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ex vivo diffusion mri  (Bruker Corporation)


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    Structured Review

    Bruker Corporation ex vivo diffusion mri
    (A) A view of the [ t − 1 , t + 1 ] layers of a deep feed forward neural network h V , E , σ , w . The input layer (left) is parsed against a “hidden” layer (middle) trained on annotated datasets, which corresponds to the correct output node depending on the weights obtained for each node. (B) The network architecture we propose for use in parameter estimation <t>from</t> <t>diffusion</t> <t>MRI</t> data, h v 0 ; H . In contrast to the traditional feed‐forward neural network, the weightings are checked against the preset test matrix of possible contributing signals. The weights given to each entry of this solution space are then used to generate the corresponding output node. This architecture is theoretically generalizable to any single‐ or multitensor representation of the diffusion MR signal.
    Ex Vivo Diffusion Mri, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 97/100, based on 3081 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/diffusion+mri/Diffusion/pmc12862189-178-1-16
    Average 97 stars, based on 3081 article reviews
    ex vivo diffusion mri - by Bioz Stars, 2026-09
    97/100 stars

    Images

    1) Product Images from "Accelerated Diffusion Basis Spectrum Imaging With Tensor Computations"

    Article Title: Accelerated Diffusion Basis Spectrum Imaging With Tensor Computations

    Journal: Human Brain Mapping

    doi: 10.1002/hbm.70460

    (A) A view of the [ t − 1 , t + 1 ] layers of a deep feed forward neural network h V , E , σ , w . The input layer (left) is parsed against a “hidden” layer (middle) trained on annotated datasets, which corresponds to the correct output node depending on the weights obtained for each node. (B) The network architecture we propose for use in parameter estimation from diffusion MRI data, h v 0 ; H . In contrast to the traditional feed‐forward neural network, the weightings are checked against the preset test matrix of possible contributing signals. The weights given to each entry of this solution space are then used to generate the corresponding output node. This architecture is theoretically generalizable to any single‐ or multitensor representation of the diffusion MR signal.
    Figure Legend Snippet: (A) A view of the [ t − 1 , t + 1 ] layers of a deep feed forward neural network h V , E , σ , w . The input layer (left) is parsed against a “hidden” layer (middle) trained on annotated datasets, which corresponds to the correct output node depending on the weights obtained for each node. (B) The network architecture we propose for use in parameter estimation from diffusion MRI data, h v 0 ; H . In contrast to the traditional feed‐forward neural network, the weightings are checked against the preset test matrix of possible contributing signals. The weights given to each entry of this solution space are then used to generate the corresponding output node. This architecture is theoretically generalizable to any single‐ or multitensor representation of the diffusion MR signal.

    Techniques Used: Diffusion-based Assay

    Axial slices of DBSI and DBSIpy analysis of one representative ex vivo mouse diffusion MRI data. Note that as the b 0 SNR degrades, features in the DBSIpy estimated parameter maps retain good conspicuity. Qualitatively, DBSI parameter maps lack the same contrast‐to‐noise as their DBSIpy counterparts even in the high‐SNR regime. Furthermore, the DBSI parameter maps match or exceed the loss in quality observed in the input data.
    Figure Legend Snippet: Axial slices of DBSI and DBSIpy analysis of one representative ex vivo mouse diffusion MRI data. Note that as the b 0 SNR degrades, features in the DBSIpy estimated parameter maps retain good conspicuity. Qualitatively, DBSI parameter maps lack the same contrast‐to‐noise as their DBSIpy counterparts even in the high‐SNR regime. Furthermore, the DBSI parameter maps match or exceed the loss in quality observed in the input data.

    Techniques Used: Ex Vivo, Diffusion-based Assay

    Related Articles

    Diffusion-based Assay:

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering
    Article Snippet: .. Diffusion MRI For diffusion MRI-scanning of the fixed mouse brain, we used a 9.4T Bruker scanner with a volume resonator for transmission and a receive surface cryo-coil. ..

    Article Title: Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability
    Article Snippet: They were immersed in 0.1M PBS for at least 120 hours before imaging and transferred to Fomblin (Fomblin Profludropolyether; Ausimont, Thorofare, NJ) just before imaging. .. Diffusion MRI were acquired on a Bruker BioSpin 4.7 T MRI (Bruker) machine for each sample using a 3D multiple spin echo diffusion tensor sequence (b=1000s/mm 2 ; 30 directions) with the following parameters: repetition time=0.7s; echo time=32.5ms. ..

