Neurolucida 360


The Leading Software for Automatic 3D Neuron Reconstruction and Quantitative Analysis

Neurolucida 360 is the premier tool used by neuroscientists to quickly and accurately reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines, varicosities and putative synapses.

With the sophistication to analyze specific neuronal structures such as axons, basal dendrites, apical dendrites, and axon-carrying dendrites, you can completely reconstruct and analyze any neuron in any species.

Machine learning and the most advanced image detection algorithms allow you to confidently reconstruct cells using a variety of labeling and microscopy techniques.

Engineered to work efficiently with even the largest 3D datasets using precognitive image handling intelligence.

Whether you are interested in analyzing individual neurons or the interactions of neurons, see why Neurolucida 360 far surpasses all other software for automatic neuron reconstruction!

No Bottom Padding

Move at the Speed of Neuroscience with the Latest Version of Neurolucida 360

We’ve re-engineered image and data handling within MBF Bioscience software solutions from the ground up to maximize your computer hardware investment. No matter the image data size, from lightsheet microscopes, confocal microscopes, or slide scanners, you are now able to work efficiently, without delay.

Image load times in Neurolucida 360 v2021 up to 5000x faster in the 3D environment and 250x faster in the 2D environment, so now your research can move as fast as you do.

With our new intelligent image loading, maximized concurrent usage of CPU cores, multiple levels of data caching, and efficient use of RAM and GPU resources, you can now display and reconstruct your images faster than ever before to you make your scientific discoveries.

Customer Reviews

"Neurolucida 360 is a remarkable system that has provided us with tools to study dendritic architecture in cultured neurons, rodent models, and humans, with outstanding precision and detail."
Jeremy Herskowitz, Ph.D.
University of Alabama at Birmingham
"Neurolucida 360 is clearly the best in the field - reliable, accurate, and very importantly, easy and intuitive to use. I would not try any other system."
Jeffrey Kordower, Ph.D.
Rush Presbyterian Medical Center
"Neurolucida 360 is very useful for doing quantitative analysis of neuronal morphology."
Yun Wang, Ph.D.
Allen Institute for Brain Science
"I am so happy to be a customer of your company. I always get great help related with your product or not. With the experienced members, you are the best team I've ever met. All of your staff are very kind and helpful. Thank you for your great help and support all the time."
Mazhar ÖZKAN, PhD
Marmara Üniversitesi Tıp Fakültesi, Turkey


The Complete Solution for Neuronal Reconstruction and Analysis

  • Axons
  • Dendrites
  • Somas
  • Dendritic spines
  • Synapses
  • Varicosities

Neurolucida 360 has been used to reconstruct thousands of neurons including pyramidal, chandelier, and projection neurons.

It leverages the expertise and experience we gained in the long history of developing our renowned Neurolucida system, the most widely used software for neuron tracing, and used in laboratories worldwide to produce over 10,000 peer reviewed citations.

Introduction to: Neurolucida 360



With hundreds of peer-reviewed citations, scientists around the world trust Neurolucida 360 to efficiently and accurately reconstruct neurons in 3D. Watch the video to see how fast, easy, and accurate our software is!

MBF Bioscience’s Data Web Viewer

Explore a variety of data that demonstrates the models you can create using MBF Bioscience image analysis software (e.g. Neurolucida 360). Interact with these data files over the web and examine the full resolution, 3D morphological models of generated from microscopy images.

View MBF Bioscience Data Web Viewer

Quantify Neuronal Morphology

Neurolucida 360 is the most widely used software for automatic neuron reconstruction for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. With the included Neurolucida Explorer software, you can perform detailed morphometric analyses of neurons, such as quantifying:

  • the number of dendrites, axons, nodes, synapses, and spines
  • the length, width, and volume of dendrites and axons
  • the area and volume of the soma
  • the complexity and extension of neurons 

+ Click here to see other analyses with Neurolucida Explorer

Case Studies

Case Study 1:

As reported in Science, Neurolucida 360 now offers more accuracy than ever before. In the paper “Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution” (2019) researchers performed a morphological analysis of extremely high resolution 3D images of dendritic spines in the fruit fly brain. Using Neurolucida 360 in combination with expansion microscopy and lattice light sheet microscopy the researchers obtained comprehensive morphometric data with more accuracy than ever before. Measurements reported in the study include the length of the entire neck of the dendritic spine, contact points where each spine attaches to its dendrite, the extent of the head and neck along the spine backbone, and most impressively, spine neck diameter.

