The Most Advanced System for Neuron Tracing and Reconstruction, Quantitative Neuron Analysis, and 3D Brain Mapping

Quantify Neuronal Morphology

Neurolucida is a microscopy system specifically designed for performing accurate neuron reconstructions directly from histological specimens. It is capable of over 500 quantitative morphometric analyses, including:

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

Researchers have reconstructed and analyzed tens of thousands of neurons using Neurolucida, leading to hundreds of advances in the understanding of neurodegenerative diseases, neuropathy, memory, and behavior, and advances in other research fields such as ophthalmology. Neurolucida is cited over 10 times more than all other available neuron tracing programs combined (Halavi, Hamilton, Parekh, & Ascoli, 2012). And, according to another study, Neurolucida is "the most widely used and versatile system to produce neuronal reconstruction." (P. Aguiar, M. Souda, P. Szucs, 2013)

No Bottom Padding


Neurolucida Works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes

Microscopy hardware and Neurolucida software work in harmony to deliver a powerful, seamless neuron reconstruction system. A typical system includes a microscope, computer, and Neurolucida software. Most of what is visible through the oculars is displayed on the computer monitor with Neurolucida. 

Neurolucida fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • control motorized stages
  • control cameras to change or save settings for future use
  • operate the focus knob or change objectives
  • change filter turrets, filter wheels, and mirror cubes when acquiring fluorescent images or image stacks
  • it can support almost all file formats


Are you looking to do automatic 3D neuron reconstruction and analysis? Check out Neurolucida 360

Fully Integrated Microscope Systems

In addition to the software for neuron tracing and analysis, a Neurolucida system includes all necessary hardware (microscope, computer, motorized stage, camera, etc.). On-site installation and training, technical support for the entire system (hardware and software) and research support (to help optimize your experimental design) are included.

No Bottom Padding

Neurolucida on a Microscope

Fully integrated system
Reduces work and speeds up data collection

Customer Reviews

"Neurolucida is one of the very few systems that combines complex morphometrical quantification with beautiful display of the results."
Ahmed Salehi, M.D., Ph.D.
Stanford Medical School
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
Bogdan A. Stoica, M.D.
University of Maryland
"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


Can I Upgrade my Existing Microscope Hardware?

  • There are two main options when purchasing a Neurolucida system:

1.Purchase a brand new system: We work with all the leading microscope manufacturers including:

● Zeiss Axio Imager M2/Z2
● Olympus BX53/BX63
● Leica DM4/DM6
2. Upgrade existing microscope hardware
  • We typically provide complete turn-key systems include all of the hardware, software and services you will need for your new system.  
  • If you already have an existing microscope, motorized stage, or camera that you would like to use in a new system, we are happy to help you determine if it would be appropriate to integrate it into a new system rather than purchase all new hardware. 
  • All of our Neurolucida systems are custom configured based on the specific research needs of each customer.  

Contact Us

Neurolucida has been cited in over 6,000 published research papers.

7 times more than all other neuron tracing programs combined.


3D Brain Mapping

Neurolucida has advanced tools for creating and analyzing 3D reconstructions of brain and spinal cord specimens.

  • Map and analyze a long neuronal pathway
  • Map the distribution of cells in a region of interest
  • Quantify volume for studies looking at volume change, such as the atrophy of the striatum in a specimen that has the Huntington's gene expressed, or the volume of lesions that appear in a region of interest.
  • Analyze the distribution of objects in a region of interest and find the proximity of one object to another or find the distance between the object and an anatomical boundary.
Read about how scientists used Neurolucida to map memories

Serial Section Reconstruction

Serial sections are tissue sections that have been cut sequentially with a microtome. To obtain morphometric data about neurons or structures that extend beyond a single tissue section, researchers often create a serial section reconstruction - a digital representation of the serial tissue sections. This method includes tracing the outline of each tissue section at low magnification and tracing the neuron or structure of interest in each tissue section at a higher magnification. This can be done at the microscope or from images with Neurolucida, which has tools to help make this process easier. For example, Neurolucida has an automatic contouring tool to help you trace the outline of the tissue specimen or trace an anatomical boundary within the specimen.


Capture Image Stacks and Whole Slide Images with Neurolucida

Neurolucida can capture 2D (x,y) and 3D (x,y,z) whole slide images (high resolution digital images of your specimen) with the addition of the 2D or 3D Slide Scanning Module, but Neurolucida also supports whole slide images from providers such as Aperio and Hamamatsu. Working with whole slide images gives you the freedom to create neuron reconstructions and analyze them on any computer (even those not connected to a microscope), and also gives you a permanent digital file of your specimen that can be easily stored on Biolucida, MBF’s image viewing, sharing, and storing application.


Watch automatic contouring in a 30 second video on YouTube

Automatic Cell Detection and Mapping

Identify labeled neurons in whole slide images using an intuitive cell detection workflow. Our sophisticated detection algorithm is robust against histologic and imaging artifacts such as edge effects, uneven illumination, and variable staining across specimens. 

Slide Scanning Workflow

A completely new slide scanning workflow is easier to use, will save time training new users and give you great slide scanning results. Use this workflow to scan at any magnification and create high resolution 2D images or 3D stacks. This workflow brings all the controls and features necessary to complete slide scanning into one location.  Feature includes:

  • An easy-to-follow guide that makes it simple for new users to scan great quality images 
  • Background correction to insure clean, even, image quality
  • Heat map allows you to spot folds and other areas that need additional focus sites
  • Validate your settings before you start a long acquire by taking a test image 

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

Neurolucida 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 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.

Each Neurolucida System We Configure Is:

  • Based upon your specific research needs. We can provide all necessary hardware.
  • Fully integrated – Neurolucida  controls motorized stages, cameras, filter wheels etc.
  • Scalable, so it fits your budget and allows room for additional capabilities via our imaging modules and hardware upgrades.
  • Supported by our team of scientists and technicians who are experts in research software and laboratory hardware.  Our scientists also can help you design your study.
  • Upgradable to new software versions that are released regularly.

Neurolucida has been developed with support from the National Institute of Mental Health (NIMH)

Learn more about neuron tracing

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.

Request More Information

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.

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

Creating effective graphics, images and videos using Neurolucida & Stereo Investigator
Creating effective graphics, images and videos for publications using Neurolucida and Stereo Investigator
brain mapping with version 11 webinar
Brain Mapping with Neurolucida and its New Automatic Advancements
Reconstructing & Analyzing Neurons with Neurolucida & its New Automated Advancements
Reconstructing & Analyzing Neurons with Neurolucida & its New Automated Advancements
Webinar: Structured Illumination Imaging and Analysis with Neurolucida and Stereo Investigator
Performing Structured Illumination Imaging and Analysis with Neurolucida and Stereo Investigator

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.

Still Have Questions? Just Ask!

Paragraphs Contact Form

This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.