    Article Title: pTx‐Pulseq in hybrid sequences: Accessible and advanced hybrid open‐source MRI sequences on Philips scanners
    Article Snippet: .. Consequently, advanced sequences have been developed in Pulseq and made available through GitHub, such as “Pulseq‐CEST” for chemical exchange saturation transfer MRI and “PulseqDiffusion” for diffusion MRI., Pulseq has previously been supported by four MRI vendors (Siemens, Bruker, GE, and United Imaging) that allow for either high‐level translation of Pulseq into their native MRI sequence format or internally function similar enough to make an interpreter possible., , Philips MRI scanners, however, use a distinct platform that leverages the repetitive nature of pulse sequences, which historically limited direct Pulseq integration. ..

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d -Het and 3 Tfap2d -KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence ( b = 1,500 s mm −2 ; 30 directions) with the following parameters : repetition time = 1,250 ms; echo time = 26 ms. ..

    Article Title: Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer’s Disease Continuum
    Article Snippet: .. Diffusion MRI was acquired using an 11.7-Tesla NMR spectrometer (Bruker Biospin, Billerica, MA, USA). .. A single-channel 30 mm Bruker volume coil was used for both radio frequency transmission and reception.

    Article Title: The subcommissural organ regulates brain development via secreted peptides.
    Article Snippet: .. Diffusion MRI Used Not used 4 n atu re p o rtfo lio | rep o rtin g su m m ary M a rc h 2 0 2 1 Preprocessing Preprocessing software Paravision 5.1 software (Bruker BioSpin) and a Linux PC running Topspin 2.0 provided the user interface. ..

    Article Title: Using temperature to analyze the neural basis of a time-based decision.
    Article Snippet: The basal ganglia are thought to contribute to decision-making and motor control.. These functions are critically dependent on timing information, which can be extracted from the evolving state of neural populations in their main input structure, the striatum.. However, it is debated whether striatal activity underlies latent, dynamic decision processes or kinematics of overt movement.

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits.
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d-Het and 3 Tfap2d-KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence (b = 1,500 s mm−2; 30 directions) with the following parameters62: repetition time = 1,250 ms; echo time = 26 ms. ..

    Magnetic Resonance Imaging:

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering
    Article Snippet: .. Diffusion MRI For diffusion MRI-scanning of the fixed mouse brain, we used a 9.4T Bruker scanner with a volume resonator for transmission and a receive surface cryo-coil. ..

    Article Title: Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability
    Article Snippet: They were immersed in 0.1M PBS for at least 120 hours before imaging and transferred to Fomblin (Fomblin Profludropolyether; Ausimont, Thorofare, NJ) just before imaging. .. Diffusion MRI were acquired on a Bruker BioSpin 4.7 T MRI (Bruker) machine for each sample using a 3D multiple spin echo diffusion tensor sequence (b=1000s/mm 2 ; 30 directions) with the following parameters: repetition time=0.7s; echo time=32.5ms. ..

    Article Title: pTx‐Pulseq in hybrid sequences: Accessible and advanced hybrid open‐source MRI sequences on Philips scanners
    Article Snippet: .. Consequently, advanced sequences have been developed in Pulseq and made available through GitHub, such as “Pulseq‐CEST” for chemical exchange saturation transfer MRI and “PulseqDiffusion” for diffusion MRI., Pulseq has previously been supported by four MRI vendors (Siemens, Bruker, GE, and United Imaging) that allow for either high‐level translation of Pulseq into their native MRI sequence format or internally function similar enough to make an interpreter possible., , Philips MRI scanners, however, use a distinct platform that leverages the repetitive nature of pulse sequences, which historically limited direct Pulseq integration. ..

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d -Het and 3 Tfap2d -KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence ( b = 1,500 s mm −2 ; 30 directions) with the following parameters : repetition time = 1,250 ms; echo time = 26 ms. ..

    Article Title: Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer’s Disease Continuum
    Article Snippet: .. Diffusion MRI was acquired using an 11.7-Tesla NMR spectrometer (Bruker Biospin, Billerica, MA, USA). .. A single-channel 30 mm Bruker volume coil was used for both radio frequency transmission and reception.

