ArticleFrontiers in neuroanatomy2011
Espina: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images.
Article in Frontiers in neuroanatomy, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 84 citations in OpenAlex.
- Layer-specific cellular composition of mouse primary somatosensory and human temporal cortex: a direct 3D confocal counting approach.Frontiers in neuroanatomy · 2026Article
- Neuroprotective mitochondria targeted small molecule restores synapses and the distribution of synaptic mitochondria in the hippocampus of APP/PS1 mice.Scientific reports · 2025Article
- Volume electron microscopy reveals unique laminar synaptic characteristics in the human entorhinal cortex.eLife · 2025Article
- Photomarking Relocalization Technique for Correlated Two-Photon and Electron Microscopy Imaging of Single Stimulated Synapses.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Volume electron microscopy analysis of synapses in primary regions of the human cerebral cortex.Cerebral cortex (New York, N.Y. : 1991) · 2024Article
- Tracing nerve fibers with volume electron microscopy to quantitatively analyze brain connectivity.Communications biology · 2024Article
- Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy.Frontiers in neuroanatomy · 2024Article
- 3D synaptic organization of layer III of the human anterior cingulate and temporopolar cortex.Cerebral cortex (New York, N.Y. : 1991) · 2023Article
- Secretagogin as a marker to distinguish between different neuron types in human frontal and temporal cortex.Frontiers in neuroanatomy · 2023Article
- Exploiting volume electron microscopy to investigate structural plasticity and stability of the postsynaptic compartment of central synapses.Frontiers in cellular neuroscience · 2023Review
- Single-Neuron Labeling in Fixed Tissue and Targeted Volume Electron Microscopy.Frontiers in neuroanatomy · 2022Article
- Automated Synapse Detection Method for Cerebellar Connectomics.Frontiers in neuroanatomy · 2022Article
- 3D Synaptic Organization of the Rat CA1 and Alterations Induced by Cocaine Self-Administration.Cerebral cortex (New York, N.Y. : 1991) · 2021Article
- Comparative 2D and 3D Ultrastructural Analyses of Dendritic Spines from CA1 Pyramidal Neurons in the Mouse Hippocampus.International journal of molecular sciences · 2021Article
- 3D Ultrastructural Study of Synapses in the Human Entorhinal Cortex.Cerebral cortex (New York, N.Y. : 1991) · 2021Article
- Estimation of the number of synapses in the hippocampus and brain-wide by volume electron microscopy and genetic labeling.Scientific reports · 2020Article
- Article
- Volume Electron Microscopy Study of the Relationship Between Synapses and Astrocytes in the Developing Rat Somatosensory Cortex.Cerebral cortex (New York, N.Y. : 1991) · 2020Article
- Area-Specific Synapse Structure in Branched Posterior Nucleus Axons Reveals a New Level of Complexity in Thalamocortical Networks.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2020Article
- Size, Shape, and Distribution of Multivesicular Bodies in the Juvenile Rat Somatosensory Cortex: A 3D Electron Microscopy Study.Cerebral cortex (New York, N.Y. : 1991) · 2020Article
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Authors and funding
6 authors at 4 institutions in 1 country.
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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.
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