Fijiyama: A registration tool for 3D multimodal time-lapse imaging

Fernandez Romain, Moisy Cédric. 2021. Fijiyama: A registration tool for 3D multimodal time-lapse imaging. Bioinformatics, 37 (10) : 1482-1484.

Url - jeu de données - Entrepôt autre : https://doi.org/10.5281/zenodo.3695736

Quartile : Q1, Sujet : BIOCHEMICAL RESEARCH METHODS / Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY

Résumé : The increasing interest of animal and plant research communities for biomedical 3D imaging devices results in the emergence of new topics. The anatomy, structure and function of tissues can be observed non-destructively in time-lapse multimodal imaging experiments by combining the outputs of imaging devices such as X-ray CT and MRI scans. However, living samples cannot remain in these devices for a long period. Manual positioning and natural growth of the living samples induce variations in the shape, position and orientation in the acquired images that require a preprocessing step of 3D registration prior to analyses. This registration step becomes more complex when combining observations from devices that highlight various tissue structures. Identifying image invariants over modalities is challenging and can result in intractable problems. Fijiyama, a Fiji plugin built upon biomedical registration algorithms, is aimed at non-specialists to facilitate automatic alignment of 3D images acquired either at successive times and/or with different imaging systems. Its versatility was assessed on four case studies combining multimodal and time series data, spanning from micro to macro scales.

Mots-clés Agrovoc : imagerie, traitement d'images, analyse de tissus, imagerie par résonance magnétique, analyse de séries chronologiques, bioinformatique

Mots-clés libres : Image registration, Time-lapse imaging, Vineyard, Image processing, Software

Classification Agris : U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : CTS 7 (2019-) - Hors champs stratégiques

Agences de financement hors UE : Ministère de l'Agriculture et de l'Alimentation, France AgriMer, Comité National des Interprofessions des Vins à Appellation d'Origine, Agropolis Fondation

Auteurs et affiliations

• Fernandez Romain, CIRAD-BIOS-UMR AGAP (FRA) - auteur correspondant
• Moisy Cédric, IFV (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/599031/)

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