Read More

science MBF magazine cover


Case Study 2:

In this case study, we demonstrate how the Dr. John Tompkins and his lab at UCLA utilized MBF Bioscience’s multi-resolution image segmentation strategies to understand the structure-function relationships of cells within the stellate ganglion. After performing electrophysiolocial recordings, the cells were labeled with a fluorescent dye and processed for imaging. Using Neurolucida 360, the Tompkins lab reconstructed select neurons from images at 40x magnification. These cells were annotated with their corresponding electrophysiological recording ID. The entire stellate ganglion was also imaged at 10X magnification and contoured using integrated FAIR anatomy terminology lists. The registration of the high-resolution cellular reconstructions to the whole stellate ganglion allowed the Tompkin’s lab to bring the physiological and morphological data into context with the entire ganglion. Dr. Tompkins is contributing this data to the SPARC program.  


Case Study 3:

Some inflammation is normal in a healthy mammalian brain. But as the brain ages, processes can break down, leading to chronic neuroinflammation. This can develop into Alzheimer’s disease, dementia, and other neurodegenerative diseases. Scientists at Prof. Gerald Muench’s lab, at Western Sydney University say that curcumin, a substance in the spice turmeric, has the potential to lower inflammation in the brain. In two recent studies, the researchers, led by Dr. Erika Gyengesi, used Stereo Investigator and Neurolucida 360 to reconstruct and quantify glial cells in the brains of mice after feeding them two different curcumin formulations.

Read More

Case Study 4:

Researchers Identify Potential Treatment for Patients at Risk for Alzheimer’s Disease

In a paper published in Science Signaling, researchers at the Herskowitz Lab, at the University of Alabama at Birmingham, used Neurolucida 360 to analyze spine density and dendritic length in hAPP mice — a mouse model of AD. Their findings describe a treatment that could protect against synapse loss and prevent the onset of dementia in patients at risk for Alzheimer’s disease.

Read More

Neurolucida 360 has been cited in over 400 published research papers.


Automatic Detection and Modeling

Neurolucida 360 is uniquely designed to automatically model, classify and quantify dendritic spines in 3D. Spines are automatically classified by type (i.e., mushroom, filipodia, stubby, thin as described in the scientific literature). It is also designed to model and quantify somas, varicosities, and synapses.

Detect and Classify Spines

Trace Branches and Detect Varicosities

Dendrite Spines Neuron Tracing branches



Works With All Types of Microscopy

Neurolucida 360 works with 3D and 2D images from virtually all forms of microscopy. It excels at handling very large images such as whole slide images or large 3D images of cleared tissue.

  • brightfield
  • confocal 
  • light sheet
  • expansion microscopy
  • Micro-CT
  • two-photon
  • fluorescence 
  • slide scanners
  • fMost 

Trace Golgi Stained Neurons

Reconstruct Neurons from Cleared Tissue

golgi stained neuron tracing reconstructing neurons from cleared tissue


Analyzing Images Acquired through Expansion Microscopy

Expansion microscopy allows imaging and analysis of structures otherwise too small for detection using light microscopy methods. By enlarging cells and subcellular components while preserving their structure, researchers can examine neural connections and networks on a much finer scale. All of the tracing and quantification features in Neurolucida 360 can be used to analyze images acquired through expansion microscopy techniques.

