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custom-built, semi-automated analysis tool coded in  (MathWorks Inc)


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    MathWorks Inc custom-built, semi-automated analysis tool coded in
    Custom Built, Semi Automated Analysis Tool Coded In, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/-coded+custom+tool/pmc05064019-196-15-20
    Average 90 stars, based on 1 article reviews
    custom-built, semi-automated analysis tool coded in - by Bioz Stars, 2026-09
    90/100 stars

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    Article Title: Quantitative abdominal sodium MRI combined with 32-channel proton pTx MRI at 7 Tesla in a large field-of-view.
    Article Snippet: Quantitative 23Na images were calculated with a semi-automated segmentation tool, self-developed in Matlab (The MathWorks Inc., Natick, MA, USA, Version R2024b) using the known concentration in the reference vials and interpolation based on a linear regression fit.

    Article Title: Semi-Automated Analysis of 4D Flow MRI to Assess the Hemodynamic Impact of Intracranial Atherosclerotic Disease
    Article Snippet: 4D flow MRI data was corrected for noise and eddy currents ( 41 , 47 , 48 ), and a 3D PC MR angiogram (PCMRA) was created using pseudo-complex difference algorithm ( 49 ) ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2. caption a7 4D flow MRI quantification including (a) segmentation of PCMRA, (b) segmentation of 3D TOF MRA registered with PCMRA, (c) centerline of major arteries of the CoW, (d) automated placement of multiple 2D analysis planes perpendicular to centerlines, (e) segmentation of lumen on TOF MRA and velocity profile at a 2D plane, (f) schematic 4D flow MRI test result showing median and interquartile range (IQR) of area and flow rate as well as maximum peak velocity of each major artery of the CoW, and (g) schematic diagram of the stenosis showing the location of two planes that were used to quantify velocity and area for pressure drop estimation Semi-automated Flow Analysis A novel in-house semi-automated analysis tool was developed in MATLAB (MathWorks, MA, USA) for volumetric quantification of 4D flow MRI using a centerline processing scheme ( 50 ).

    Article Title: A self-organized synthetic morphogenic liposome responds with shape changes to local light cues.
    Article Snippet: The defined protein concentration in the bulk was used to calculate the protein densities on the membrane using a semi-automated tool in Matlab MathWorks, Natick, U.S.

    Article Title: A self-organized synthetic morphogenic liposome responds with shape changes to local light cues
    Article Snippet: The defined protein concentration in the bulk was used to calculate the protein densities on the membrane using a semi-automated tool in Matlab MathWorks, Natick, U.S.A.) .

    Article Title: Semi-Automated Analysis of 4D Flow MRI to Assess the Hemodynamic Impact of Intracranial Atherosclerotic Disease
    Article Snippet: Flow Analysis 4D flow MRI data was corrected for noise and eddy currents ( 41 , 47 , 48 ), and a 3D PC MR angiogram (PCMRA) was created using pseudo-complex difference algorithm ( 49 ) ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2. caption a7 4D flow MRI quantification including (a) segmentation of PCMRA, (b) segmentation of 3D TOF MRA registered with PCMRA, (c) centerline of major arteries of the CoW, (d) automated placement of multiple 2D analysis planes perpendicular to centerlines, (e) segmentation of lumen on TOF MRA and velocity profile at a 2D plane, (f) schematic 4D flow MRI test result showing median and interquartile range (IQR) of area and flow rate as well as maximum peak velocity of each major artery of the CoW, and (g) schematic diagram of the stenosis showing the location of two planes that were used to quantify velocity and area for pressure drop estimation Semi-automated Flow Analysis A novel in-house semi-automated analysis tool was developed in MATLAB (MathWorks, MA, USA) for volumetric quantification of 4D flow MRI using a centerline processing scheme ( 50 ).

    Magnetic Resonance Imaging:

    Article Title: Semi-Automated Analysis of 4D Flow MRI to Assess the Hemodynamic Impact of Intracranial Atherosclerotic Disease
    Article Snippet: .. A novel in-house semi-automated analysis tool was developed in MATLAB (MathWorks, MA, USA) for volumetric quantification of 4D flow MRI using a centerline processing scheme ( 50 ). ..



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    We developed two approaches (AD-ADOLC and AD-Recorder) to make an OpenSim function F and its forward ( F fwd ) and reverse ( F rev ) directional derivatives available within the CasADi environment for use by the NLP solver during the optimization. In the AD-ADOLC approach (top), ADOL-C’s algorithms are used in a C++ code to provide F fwd and F rev . In the AD-Recorder approach (bottom), Recorder provides the expression graph of F as MATLAB source code from which CasADi’s C-code generator generates C-code containing F , F fwd , and F rev . The AD-Recorder approach combines operator overloading, when generating the expression graph, and source code transformation, when processing the expression graph to generate C-code for F , F fwd , and F rev . In both approaches, the code comprising F , F fwd , and F rev is compiled as a Dynamic-link Library (DLL), which is imported as an external function within the CasADi environment. In our application, F represents the multi-body dynamics and is called when formulating the optimal control problem. The latter is then composed into a differentiable optimal control transcription using CasADi. During the optimization, CasADi provides the NLP solver with evaluations of the NLP objective function ( nlp f ), constraints ( nlp g ), objective function gradient ( nlp grad f ), constraint Jacobian ( nlp jac g ), and Hessian of the Lagrangian ( nlp hess l ). CasADi efficiently queries F fwd and F rev to construct the full derivative matrices.

    Journal: PLoS ONE

    Article Title: Algorithmic differentiation improves the computational efficiency of OpenSim-based trajectory optimization of human movement

    doi: 10.1371/journal.pone.0217730

    Figure Lengend Snippet: We developed two approaches (AD-ADOLC and AD-Recorder) to make an OpenSim function F and its forward ( F fwd ) and reverse ( F rev ) directional derivatives available within the CasADi environment for use by the NLP solver during the optimization. In the AD-ADOLC approach (top), ADOL-C’s algorithms are used in a C++ code to provide F fwd and F rev . In the AD-Recorder approach (bottom), Recorder provides the expression graph of F as MATLAB source code from which CasADi’s C-code generator generates C-code containing F , F fwd , and F rev . The AD-Recorder approach combines operator overloading, when generating the expression graph, and source code transformation, when processing the expression graph to generate C-code for F , F fwd , and F rev . In both approaches, the code comprising F , F fwd , and F rev is compiled as a Dynamic-link Library (DLL), which is imported as an external function within the CasADi environment. In our application, F represents the multi-body dynamics and is called when formulating the optimal control problem. The latter is then composed into a differentiable optimal control transcription using CasADi. During the optimization, CasADi provides the NLP solver with evaluations of the NLP objective function ( nlp f ), constraints ( nlp g ), objective function gradient ( nlp grad f ), constraint Jacobian ( nlp jac g ), and Hessian of the Lagrangian ( nlp hess l ). CasADi efficiently queries F fwd and F rev to construct the full derivative matrices.

    Article Snippet: First, we enabled the use of AD in OpenSim through a custom source code transformation tool and through the operator overloading tool ADOL-C. Second, we developed an interface between OpenSim and CasADi to solve trajectory optimization problems.

    Techniques: Expressing, Transformation Assay, Control, Construct