gunn ◽  
Jérémie Kalfon ◽  
Sue Ann Koay ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Calcium Imaging ◽  
High Performance ◽  
Human Performance ◽  
Ground Truth ◽  
Streaming Data ◽  
Imaging Data ◽  
Two Photon

AbstractAdvances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

scholarly journals Optimal Short-Time Acquisition Schemes in High Angular Resolution Diffusion-Weighted Imaging

2013 ◽  
Vol 2013 ◽  
pp. 1-17 ◽  
Author(s):  
V. Prčkovska ◽  
H. C. Achterberg ◽  
M. Bastiani ◽  
P. Pullens ◽  
E. Balmashnova ◽  
...  
Keyword(s):  
High Performance ◽  
Angular Resolution ◽  
Diffusion Imaging ◽  
High Angular Resolution ◽  
Brain Scans ◽  
Reconstruction Methods ◽  
Pdf Estimation ◽  
Non Gaussian ◽  
Short Time

This work investigates the possibilities of applying high-angular-resolution-diffusion-imaging- (HARDI-) based methods in a clinical setting by investigating the performance of non-Gaussian diffusion probability density function (PDF) estimation for a range ofb-values and diffusion gradient direction tables. It does so at realistic SNR levels achievable in limited time on a high-performance 3T system for the whole human brainin vivo. We use both computational simulations andin vivobrain scans to quantify the angular resolution of two selected reconstruction methods: Q-ball imaging and the diffusion orientation transform. We propose a new analytical solution to the ODF derived from the DOT. Both techniques are analytical decomposition approaches that require identical acquisition and modest postprocessing times and, given the proposed modifications of the DOT, can be analyzed in a similar fashion. We find that an optimal HARDI protocol given a stringent time constraint (<10 min) combines a moderateb-value (around 2000 s/mm2) with a relatively low number of acquired directions (>48). Our findings generalize to other methods and additional improvements in MR acquisition techniques.

Click Chemistry Expedited Radiosynthesis: Sulfur [18F]fluoride Exchange of Aryl Fluorosulfates

2019 ◽  
Author(s):  
Qinheng Zheng ◽  
Hongtao Xu ◽  
Hua Wang ◽  
Wen-Ge Han Du ◽  
Nan Wang ◽  
...  
Keyword(s):  
Click Chemistry ◽  
High Performance ◽  
Isotopic Exchange ◽  
Tumor Imaging ◽  
Radiochemical Yield ◽  
Exchange Method ◽  
Molar Activity ◽  
Positron Emission ◽  
Sulfur Fluoride

The lack of simple, efficient [<sup>18</sup>F]fluorination processes and new target-specific organofluorine probes remains the major challenge of fluorine-18-based positron emission tomography (PET). We report here a fast isotopic exchange method for the radiosynthesis of aryl [<sup>18</sup>F]fluorosulfate based PET agents enabled by the emerging sulfur fluoride exchange (SuFEx) click chemistry. The method has been applied to the fully-automated <sup>18</sup>F-radiolabeling of twenty-five structurally diverse aryl fluorosulfates with excellent radiochemical yield (83–100%) and high molar activity (up to 281 GBq µmol<sup>–1</sup>) at room temperature in 30 seconds. The purification of radiotracers requires no time-consuming high-performance liquid chromatography (HPLC), but rather a simple cartridge filtration. The utility of aryl [<sup>18</sup>F]fluorosulfate is demonstrated by the <i>in vivo</i> tumor imaging by targeting poly(ADP-ribose) polymerase 1 (PARP1).

Evaluation of New 99mTc(CO)3 + Radiolabeled Glycylglycine In Vivo

2019 ◽  
Vol 19 (11) ◽  
pp. 1382-1387
Author(s):  
Ahmet M. Şenışık ◽  
Çiğdem İçhedef ◽  
Ayfer Y. Kılçar ◽  
Eser Uçar ◽  
Kadir Arı ◽  
...  
Keyword(s):  
High Performance ◽  
The Body ◽  
Biological Behavior ◽  
In Vivo Evaluation ◽  
Radiolabeled Peptides ◽  
Tumor Bearing ◽  
Biodistribution Data ◽  
Good Accordance ◽  
Rapid Clearance

Background: Peptide-based agents are used in molecular imaging due to their unique properties, such as rapid clearance from the circulation, high affinity and target selectivity. Many of the radiolabeled peptides have been clinically experienced with diagnostic accuracy. The aim of this study was to investigate in vivo biological behavior of [99mTc(CO)3(H2O)3]+ radiolabeled glycylglycine (GlyGly). Methods: Glycylglycine was radiolabeled with a high radiolabeling yield of 94.69±2%, and quality control of the radiolabeling process was performed by thin layer radiochromatography (TLRC) and High-Performance Liquid Radiochromatography (HPLRC). Lipophilicity study for radiolabeled complex (99mTc(CO)3-Gly-Gly) was carried out using solvent extraction. The in vivo evaluation was performed by both biodistribution and SPECT imaging. Results: The high radiolabelling yield of 99mTc(CO)3-GlyGly was obtained and verified by TLRC and HPLRC as well. According to the in vivo results, SPECT images and biodistribution data are in good accordance. The excretion route from the body was both hepatobiliary and renal. Conclusion: This study shows that 99mTc(CO)3-GlyGly has the potential to be used as a peptide-based imaging agent. Further studies, 99mTc(CO)3-GlyGly can be performed on tumor-bearing animals.

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