An advanced system for neuron tracing and reconstruction, neuron analysis, and 3D brain mapping

Quantify neuronal morphology

Neurolucida is a powerful tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis 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 a recently published paper, Neurolucida is "the most widely used and versatile system to produce neuronal reconstruction is Neurolucida." (P. Aguiar, M. Souda, P. Szucs, 2013

In addition to the software for neuron tracing and analysis, a Neurolucida system includes any hardware you need, such as a microscope, computer, motorized stage, camera, etc., and comes with MBF’s technical support for the entire system as well as research support to help optimize your experimental design.

Neurolucida can be used to trace neurons directly from a brightfield or widefield fluorescence microscope, or from image stacks. 

Neurolucida on a microscope

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

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

Neurolucida works with brightfield, multi-channel fluorescence, confocal, structured illumination, and two-photon microscopes.


Neuron tracing with image stacks


There are three different options for tracing and analyzing neurons in image stacks.

1) Pair Neurolucida with the Image Stack extension module to acquire image stacks and analyze them at the microscope

2) Use Neurolucida Desktop to trace and analyze neurons on any desktop PC. Works with image stacks acquired with the Image Stack module or with third party software

3) Acquire image stacks at the microscope with Neurolucida and the Image Stack module, and then analyze them on a different computer with Neurolucida Desktop

When you acquire image stacks with Neurolucida, the software directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes. This means that Neurolucida automatically captures the images so you can work on other projects. Image stacks can also be saved to the Biolucida Cloud for easy retrieval.

+ Read about how to analyze tissue clarified with CLARITY, SeeDB, 3DISCO, and more

Neurolucida on whole slide images

Neurolucida also works with whole slide images (digital scans of your specimen) from providers such as Aperio and Hamamatsu, and it can capture whole slide images of your entire specimen in 3D (x, y, and z) or 2D (x, y) with the addition of the Virtual Tissue 3D or 2D module. 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 Cloud, MBF’s image viewing, sharing, and storing software.

Serial section reconstructions

Use serial section reconstructions to trace and analyze neurons through multiple sections, or to create a 3D model of the organ and its regions for brain mapping and quantification. The 3D visualization capabilities in Neurolucida allow you to view the structures the way they were in the model organism, from any angle.

After mounting the sections, they are certain to be in different orientations on the slide. Neurolucida has tools to help align the tracing of the section or sections you have already traced to the image of the section you are about to trace. The automatic contouring tool in Neurolucida automatically traces anatomical boundaries to make serial section reconstruction easier and faster.

+ Watch automatic contouring in a 30 second video on YouTube


3D brain mapping

Neurolucida has advanced tools and analyses for 3D brain mapping.  Map and analyze a long neuronal pathway, or map the distribution of cells in a region of interest.

  • Use the full power of Neurolucida to quantitatively analyze brain maps. 
  • 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

Customized neuron tracing & analysis solutions

Each Neurolucida system is customized for your lab. We can provide solely software and integration to labs that already have all the necessary equipment, or we can provide complete systems including microscopes, motorized stages, cameras, computers and software. Either way, our systems are fully integrated, allowing our software to drive motorized parts of the microscope system. Extension modules and additional hardware can be added to your system as your needs evolve.

Each Neurolucida system we configure is:

  • Based upon individual research needs.
  • Fully integrated - Neurolucida software drives motorized stages, cameras, filter wheels etc.
  • Scalable to fit your budget and allow room for additional capabilities via our extension modules.
  • Supported by our team of scientists and technicians including five PhDs in neuroscience and four PhDs in image processing.  Our scientists can also help you design your study.
  • Upgradable to new software versions that are released regularly.

+ Learn more about neuron tracing

Neurolucida has been developed with support from SBIR grants awarded by the NIMH.

Halavi M., Hamilton K.A., Parekh R. and Ascoli G.A. (2012). Digital reconstructions of neuronal morphology: three decades of research trends. Front. Neurosci. 6:49. doi:10.3389/fnins.2012.00049