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

Morales, Juan and Alonso Nanclares, Lidia and Rodrigo Rodriguez, Jose and Felipe Oroquieta, Javier de and Rodriguez Herrero, Agustin and Merchan Perez, Angel (2011). ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images. "Frontiers Neuroanatomy", v. 5 (n. 18); pp. 5-18. ISSN 1662-5129. https://doi.org/10.3389/fnana.2011.00018.

Description

Title: ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images
Author/s:
  • Morales, Juan
  • Alonso Nanclares, Lidia
  • Rodrigo Rodriguez, Jose
  • Felipe Oroquieta, Javier de
  • Rodriguez Herrero, Agustin
  • Merchan Perez, Angel
Item Type: Article
Título de Revista/Publicación: Frontiers Neuroanatomy
Date: 2011
ISSN: 1662-5129
Volume: 5
Subjects:
Faculty: E.T.S.I. y Sistemas de Telecomunicación (UPM)
Department: Sistemas Electrónicos y de Control [hasta 2014]
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

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 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope 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 3D 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.

More information

Item ID: 13671
DC Identifier: http://oa.upm.es/13671/
OAI Identifier: oai:oa.upm.es:13671
DOI: 10.3389/fnana.2011.00018
Official URL: http://www.frontiersin.org/Neuroanatomy/10.3389/fnana.2011.00018/abstract
Deposited by: Memoria Investigacion
Deposited on: 10 Oct 2012 10:44
Last Modified: 07 Apr 2019 10:25
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