UNIGE document Scientific Article
previous document  unige:83906  next document
add to browser collection
Title

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

Authors
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
Identifiers
PMID: 25956038
Full text
Article (Published version) (2.8 MB) - document accessible for UNIGE members only Limited access to UNIGE
Structures
Research group Molécules d'adhésion et processus de migration cellulaire (167)
Citation
(ISO format)
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. https://archive-ouverte.unige.ch/unige:83906

113 hits

0 download

Update

Deposited on : 2016-05-27

Export document
Format :
Citation style :