    Article Title: The subcommissural organ regulates brain development via secreted peptides.
    Article Snippet: .. Diffusion MRI Used Not used 4 n atu re p o rtfo lio | rep o rtin g su m m ary M a rc h 2 0 2 1 Preprocessing Preprocessing software Paravision 5.1 software (Bruker BioSpin) and a Linux PC running Topspin 2.0 provided the user interface. ..

    Article Title: Using temperature to analyze the neural basis of a time-based decision.
    Article Snippet: The basal ganglia are thought to contribute to decision-making and motor control.. These functions are critically dependent on timing information, which can be extracted from the evolving state of neural populations in their main input structure, the striatum.. However, it is debated whether striatal activity underlies latent, dynamic decision processes or kinematics of overt movement.

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits.
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d-Het and 3 Tfap2d-KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence (b = 1,500 s mm−2; 30 directions) with the following parameters62: repetition time = 1,250 ms; echo time = 26 ms. ..

    Transmission Assay:

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering
    Article Snippet: .. Diffusion MRI For diffusion MRI-scanning of the fixed mouse brain, we used a 9.4T Bruker scanner with a volume resonator for transmission and a receive surface cryo-coil. ..

    Sequencing:

    Article Title: Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability
    Article Snippet: They were immersed in 0.1M PBS for at least 120 hours before imaging and transferred to Fomblin (Fomblin Profludropolyether; Ausimont, Thorofare, NJ) just before imaging. .. Diffusion MRI were acquired on a Bruker BioSpin 4.7 T MRI (Bruker) machine for each sample using a 3D multiple spin echo diffusion tensor sequence (b=1000s/mm 2 ; 30 directions) with the following parameters: repetition time=0.7s; echo time=32.5ms. ..

    Article Title: pTx‐Pulseq in hybrid sequences: Accessible and advanced hybrid open‐source MRI sequences on Philips scanners
    Article Snippet: .. Consequently, advanced sequences have been developed in Pulseq and made available through GitHub, such as “Pulseq‐CEST” for chemical exchange saturation transfer MRI and “PulseqDiffusion” for diffusion MRI., Pulseq has previously been supported by four MRI vendors (Siemens, Bruker, GE, and United Imaging) that allow for either high‐level translation of Pulseq into their native MRI sequence format or internally function similar enough to make an interpreter possible., , Philips MRI scanners, however, use a distinct platform that leverages the repetitive nature of pulse sequences, which historically limited direct Pulseq integration. ..

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d -Het and 3 Tfap2d -KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence ( b = 1,500 s mm −2 ; 30 directions) with the following parameters : repetition time = 1,250 ms; echo time = 26 ms. ..

    Article Title: Specification of claustro-amygdalar and palaeocortical neurons and circuits.
    Article Snippet: Nine postmortem mouse brains (3 wild-type control, 3 Tfap2d-Het and 3 Tfap2d-KO) were perfusion-fixed in with 4% paraformaldehyde solution in 0.1 M PBS for 24 h. Following perfusion–fixation, mouse brains were immersed and stored in 0.1 M PBS for 24 h and were transferred to Fomblin (SPI Supplies 69991-67-9) just before imaging. .. Diffusion MRI was acquired on a BioSpin 9.4 T MRI (Bruker) machine for each subject using a 3D echo-planner-imaging diffusion sequence (b = 1,500 s mm−2; 30 directions) with the following parameters62: repetition time = 1,250 ms; echo time = 26 ms. ..

    Imaging:

    Article Title: pTx‐Pulseq in hybrid sequences: Accessible and advanced hybrid open‐source MRI sequences on Philips scanners
    Article Snippet: .. Consequently, advanced sequences have been developed in Pulseq and made available through GitHub, such as “Pulseq‐CEST” for chemical exchange saturation transfer MRI and “PulseqDiffusion” for diffusion MRI., Pulseq has previously been supported by four MRI vendors (Siemens, Bruker, GE, and United Imaging) that allow for either high‐level translation of Pulseq into their native MRI sequence format or internally function similar enough to make an interpreter possible., , Philips MRI scanners, however, use a distinct platform that leverages the repetitive nature of pulse sequences, which historically limited direct Pulseq integration. ..

