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ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

Frontiers in Neuroanatomy. 2011;5 DOI 10.3389/fnana.2011.00018

 

Journal Homepage

Journal Title: Frontiers in Neuroanatomy

ISSN: 1662-5129 (Online)

Publisher: Frontiers Media S.A.

LCC Subject Category: Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry | Science: Human anatomy

Country of publisher: Switzerland

Language of fulltext: English

Full-text formats available: PDF, HTML, ePUB, XML

 

AUTHORS


Juan eMorales (Universidad Politécnica de Madrid)

Juan eMorales (Universidad Politécnica de Madrid)

Lidia eAlonso-Nanclares (Universidad Politécnica de Madrid)

Lidia eAlonso-Nanclares (CSIC)

Lidia eAlonso-Nanclares (Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas)

José-Rodrigo eRodriguez (Universidad Politécnica de Madrid)

José-Rodrigo eRodriguez (CSIC)

José-Rodrigo eRodriguez (Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas)

Javier eDefelipe (Universidad Politécnica de Madrid)

Javier eDefelipe (CSIC)

Javier eDefelipe (Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas)

Ángel eRodriguez (Universidad Politécnica de Madrid)

Angel eMerchan-Perez (Universidad Politécnica de Madrid)

Angel eMerchan-Perez (Universidad Politécnica de Madrid)

Angel eMerchan-Perez (Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas)

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 14 weeks

 

Abstract | Full Text

The synapses in the cerebral cortex can be classified into two main types, Gray’s type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze three-dimensional samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using FIB/SEM microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed and quantified from large three-dimensional tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.