Neuron tracing & analysis directly on the microscope. The gold standard for neuron tracing
MBF Bioscience > Neurolucida®

Product Overview

The Neurolucida system is specifically designed for accurately tracing neuronal structures directly from histological specimens and generating quantitative morphometric data. Neuroscientists around the world trust Neurolucida as the gold standard for producing accurate anatomical models that can be quantitatively analyzed in hundreds of different ways to address perplexing biological questions. With over 6000 citations, research conducted with the help of the Neurolucida system has led to hundreds of advances in the understanding of neurodegenerative diseases, neuropathy, memory, and behavior.

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Key Benefits

The Neurolucida system is widely recognized by neuroscientists as the gold standard for neuron reconstruction because it is based on the ground truth—you trace directly from the specimen on the microscope or from previously captured images. The tracing tools are specialized for neuronal structures, making it clear which tool to use and why; in addition, you can also edit traced structures as needed. Neurolucida offers a wide array of other powerful capabilities, including anatomical region mapping, 3D serial section reconstruction, automatic cell detection, and slide scanning.

Neurolucida fully integrates with your microscope system hardware to control motorized stages, focus, cameras, objective changers, and optical filters. Whether you need a new microscope system or want to use Neurolucida with your existing microscope hardware, our technical sales specialists will work with you to understand your current and future research interests, and choose microscope components that will help you achieve your research goals and fit your budget.

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

Minimum System Requirements

Operating System

Windows 10, 64-bit




16 GB


>6 GB

Recommended System Requirements

Operating System

Windows 10, 64-bit




64 GB


>8 GB


Solid state drive(s)

File Input Options

Supported image file formats


Output Specifications

Data output formats



* Our XML data file format, the Neuromorphological File Specification (NFS), is endorsed as a standard by the INCF.

Image file output formats


Movie export format


Hardware Compatibility










Computer controlled microscopes

Leica supported microscopes:

  • DM6B
  • DM4
  • DM 3000
  • DM 4000
  • DM 4500
  • DM 5000
  • DM 5500
  • DM 6000
  • DM 6000-FS
  • DM 8000M
  • DM12000M
  • DM4
  • DM6
  • DMI4000
  • DMI 5000
  • DMI 6000
  • DMI8



Zeiss supported microscopes:

  • AxioImager 1 and 2 series
  • Vario
  • AxioVert 200M
  • Zeiss Axioplan/phot 2(i)(ie)


Nikon supported microscopes

  • 90i/80i
  • TE2000
  • Ti
  • Ni-U
  • Ni-E
  • Ci-E


Olympus BX and IX Series:

  • BX63
  • BX53
  • IX83
  • IX2/BX2 UCB control boxes

Manual microscopes

Most models after 2002 of Zeiss, Olympus, Nikon, Leica


Structured illumination

  • Zeiss Apotome I, II, III
  • Olympus DSU
  • CarvII
  • Optigrid

Filter wheels and shutters

Zeiss, Olympus, Leica, Nikon, LEP, Prior, Sutter




Color video cameras

  • Qimaging Retiga 2000R
  • Lumenera Lumen HR
  • Optronics Microfire
  • Zeiss Axiocam MRc, 305, 506, 512, 705, 712
  • DVC 2000C
  • Leica DFC
  • Basler



Monochrome video cameras

  • Hamamatsu
  • Zeiss Axiocam MRm, 305, 506, 512, 702, 705, 712
  • Leica DFC
  • Cooke Sensicam QE, EM
  • Cooke PCO

Light sources

  • Lumencore Sola
  • X-Cite 120PC, 120LED, Exacte, XYLIS, XLED1, TURBO, NOVEM

Supported Image File Formats: PDF

Contact us for an up-to-date list or question about specific models

Neurolucida helps to reveal new findings in a follow-up to a 40 year old study
>> Learn More

Researchers Observe Altered Neuropathology in CTE Brains
>> Learn More

Scientists Discover New “Rosehip” Neuron in Human Brain
>> Learn More

NeuroMorpho.Org Releases Nearly 10,000 New Neuron Reconstructions and Neurolucida leads the way
>> Learn More

Exercise changes astrocytes and eases symptoms of neurodegenerative disorders
>> Learn More

Uncovering the role of microglia in fetal alcohol spectrum disorders
>> Learn More

Scientists Observe Differences Between Brains of Stressed and Unstressed Rats After Fear Conditioning
>> Learn More

Hippocampal Neurons Change After Melatonin Injection
>> Learn More

Dendritic Spine Loss Reported in Schizophrenia and Bipolar Disorder
>> Learn More

Two 2014 Nobel Laureates Used Neurolucida to Create 3D Reconstructions of Neurons That Help Rats and Humans Navigate the World
>> Learn More