    Nuclear Magnetic Resonance:

    Article Title: Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer’s Disease Continuum
    Article Snippet: .. Diffusion MRI was acquired using an 11.7-Tesla NMR spectrometer (Bruker Biospin, Billerica, MA, USA). .. A single-channel 30 mm Bruker volume coil was used for both radio frequency transmission and reception.

    Software:

    Article Title: The subcommissural organ regulates brain development via secreted peptides.
    Article Snippet: .. Diffusion MRI Used Not used 4 n atu re p o rtfo lio | rep o rtin g su m m ary M a rc h 2 0 2 1 Preprocessing Preprocessing software Paravision 5.1 software (Bruker BioSpin) and a Linux PC running Topspin 2.0 provided the user interface. ..

    Article Title: Using temperature to analyze the neural basis of a time-based decision.
    Article Snippet: The basal ganglia are thought to contribute to decision-making and motor control.. These functions are critically dependent on timing information, which can be extracted from the evolving state of neural populations in their main input structure, the striatum.. However, it is debated whether striatal activity underlies latent, dynamic decision processes or kinematics of overt movement.



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    Image Search Results


    (A) A view of the [ t − 1 , t + 1 ] layers of a deep feed forward neural network h V , E , σ , w . The input layer (left) is parsed against a “hidden” layer (middle) trained on annotated datasets, which corresponds to the correct output node depending on the weights obtained for each node. (B) The network architecture we propose for use in parameter estimation from diffusion MRI data, h v 0 ; H . In contrast to the traditional feed‐forward neural network, the weightings are checked against the preset test matrix of possible contributing signals. The weights given to each entry of this solution space are then used to generate the corresponding output node. This architecture is theoretically generalizable to any single‐ or multitensor representation of the diffusion MR signal.

    Journal: Human Brain Mapping

    Article Title: Accelerated Diffusion Basis Spectrum Imaging With Tensor Computations

    doi: 10.1002/hbm.70460

    Figure Lengend Snippet: (A) A view of the [ t − 1 , t + 1 ] layers of a deep feed forward neural network h V , E , σ , w . The input layer (left) is parsed against a “hidden” layer (middle) trained on annotated datasets, which corresponds to the correct output node depending on the weights obtained for each node. (B) The network architecture we propose for use in parameter estimation from diffusion MRI data, h v 0 ; H . In contrast to the traditional feed‐forward neural network, the weightings are checked against the preset test matrix of possible contributing signals. The weights given to each entry of this solution space are then used to generate the corresponding output node. This architecture is theoretically generalizable to any single‐ or multitensor representation of the diffusion MR signal.

    Article Snippet: The ex vivo diffusion MRI experiments conducted for this work were performed on a 9.4 T Bruker BioSpec small‐animal MRI system equipped with a volume transmitter coil (RF RES 400 1H 112/086 QSN TO AD) and a H 2 × 2 mouse brain surface array receiver coil (RF ARR 400 1H M.BR.

    Techniques: Diffusion-based Assay

    Axial slices of DBSI and DBSIpy analysis of one representative ex vivo mouse diffusion MRI data. Note that as the b 0 SNR degrades, features in the DBSIpy estimated parameter maps retain good conspicuity. Qualitatively, DBSI parameter maps lack the same contrast‐to‐noise as their DBSIpy counterparts even in the high‐SNR regime. Furthermore, the DBSI parameter maps match or exceed the loss in quality observed in the input data.

    Journal: Human Brain Mapping

    Article Title: Accelerated Diffusion Basis Spectrum Imaging With Tensor Computations

    doi: 10.1002/hbm.70460

    Figure Lengend Snippet: Axial slices of DBSI and DBSIpy analysis of one representative ex vivo mouse diffusion MRI data. Note that as the b 0 SNR degrades, features in the DBSIpy estimated parameter maps retain good conspicuity. Qualitatively, DBSI parameter maps lack the same contrast‐to‐noise as their DBSIpy counterparts even in the high‐SNR regime. Furthermore, the DBSI parameter maps match or exceed the loss in quality observed in the input data.

    Article Snippet: The ex vivo diffusion MRI experiments conducted for this work were performed on a 9.4 T Bruker BioSpec small‐animal MRI system equipped with a volume transmitter coil (RF RES 400 1H 112/086 QSN TO AD) and a H 2 × 2 mouse brain surface array receiver coil (RF ARR 400 1H M.BR.

    Techniques: Ex Vivo, Diffusion-based Assay