Interactive Neuron Analyzer
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EspINA is a user-friendly tool which performs segmentation and analysis of elements in a reconstructed 3D volume of the brain, and greatly facilitates and accelerates these processes. It allows visualization and segmentation of large image stacks datasets, both from electron micrsocopy (e.g. FIB/SEM) and confocal laser microscopy.

  • Explore

    Natural 3D navigation over the orthogonal planes

    Fluent navigation through the different sections of the stack using three planar views. Simultaneous different channel visualization can be performed in a customized stainings and intensity/contrast properties. Navigation bookmarks helps to easily find stack spots.

  • Segment

    Brain structures can be individually segmented to later analysis

    Identify as many elements as you want using our classification or expand it as needed. Reconstruct them using our manual or semi-automated tools.

  • Edit

    Asortment of tools to improve segmentations

    If the result of the segmentation is not completely satisfactory, we provide a set of tools to enhance their morphology automatically or manually.

  • Visualize

    Several 2D and 3D representations

    Geometrical features of segmented elements are relevant to their function. Different 3D visualizations provide detailed views for every segmented element.

  • Analyze

    Obtain multiple measures from segmented structures

    The final step of the working session is the extraction of measurements for each object segmented. A list of morphometric features and parameters can be selected to be easily exported to standard .csv or .xls spreadsheet format.

  • And more...

    Expand EspINA capabilities with plugins

    New tools, visualizations and reports can be added via our plugin system. You can even add your own.


Basic Workflow

Learn the basics to start

Grey Level Segmentation

Segment based on grey level similarity

Freehand Segmentation

Segment exactly what you want

Edition Tools

Enhance segmentations

Visual Representations

Flexible segmentation visualization

Reports and Analyze

Segmentation data and measurements

Getting Started


You can download the latest binaries for Windows or Linux machines.

Sample Datasets

Download our FIB/SEM stack sample from mouse brain to start testing out EspINA without delay.


Some researchers have successfully used EspINA software to get results. A selection of such scientific papers is shown below:

3D Analysis of the Synaptic Organization in the Entorhinal Cortex in Alzheimer's Disease

Domínguez-Álvaro et al., 2021.
eNeuro 8: ENEURO.0504-20.2021. doi:10.1523/ENEURO.0504-20.2021

Three-Dimensional Synaptic Organization of Layer III of the Human Temporal Neocortex

Cano-Astorga et al., 2021.
Cerebral Cortex, bhab120

3D Synaptic Organization of the Rat CA1 and Alterations Induced by Cocaine Self-Administration

Blazquez-Llorca et al.
Cereb Cortex. 2021 Mar 5;31(4):1927-1952.
doi: 10.1093/cercor/bhaa331

Three-dimensional analysis of synaptic organization in the hippocampal CA1 field in Alzheimer’s disease

Montero-Crespo et al., 2021.
Brain 144 (2): 553–573.

3D Ultrastructural Study of Synapses in the Human Entorhinal Cortex

Domínguez-Álvaro et al., 2021.
Cereb Cortex, 31(1):410–425.

Estimation of the number of synapses in the hippocampus and brain-wide by volume electron microscopy and genetic labeling

Santuy et al., 2020
Sci Rep 10, 14014.

Area-Specific Synapse Structure in Branched Posterior Nucleus Axons Reveals a New Level of Complexity in Thalamocortical Networks

Rodriguez-Moreno et al., 2020.
J Neurosci, 40 (13): 2663-2679.

Three-dimensional synaptic organization of the human hippocampal CA1 field

Montero-Crespo et al., 2020.
Elife. 9: e57013.

Volume electron microscopy study of the relationship between synapses and astrocytes in the developing rat somatosensory cortex

Kikuchi et al., 2020.
Cereb Cortex. 30(6):3800-3819.

Size, Shape, and Distribution of Multivesicular Bodies in Juvenile Rat Somatosensory Cortex: A 3D Electron Microscopy Study

Turegano-Lopez et al., 2020.
Cereb Cortex. 2020 Mar 14;30(3):1887-1901.

3D Electron Microscopy Study of Synaptic Organization of the Normal Human Transentorhinal Cortex and Its Possible Alterations in Alzheimer's Disease.

Domínguez-Álvaro et al.,2019.
eNeuro. 6(4): ENEURO.0140-19.2019.

Major Feedforward Thalamic Input Into Layer 4C of Primary Visual Cortex in Primate

Garcia-Marin et al., 2019.
Cereb Cortex. 29 (1): 134–149

Ultrastructural, Molecular and Functional Mapping of GABAergic Synapses on Dendritic Spines and Shafts of Neocortical Pyramidal Neurons

Kwon et al., 2019.
Cereb Cortex. 29(7):2771-2781.

A Quantitative Study on the Distribution of Mitochondria in the Neuropil of the juvenile Rat Somatosensory Cortex

Santuy et al. 2018.
Cereb Cortex. 28(10):3673-3684.

Study of the Size and Shape of Synapses in the Juvenile Rat Somatosensory Cortex

Santuy et al. 2018.
eNeuro. 5(1)

Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex

Santuy et al. 2018.
Brain Struct Funct. 223(1):77-90.

Quantitative 3D Ultrastructure of Thalamocortical Synapses from the "Lemniscal" Ventral Posteromedial Nucleus in Mouse Barrel Cortex

Rodriguez-Moreno et al. 2018.
Cereb Cortex. 28(9):3159-3175.

Three-dimensional analysis of synapses in the transentorhinal cortex of Alzheimer’s disease patients

Domínguez-Álvaro et al. 2018.
Acta Neuropathol Commun. 6(1):20.

Reelin Regulates the Maturation of dendritic Spines, Synaptogenesis and Glial Ensheathment of Newborn Granule Cells

Bosch et at. 2016.
Cereb Cortex. 2016 Oct 17;26(11):4282-4298.

A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria

Márquez-Neila et al. 2016.
Neuroinformatics. 14(2):235-250.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

Bosch et al. 2015.
Front Neuroanat. 9:60.

Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study

Merchán-Pérez et al. 2014.
Cereb Cortex. 24(6): 1579–1588

Characterization and extraction of the synaptic apposition surfaces for synaptic geometry analysis

Morales et al. 2013.
Front Neuroanat. 7:20.

FIB/SEM Technology and Alzheimer’s Disease: three-dimensional analysis of human cortical synapses.

Blazquez-Llorca et al. 2013.
J Alzheimers Dis. 34(4):995-1013.

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

Morales et al. 2011.
Front. Neuroanat. 5:18

If you have used EspINA to get your results and you have published them (congratulations!!) please, let us know and your publication will also appear here. Reviews of image processing software which include EspINA are also welcome.

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