Anorexia Accelerates the Development of the Rat Hippocampus
>> Learn More

Scientists Use Neurolucida to Create 3D Reconstructions of Placental Villous Trees
>> Learn More

New Neurons Erase Memories
>> Learn More

Brain Cleans Itself During Sleep; Scientists Image Cerebral Fluid Flow With Neurolucida
>> Learn More

3D Reconstructions of Neurons Reveal More Branching in Sedentary Rats
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Neurons in the Basal Forebrain are Exquisitely Organized
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Scientists Discover Anorexia-Driven Changes to Dendrites With Neurolucida
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Neurolucida Helps Scientists Discover that Gorillas are Relevant in the Study of Alzheimer’s Disease
>> Learn More

Ohio State Neuroscientists Use Neurolucida to Analyze Brain Cells in Sexually Active Hamsters
>> Learn More

Japanese Researchers Develop New Optical Clearing Agent; Neurolucida Used For 3D Imaging in Study
>> Learn More

Drug for Treating Asthma Improves Cognitive Function in Down Syndrome Mouse Model
>> Learn More

Neurolucida Helps Ohio State Scientists Study Melatonin’s Effects on Brain Plasticity in Mice
>> Learn More

Researchers at the University of Michigan Analyze Spine Density in Addiction-Prone Rats with Neurolucida
>> Learn More

Scientists Use Neurolucida in Study of Calcium Signaling During Spontaneous Brain Activity
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Scientists in Portugal Use Neurolucida Explorer to Analyze Neuroplasticity in Depression
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Cincinnati Scientists Use Neurolucida in Epilepsy Study
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Michigan Scientists Analyze Brain Cells Born During Puberty With Neurolucida
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Stanford Scientists Render Mouse Brain Transparent, Offering New Possibilities For 3D Analysis
>> Learn More

Scientists Use Neurolucida in Study Describing New Cell Population in Juvenile CA3 Hippocampus
>> Learn More

Scientists in Japan Identify Two Brain Circuits Involved in Image Recognition; Neurolucida Plays Part
>> Learn More

UVA Scientists Use Neurolucida in Study Identifying Two New Circuits in Rat Neocortex
>> Learn More

Neurolucida Helps Scientists Map Rett Syndrome’s Brain Dysfunction in Mouse Model
>> Learn More

Scientists Map Diaphragm’s Motor Nerve and Arteriolar Networks With Neurolucida
>> Learn More

Neuroscientists in Germany Outline Protocol for Best Accuracy in Neuron Reconstruction, including Use of Neurolucida
>> Learn More

Gene Therapy May Be Answer to Effective Parkinson’s Treatment; Neurolucida Plays Role in Study
>> Learn More

Yale Researchers Make Breakthrough in Possible Depression Treatment
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Neurolucida Helps Scientists in Jerusalem Study Synaptic Density in Lactating Mice
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Dr. Henry Markram’s Team Uses Neurolucida in New Blue Brain Study
>> Learn More

UVM Scientists Use Neurolucida and Stereo Investigator to Study Neurons in the Avian Iris
>> Learn More

French Scientists Use Neurolucida to Study Plasticity in Adult Neurons
>> Learn More

Neurolucida Helps Florida Researchers Reconstruct a Region of the Rat Brain
>> Learn More

In the Forest of the Mind
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Columbia Scientists Map Neocortical Circuit Connectivity with Neurolucida
>> Learn More

Scientists use Neurolucida Reconstructions to Analyze Dendritic Trees
>> Learn More

Bethesda Scientists Use Neurolucida to Map Memories in the Brain
>> Learn More

Neurolucida Helps Look at Whether Dendrites Can Tell Inputs Apart
>> Learn More

It’s Not You, It’s Your Hormones. Scientists Study Estrogen’s Role in Stress.
>> Learn More

Multiple Sclerosis and Schizophrenia Research May Benefit From New Findings
>> Learn More

University of Maryland Scientists Reconstruct Neuronal Processes in 3D with Neurolucida
>> Learn More

Neurolucida Helps Scientists Better Understand Sound Localization
>> Learn More

Using Neurolucida for Dendritic Spine Analysis
>> Learn More


Visit our blog to read more case studies

Download Neurolucida product sheet here.

Neurolucida® Version 2023.1.2 
Released April 2023

New Features and Enhancements

  • Added support for Leica K5 and K3C cameras’
  • Decimal points can now be entered during setup in the Slide Scanning workflow
  • Smart optimization feature is off by default


View Full Version History Here.

Who Is Using Neurolucida?

Neurolucida is used across the globe by the most prestigious laboratories. 

News About Neurolucida

Cited in Peer Reviewed Scientific Publications

NeuroIucida’s utility is underscored by the number of references it receives in the worlds most important scientific publications.

