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For3D: Full organ reconstruction in 3D, an automatized tool for deciphering the complexity of lymphoid organs

Bailly, Anne-Laure
Published in Journal of immunological methods. 2015, vol. 424, p. 32-42
Abstract To decipher the complex topology of lymphoid structures, we developed an automated process called Full Organ Reconstruction in 3D (For3D). A dedicated image-processing pipeline is applied to entire collections of immunolabeled serial sections, acquired with a slide-scanning microscope. This method is automated, flexible and readily applicable in two days to frozen or paraffin-embedded organs stained by fluorescence or brightfield immunohistochemistry. 3D-reconstructed organs can be visualized, rotated and analyzed to quantify substructures of interest. Usefulness of For3D is exemplified here through topological analysis of several mouse lymphoid organs exhibiting a complex organization: (i) the thymus, composed of two compartments, a medulla intricately imbricated into a surrounding cortex, (ii) lymph nodes, also highly compartmentalized into cortex, paracortex and medulla and (iii) the vascularization of an EG7 primary thymoma. This open-source algorithm, based on ImageJ and Matlab scripts, offers a user-friendly interface and is widely applicable to any organ or tissue, hence readily adaptable to a broad range of biomedical samples.
Keywords AnimalsCell Line, TumorImage Processing, Computer-Assisted/methodsImaging, Three-Dimensional/methodsLymph NodesLymphoid Tissue/anatomy & histologyMiceNeoplasms/blood supply/pathologyNeovascularization, Pathologic/pathologyThymus Gland/anatomy & histology
PMID: 25956038
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Research group Molécules d'adhésion et processus de migration cellulaire (167)
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SERGE, Arnauld et al. For3D: Full organ reconstruction in 3D, an automatized tool for deciphering the complexity of lymphoid organs. In: Journal of immunological methods, 2015, vol. 424, p. 32-42. doi: 10.1016/j.jim.2015.04.019 https://archive-ouverte.unige.ch/unige:83906

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Deposited on : 2016-05-27

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