The Most Advanced System for Neuron Tracing and Reconstruction,

Quantitative Neuron Analysis, and 3D Brain Mapping


Quantify Neuronal Morphology

Neurolucida is the gold standard for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. 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  

Researchers have reconstructed and analyzed tens of thousands of neurons using Neurolucida, leading to advances in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, and advances in other research fields such as ophthalmology. Neurolucida is cited over 7 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)










Neurolucida Version 2019

State of the art software for state of the art research

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.

Neurolucida on a Microscope

Fully integrated system
Reduces work and speeds up data collection


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


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



Can I upgrade my existing microscope hardware?

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

1.Purchase a brand new system

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.


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.

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 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

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 

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


Media Library

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

Still Have Questions? Just Ask!

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Neurolucida | Neuron Tracing Software | MBF Bioscience


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