Both automated and user-guided tracing tools can be used in conjunction with model scaling adjustments to allow researchers to obtain correct measurements of structures both in the expanded volume and of the original volume of the tissue (based on the calculated scale factor). One of the many advantages of analyzing expanded tissues in Neurolucida 360 is that the expansion process permits visualization of sub-cellular neuronal processes such as dendritic spine neck length and diameter that are otherwise too small to measure accurately in unexpanded tissues. Dendritic spines analysis in Neurolucida 360 has been adjusted to make the most from this increased resolution to improve spine detection, classification, and morphometric analyses.


Our New Machine Learning Algorithms Allow you to Make New Discoveries


Puncta detection in the 3D environment allows you to detect anything from cells to punctate subcellular structures synapses. The feature includes the ability to utilize machine learning to generate more accurate reconstructions. The machine learning detection mechanism employs specific models of object size and appearance (e.g. for puncta, cell nuclei) that accept or reject locations in your image that meet general detection parameters. Only objects that meet the requirements of the specialized machine learning model are further considered for detection and reconstruction, leading to a more accurate selection of puncta of interest.


Our New High-Tech Imaging Engine also has New Tools Available Allows you to make your Scientific Discoveries Flow with Ease. These Include:

No Bottom Padding




The subvolume function enables seamless, dynamic tracing on systematically selected focus sites of 2D and 3D image stacks within the 3D environment.

No Padding

No Top Padding




Color channel specification allows you to select one or multiple channels to view, hide, and reconstruct your images by associating traced structures with specific color channels in the 3D environment to facilitate multiplexed analyses.


A Full Suite of Tools to Edit Structures in 3D and Deliver Ground-Truth Data

With Neurolucida 360's full suite of tools you can manually trace and edit your reconstructions, creating a ground-truth representation of your neuron data.

You can also fine-tune and correct the automatic reconstructions in cases of particularly challenging image data. Some of the edit functions available are:

  • Detach dendrite/axon branch segments
  • Connect dendrite/axon branch segments
  • Remove dendrite/axon trees or branch segments
  • Adjust dendrite/axon diameters
  • Move location of individual axon/dendrite points in X, Y and Z
  • Change dendritic spines by splitting, or merging, or reclassifying


Are you looking for a microscope based neuron tracing system? Check out Neurolucida


Comprehensive Quantitative Analyses

Our rigorously tested analyses provide accurate and robust results that you and others can trust in publications.

Use Neurolucida Explorer, Neurolucida 360 companion analysis software, to perform sophisticated analyses that help answer your research questions.

We provide dozens of analyses that analyze and graph hundreds of metrics and parameters, including: 

  • Structure
  • Distribution
  • Orientation
  • Colocalization


Real-time Interactive 3D Visualization

As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable to effective data interpretation. 

Our software includes a highly versatile 3D visualization environment suitable to most microscopy images with state-of-the-art functionalities to support your analysis and publication needs.

  • Visualize large, complex 3D images (including multichannel images) and reconstructions
  • 2D and 3D image data from two-photon, confocal, brightfield or light sheet microscopy
  • 3D volume, image slicing, and simultaneous views
  • Multiple projections: XY, YZ, XZ, alpha, minimum, and maximum
  • Transparency, rendering (wireframe, centerline, surface, texture) and other display options for image and traces that can be adjusted on the fly
  • Create dynamic movies
  • Export options including exporting 3D graphics to third-party applications
  • Loads complex surfaces in seconds
  • Works with the most advanced “gaming class” graphics cards to deliver high performance at an affordable price
  • Supports almost all file formats

Our File Format is Now Open and FAIR to Allow Collaboration Between the Scientific Community

Neurolucida 360 supports the collaborative goals of Open Science through the practice of data openness, integrity, and reproducibility, by using MBF Bioscience’s published digital reconstruction data file format, the Neuromorphological File Specification (NFS).

The data elements in this NFS format were specifically implemented to ensure the files are Findable, Accessible, Interoperable, and Reusable (FAIR). Abiding by these data standards and providing microscopy image and experimental data provenance enhances the ease of repurposing this data. Encoded in the well-recognized and readable format, the modeling elements specify microscopic neuroanatomies in a calibrated 3D coordinate system with appropriate units.

