FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t
Quantitative Magnetic Resonance Imaging (MRI) is a relevant technique to measure water availability and binding in animal or vegetal tissues. Among others, MRI is useful to decipher the impact of stresses on living samples (Sidi-Boulenouar et al., 2019). Reproducible measurements of anatomical and physiological changes can be obtained by quantitative mapping of biomarkers (see Figure 1-a) such as proton density (PD) and magnetization relaxation times (T1, T2) in 2D images (Borisjuk et al., 2012 ; Dusschoten et al., 2016). However, the application of quantitative MRI to 3D + t microscopic imaging is still challenging. Detection of weak signals associated with small voxels requires longer acquisition times, which favors spatial drift and tissue deformations (Han et al., 2015). In addition, low signal-to-noise ratio (SNR) environments dramatically reduce the estimation accuracy of the parameters (Raya et al., 2010). Non-specialists facing these issues with multi-echo spin-echo data may be discouraged when using available open implementations of T1-T2 relaxometry: there is a lack of a user-friendly tools capable of processing large data in a reasonable time. We propose FijiRelax, an efficient Fiji plugin for the estimation of relaxation parameter maps from 3D + t multi-echo spin-echo sequences, integrating Rician noise and spatial drift corrections. The plugin is distributed and documented as an ImageJ plugin (Plugin page), available in a graphical interface and scriptable in BeanShell to allow batch processing for high-throughput experiments.
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Subjects: | U30 - Méthodes de recherche, U10 - Informatique, mathématiques et statistiques, imagerie par résonance magnétique, cartographie, mesure (activité), eau magnétique, http://aims.fao.org/aos/agrovoc/c_36764, http://aims.fao.org/aos/agrovoc/c_1344, http://aims.fao.org/aos/agrovoc/c_4668, http://aims.fao.org/aos/agrovoc/c_35207, http://aims.fao.org/aos/agrovoc/c_2895, |
Online Access: | http://agritrop.cirad.fr/604609/ http://agritrop.cirad.fr/604609/3/Joss_rfernandez_fijirelax.pdf |
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dig-cirad-fr-6046092024-01-29T05:56:15Z http://agritrop.cirad.fr/604609/ http://agritrop.cirad.fr/604609/ FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t. Fernandez Romain, Moisy Cédric. 2023. Journal of Open Source Software, 8 (81):4981, 4 p.https://doi.org/10.21105/joss.04981 <https://doi.org/10.21105/joss.04981> FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t Fernandez, Romain Moisy, Cédric eng 2023 Journal of Open Source Software U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 Fidji http://aims.fao.org/aos/agrovoc/c_2895 Quantitative Magnetic Resonance Imaging (MRI) is a relevant technique to measure water availability and binding in animal or vegetal tissues. Among others, MRI is useful to decipher the impact of stresses on living samples (Sidi-Boulenouar et al., 2019). Reproducible measurements of anatomical and physiological changes can be obtained by quantitative mapping of biomarkers (see Figure 1-a) such as proton density (PD) and magnetization relaxation times (T1, T2) in 2D images (Borisjuk et al., 2012 ; Dusschoten et al., 2016). However, the application of quantitative MRI to 3D + t microscopic imaging is still challenging. Detection of weak signals associated with small voxels requires longer acquisition times, which favors spatial drift and tissue deformations (Han et al., 2015). In addition, low signal-to-noise ratio (SNR) environments dramatically reduce the estimation accuracy of the parameters (Raya et al., 2010). Non-specialists facing these issues with multi-echo spin-echo data may be discouraged when using available open implementations of T1-T2 relaxometry: there is a lack of a user-friendly tools capable of processing large data in a reasonable time. We propose FijiRelax, an efficient Fiji plugin for the estimation of relaxation parameter maps from 3D + t multi-echo spin-echo sequences, integrating Rician noise and spatial drift corrections. The plugin is distributed and documented as an ImageJ plugin (Plugin page), available in a graphical interface and scriptable in BeanShell to allow batch processing for high-throughput experiments. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/604609/3/Joss_rfernandez_fijirelax.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.21105/joss.04981 10.21105/joss.04981 info:eu-repo/semantics/altIdentifier/doi/10.21105/joss.04981 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.21105/joss.04981 info:eu-repo/semantics/dataset/purl/https://doi.org/10.5281/zenodo.4518730 info:eu-repo/grantAgreement/////(FRA) Utilisation d'imagerie non destructive pour un suivi dynamique de la colonisation du bois par les pathogènes responsables des maladies du bois/VITIMAGE-2024 info:eu-repo/grantAgreement/////(FRA) Advanced Plant Life Imaging and Metrology/APLIM |
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U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 http://aims.fao.org/aos/agrovoc/c_2895 U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 http://aims.fao.org/aos/agrovoc/c_2895 |
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U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 http://aims.fao.org/aos/agrovoc/c_2895 U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 http://aims.fao.org/aos/agrovoc/c_2895 Fernandez, Romain Moisy, Cédric FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
description |
Quantitative Magnetic Resonance Imaging (MRI) is a relevant technique to measure water availability and binding in animal or vegetal tissues. Among others, MRI is useful to decipher the impact of stresses on living samples (Sidi-Boulenouar et al., 2019). Reproducible measurements of anatomical and physiological changes can be obtained by quantitative mapping of biomarkers (see Figure 1-a) such as proton density (PD) and magnetization relaxation times (T1, T2) in 2D images (Borisjuk et al., 2012 ; Dusschoten et al., 2016). However, the application of quantitative MRI to 3D + t microscopic imaging is still challenging. Detection of weak signals associated with small voxels requires longer acquisition times, which favors spatial drift and tissue deformations (Han et al., 2015). In addition, low signal-to-noise ratio (SNR) environments dramatically reduce the estimation accuracy of the parameters (Raya et al., 2010). Non-specialists facing these issues with multi-echo spin-echo data may be discouraged when using available open implementations of T1-T2 relaxometry: there is a lack of a user-friendly tools capable of processing large data in a reasonable time. We propose FijiRelax, an efficient Fiji plugin for the estimation of relaxation parameter maps from 3D + t multi-echo spin-echo sequences, integrating Rician noise and spatial drift corrections. The plugin is distributed and documented as an ImageJ plugin (Plugin page), available in a graphical interface and scriptable in BeanShell to allow batch processing for high-throughput experiments. |
format |
article |
topic_facet |
U30 - Méthodes de recherche U10 - Informatique, mathématiques et statistiques imagerie par résonance magnétique cartographie mesure (activité) eau magnétique http://aims.fao.org/aos/agrovoc/c_36764 http://aims.fao.org/aos/agrovoc/c_1344 http://aims.fao.org/aos/agrovoc/c_4668 http://aims.fao.org/aos/agrovoc/c_35207 http://aims.fao.org/aos/agrovoc/c_2895 |
author |
Fernandez, Romain Moisy, Cédric |
author_facet |
Fernandez, Romain Moisy, Cédric |
author_sort |
Fernandez, Romain |
title |
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
title_short |
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
title_full |
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
title_fullStr |
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
title_full_unstemmed |
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t |
title_sort |
fijirelax: fast and noise-corrected estimation of mri relaxation maps in 3d + t |
url |
http://agritrop.cirad.fr/604609/ http://agritrop.cirad.fr/604609/3/Joss_rfernandez_fijirelax.pdf |
work_keys_str_mv |
AT fernandezromain fijirelaxfastandnoisecorrectedestimationofmrirelaxationmapsin3dt AT moisycedric fijirelaxfastandnoisecorrectedestimationofmrirelaxationmapsin3dt |
_version_ |
1792500535932223488 |