title: For3D: Full organ reconstruction in 3D, an automatized tool for deciphering the complexity of lymphoid organs.
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.
authors.affiliation: Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Université UM105, France. Electronic address: arnauld.serge@univ-amu.fr.
authors.forename: Arnauld
authors.initials: A
authors.lastname: Sergé
authors.affiliation: Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Université UM105, France.
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Bailly
authors.affiliation: Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Université UM105, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Aurrand-Lions
authors.affiliation: Centre Médical Universitaire, Département Pathologie et Immunologie, Faculté de Médecine, Université de Genève, 1, rue Michel Servet, 1211 Genève, Switzerland.
authors.forename: Beat A
authors.initials: BA
authors.lastname: Imhof
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Inserm U1104, CNRS UMR7280, Aix-Marseille Université UM2, France. Electronic address: magali.irla@inserm.fr.
authors.forename: Magali
authors.initials: M
authors.lastname: Irla
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008198:Lymph Nodes; D008221:Lymphoid Tissue / Q000033:anatomy & histology*; D051379:Mice; D009369:Neoplasms / Q000098:blood supply / Q000473:pathology; D009389:Neovascularization, Pathologic / Q000473:pathology; D013950:Thymus Gland / Q000033:anatomy & histology
keywords: 3D reconstruction; Image processing; Lymph node; Organ topology; Primary lymphoid tumor; Thymus