These Neurolucida 360 files can also easily be viewed and parsed in a variety of software, e.g. MATLAB and Python. To learn more about the key elements of the file format and their relevant structural advantages, view our manuscript, A comprehensive, FAIR file format for neuroanatomical structure modeling.

Designed by Neuroscientists for Neuroscientists

Developed with support from the National Institute of Mental Health (NIMH), Neurolucida 360 was specifically conceived for the neuroscience community by neuroscientists who understand the challenges and breadth of neuroscience research. We are constantly pushing the technological boundaries of our software to support your needs in addressing cutting-edge research questions. Our scientists are regularly in dialogue with our customers, incorporating their suggestions into the design of Neurolucida 360 to aid discoveries in neuroscience worldwide.

Neurolucida 360 is an invaluable tool to advance connectomics and handle the “big data” necessary to map neural pathways at the level of synaptic connections comprehensively. It can also be automated to perform repeated neuronal analyses.

Consult with our staff neuroscientists to determine the best course of action to make sense of your data.


Learn How to Best Prepare and Image Neurons for Analysis

Our scientists collaborated with researchers from the Icahn School of Medicine at Mount Sinai in New York to develop a set of guidelines on preparing and imaging confocal image data for Neurolucida 360. The guidelines, published in Current Protocols in Neuroscience, will help you get the best results for spine quantification and neuron reconstruction.

+ Read the publication


How can Neurolucida 360 help you?

  • Run analyses that exactly match your research questions
  • A ready to use solution with no need for programming skills or the creation of supplementary scripts (e.g., MatLab)
  • Use it on a wide range of research specimens, from the sub-micrometer level (synapses) to the macrolevel (mapping projection neurons)
  • Use the stains and visualization techniques that fit your research paradigm including Golgi, 2D, expansion microscopy, clarity, iDISCO, uDISCO, confocal, two-photon
  • Work with an equipment in your facility, virtually all microscope image formats are supported.
  • Consult with our expert neuroscientists to get recommendations on the best means to analyze your experimental data.

Image courtesy (right): Neuron Tracing of confocal microscopy image of a human neocortical neuron injected with Lucifer Yellow, showing 3D-reconstructed dendrites and spines superimposed on the confocal image. Authors: Ruth Benavides-Piccione, Isabel Fernaud, Asta Kastenauskaite and Javier DeFelipe.


Affordable Packages

Our three most popular packages are Neurolucida 360 Lite, Essentials, and Studio.

There are different options to set up Neurolucida 360 in your lab: a one-time upfront cost for the software, an annual subscription plan, mobile licenses to move Neurolucida 360 from one computer to another, and more.

Learn more about the differences between Neurolucida and Neurolucida 360


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.

Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

Contract Services for Neuron Reconstruction

Our Neuron Reconstruction services gives your lab the ability to have industry-leading experts create a 3D digital reconstruction of individual or multiple neurons, for your research. MBF Labs will reconstruct your neurons giving you a breadth of quantitative information. The process is simple and practical. Provide us with slides or images, and MBF Labs experts do the rest.

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MBF Bioscience Forum

Get answers to your most pressing research and technical questions from MBF scientists and fellow researchers.


Visit MBF Bioscience Forum


Watch These Webinars About Neurolucida 360

See the New Features of Neurolucida 360 2020.3.1
See the New Features of Neurolucida 360 2020.3.1
Neuronal imaging protocols and techniques to achieve accurate, automated 3D neuron reconstruction
Neuronal imaging protocols and techniques to achieve accurate, automated 3D neuron reconstruction
Using Neurolucida 360 for Automatic Neuron Reconstruction and Analysis
Using Neurolucida 360 for Automatic Neuron Reconstruction and Analysis
Webinar: Reconstruct neurons in large image volumes with Neurolucida 360
Reconstruct neurons in large image volumes with Neurolucida 360
Webinar: All's FAIR in Image Segmentation
All's FAIR in Image Segmentation
Online Q/A session: Automatic Neuron Reconstruction and Analysis using Neurolucida 360
Online Q/A session: Automatic Neuron Reconstruction and Analysis using Neurolucida 360

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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