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J Immunol Methods. 2015 Sep;424:32-42. doi: 10.1016/j.jim.2015.04.019. Epub 2015 May 5.

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

Author information

1
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.
2
Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Inserm U1068, CNRS UMR7258, Aix-Marseille Université UM105, France.
3
Centre Médical Universitaire, Département Pathologie et Immunologie, Faculté de Médecine, Université de Genève, 1, rue Michel Servet, 1211 Genève, Switzerland.
4
Centre d'Immunologie de Marseille-Luminy, Inserm U1104, CNRS UMR7280, Aix-Marseille Université UM2, France. Electronic address: magali.irla@inserm.fr.

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:

3D reconstruction; Image processing; Lymph node; Organ topology; Primary lymphoid tumor; Thymus

PMID:
25956038
DOI:
10.1016/j.jim.2015.04.019
[Indexed for MEDLINE]

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