Frequently Asked Questions (FAQ)

Do I need a microscope to run Neurolucida?

There are editions of Neurolucida available that work with, or without, a microscope.  If the processes from your cells span multiple sections or dozens of fields of view, you may find it quicker and easier to reconstruct your cells with a microscope, using Neurolucida – Microscope Edition.  If you’re reconstructing cells that are relatively easy to image, you may benefit from the automatic reconstruction features available in Neurolucida 360.

Can I use my existing microscope with Neurolucida?

Neurolucida systems can be integrated with all 4 major microscope manufacturers (Zeiss, Olympus, Leica and Nikon). Depending on your microscope model, components, and experimental needs, your current microscope system may require hardware upgrades. Some of the most important components are stage, focus drive, cameras, and light sources. Contact us to assess your microscope system and help you determine a configuration that facilitates your research goals and fits your  budget.

Is Neurolucida only for neuron tracing?

Neurolucida is ideal for reconstructing any cell or structure that has tree-like processes–many researchers use Neurolucida to reconstruct astrocytes, for example.  Neurolucida also enables you to map and reconstruct anatomical regions through serial sections to create 3D models.  You can acquire 3D image stacks and 2D or 3D scans of slides for publication or archival or image analysis away from the microscope.

Which MBF software modules enhance the capture & clarity of microscopic imaging process in Neurolucida Microscope Edition?

The following MBF software modules require Neurolucida to function and can help improve your microscopic imaging process:


  • 2D Slide Scanning Module allows you to create extremely high-resolution montages composed of images obtained from multiple microscopic fields-of-view. The resolution of the individual fields is maintained in the montage, allowing for the capacity to zoom in and out without loss of resolution. You can also combine high magnification detail resolution with a large field of view that is provided by lower power objectives. Scan the entire slide, or only specified sections or regions of interest within a section.


  • 3D Slide Scanning Module allows you to create 3D (focusable) Virtual Tissue images. This module also includes the 2D Slide Scanning  module. 


  • 3D Serial Section Reconstruction Module allows you to create 3D models from serial sections, align serial sections swiftly and precisely and implement shrinkage correction


  • Image Montaging Module allows you to automatically align and stitch together previously acquired 3D image stacks or 2D images to create a high resolution 3D montage of a region of interest


  • Image Stack Module allows you to acquire and analyze confocal, brightfield and widefield fluorescence 3D image stacks. It also adds the capability to create and export brightfield and widefield fluorescence image stacks to Neurolucida offline workstations, and includes 3D image visualization.


  • MRI Extension Module allows you to analyze 3D MRI images.
How do I analyze my data out of Neurolucida?

Every license of Neurolucida and Neurolucida 360 includes access to Neurolucida Explorer companion software. This data-analysis tool can quickly and easily export your data to Excel or to the clipboard.  It even includes batch exporting so that you can process hundreds of data files with just a few clicks!

Do I have to pay extra for Neurolucida Explorer?

No, you will be given access to a free copy of Neurolucida Explorer with every copy of Neurolucida or Neurolucida 360 you purchase.  If you don’t own Neurolucida or you need more licenses for use on analysis-only computers, you can purchase stand-alone Neurolucida Explorer licenses.

What is the difference between Neurolucida and Neurolucida 360?

Neurolucida enables reconstruction of neurons directly from slides, and can connect to a wide range of microscopes, stages, and cameras. You can also import images and trace manually plane by plane in a 2D view. In contrast, Neurolucida 360 does not connect directly to microscope systems; it is designed for automatic, semi-automatic, and manual reconstruction of neuronal architecture from previously acquired images in a 3D environment. You can rotate, pan, and zoom while semi-automatically tracing or editing the computer-generated trace.

Neurolucida is ideal if your cells span across multiple sections or have distances across many fields of view, because reconstructing directly from the slide in live image mode tends to be faster than acquiring many images.  If you’re working from images acquired on a confocal, 2-photon, or other microscope, we recommend Neurolucida 360.

Both Neurolucida and Neurolucida 360 support 3D serial section reconstructions, and offer modules for opening images and image stacks, MRI images, slide scans and other third-party formats.


Robust Professional Support

Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing.  We’ve also developed a host of additional support services, including:

  • Forums
    We have over 25 active forums where open discussions take place.
    >> Learn More
  • On-Site/Training
    We’ve conducted over 750 remote software installations.
    >> Learn More
  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
    >> Learn More

Request an Expert Demonstration

We offer a free expert demonstration of Neurolucida. During your demonstration you’ll also have the opportunity to talk to us about your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, neuron tracing, and image processing.

Related Products

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Recorded Webinars and Videos

Webinar: Introduction to Neurolucida

Webinar: Q&A session on the quantitative analysis capabilities of Neurolucida Explorer

Introduction to Neurolucida