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:

EspINA: a tool for the automated segmentation and counting ...

EspINA software calculates the number of synapses per unit volume to analyze 3D samples reconstructed from serial sections obtained from brain tissue.

Three-Dimensional Spatial Distribution of Synapses in the Neocortex...

Specific software tools allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods.

FIB/SEM Technology and Alzheimer’s Disease...

We examined the cerebral cortex of Alzheimer's disease patients to find new aspects of the pathological process associated with the disease.

Characterization and extraction of the synaptic apposition surfaces...

Efficient computational technique to automatically extract the synaptic apposition surfaces of three-dimensionally reconstructed synapses.

A Fast Method for the Segmentation of Synaptic Junctions and Mitochondria

Description of a method that works with anisotropic voxels and that is computationally efficient allowing the automatic segmentation of large image stacks.

FIB/SEM Reconstruction of identified neurons

Efficient, complete and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM.

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

3D-electron-microscopy and 3D-confocal imaging of thalamic buttons showed the total synaptic and cell densities were as much as 150% of currently accepted values. The new estimates of contributions of feedforward synaptic inputs into visual cortex call for a major revision of the design of the canonical cortical circuit.

Distribution of synapses in the neuropil

In this paper, we identify the structures onto which synapses are established, either dendritic shafts or spines, and the differences in the distribution between excitatory and inhibitory synapses.

Size and Shape of Synapses in the Rat Somatosensory Cortex

Comparison of the size and shape of excitatory and inhibitory synapses through the six cortical layers of the young rat somatosensory cortex.

Distribution of mitochondria in Synapses in the Rat Somatosensory Cortex

Estimation of the volume fraction of the cortex occupied by mitochondria and their distribution on dendrites and axons of the young rat somatosensory cortex.

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

Combined functional, molecular, and ultrastructural mapping of the location of GABAergic inputs onto dendrites of pyramidal neurons from upper layers of juvenile mouse somatosensory cortex.

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

Detailed 3D ultrastructural analysis using focused ion beam/scanning electron microscopy (FIB/SEM) to investigate possible synaptic alterations in the TEC of patients with Alzheimer's disease.

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

Three dimensional reconstructed and quantitatively analyzed anterogradely labeled VPMdm axons in L4 of adult mouse S1.

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

Investigation of the impact of the Reelin/Dab1 pathway on the synaptogenesis of newborn granule cells (GCs) in the young-adult mouse hippocampus.

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

Analysis of density, volume, and spatial distribution of 1618 MVBs across the cortical layers of the somatosensory cortex as well as their location within axons or dendrites.

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

3D analysis of the relationship of synapses with astrocytes that were previously labeled by intracellular injections in the layer IV of the rat somatosensory cortex.

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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