Neurolucida Explorer


Neurolucida® Explorer

Obtain Quantitative Morphometric Data Using Neurolucida Explorer

Neurolucida Explorer is the analytical software companion for Neurolucida and Neurolucida 360 and is designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions and brain maps that were created by Neurolucida and Neurolucida 360. It also allows you to visualize and analyze data in a 3D environment while exploring the quantitative measurements. Neurolucida Explorer is highly interactive, allowing researchers to explore their data models and see quantitative metrics generated directly from the models.

Neurolucida Explorer is the most comprehensive solution available for neuroanatomical morphometric analysis. It contains dozens of analyses that allow you to analyze thousands of parameters. With Neurolucida Explorer, you can customize many of the analyses to address your specific research questions. You can also easily export the results to most statistical software and spreadsheet software for analysis of populations. 

No Padding


The importance and value of quantitative metrics in Neuroscience is well known but sometimes overlooked. Characterizing the 3D distribution of neurons with quantitative metrics not only reduces experimenter biases in interpretations of results but also allows for developing accurate computational models of anatomy and neurological processes. A large number of neurological disorders can now be characterized with high accuracy using quantitative metrics in addition to behavioral measures. Empowering researchers with the analytical tools needed to produce accurate quantitative metrics results in a greater proportion of the scientific community adopting data analysis methods that are more reproducible and Neurolucida Explorer has been at the forefront of quantitative metrics in Neuroscience for decades with thousands of research citations.

Sophisticated Tools for Each Unique Scientific Investigation

We have removed the obstacles for rapid, high-volume, quantitative data analysis by programming all the complex analyses so you don’t have to. Users can load multiple data sets into Neurolucida Explorer for batch analysis, sparing researchers the time and effort of performing repetitive data analysis steps. Neurolucida Explorer performs multiple analyses efficiently and additively for each data file. No scripting or programming skills are needed to use Neurolucida Explorer to its full capacity. For researchers who prefer to program custom analyses and operations, data can be exported as separate files for loading into other software like Excel, Matlab, Python, and R. 

In addition to the sophisticated and comprehensive display of quantitative data in that is displayed in detailed numerical tables, Neurolucida Explorer also shows many graphical displays that allow you to visualize the quantitative data in intuitive ways. These high-quality displays can be easily turned into figures for publications and presentations.

The analyses in Neurolucida Explorer are the result of many years of our collaboration with researchers around the world, and include many requests from neuroscientists who have used our products in their labs and envisioned new analyses that help them better understand the brain and nervous system. All of the analyses in Neurolucida Explorer have been rigorously tested and validated, so that you can be assured of getting the most accurate, reliable and reproducible results.


Neurolucida Explorer can Perform Neuronal and Regional Analyses Including




  • Branched Structure – trees, terminals, segments, nodes, synapses, spines, and more
  • Branch Angle – Planar, Local, and Local Spine angles
  • Vertex - Compare the connectivity between trees such as bifurcation points
  • Dendrogram – Visual representation of a tree structure illustrating branches and nodes
  • Spines – Quantify features of dendritic spines such as length, volume, branching, and spine type


Dedogram Spine NL
Dendrogram Spine analysis


Anatomical regions

  • Closed Surface – Measurements about processes within a 3D structure
  • Proximity – Analyze the distance between two trees or structures
  • Tangential Distribution – Analyze the length and distribution of neuronal processes




  • 3D Wedge – Analyze the distribution of neuronal processes extending from the centroid of the cell body
  • Convex Hull – Measure the size of the dendritic field
  • Layer Length – Quantify neuronal nodes, spines, and processes within anatomical regions
  • Sholl Analysis – Quantify the branching of individual neurons
  • Wedge – Quantify differential growth or retractions of dendritic processes


Conves hull Sholl NL
Convex Hull Sholl



  • Polar Histogram – Quantify and illustrate the directions of dendritic growth
  • Fan In Diagram – Quantify and visualize the orientation of dendritic processes
  • Colocalization – Determine a cell’s location based on multiple markers used in double labeling


Polar Histogram  Fan In
Polar Histogram Fan In Diagram


Puncta Analyses



Puncta analyses allow you to perform morphometric and quantitative measurements on the puncta that were detected in Neurolucida 360. The specific channels used for the detections are respected and can be used to compare the different populations of puncta to each other and to other structures. The analyses include area, volume, colocalization, nearest neighbor, distance to structures, and number of puncta in closed contours, closed surface and layers. These results can be easily exported to most statistical and spreadsheet software.


Users can see specific details of each analysis such as the equations used to analyze the data. Your reconstruction data can be explored in a 3D environment with full control over navigation functions. Special publishing features include exporting your data files to third-party programs such as Microsoft Excel.

Neurolucida Explorer is included with every software license of Neurolucida and Neurolucida 360.  Additional licenses of Neurolucida Explorer can also be purchased separately if you need to share your data with more colleagues.


Neurolucida 360 FAIR forum


With the new release of the neuromophological file format specification, MBF Bioscience is committed to making morphology data FAIR and open. It details each element of the MBF XML data file in an effort to encourage the reuse of these rich data files for alternative analysis. Help us shape software development for the coming year.

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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