Neurolucida

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 and whole slide images (virtual slides). 

Neurolucida on a microscope

Microscope 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. Add the Lucivid to Neurolucida and you can trace neurons while looking through the oculars.    

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.

 

Neurolucida for neuron tracing from image stacks

Tracing neurons at the microscope from fluorescent tissue specimens can be problematic since exposure to light degrades fluorescent tissue. Therefore, many researchers capture images of their fluorescent tissue and then reconstruct and analyze neurons. Neurolucida can acquire image stacks and virtual tissues, or, if you already have images, you can use Neurolucida Desktop for neuron reconstruction and analysis. Neurolucida Desktop is a Neurolucida system that's not connected to a microscope. A Neurolucida Desktop system typically includes high-powered PC running Neurolucida and any necessary software extension modules. 

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

1) Acquire image stacks at the microscope with Neurolucida and the Image Stack module, and then analyze the image stacks on the computer that's connected to the microscope.

2) Use Neurolucida Desktop to trace and analyze neurons on a desktop PC not connected to a microscope. Works with image stacks acquired 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 Biolucida, an application for managing and sharing large image data sets.

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

 

Neurolucida on whole slide images

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 Virtual Tissue 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 Cloud, MBF’s image viewing, sharing, and storing application.

Serial section reconstructions

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.

+ Watch automatic contouring in a 30 second video on YouTube

 

3D brain mapping

After reconstructing serial sections of an entire brain, Neurolucida has advanced tools and analyses for analyzing the 3D representation of a brain specimen (see image below).

  • 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
 

Customized neuron tracing & analysis solutions

Each Neurolucida system is customized for your lab. We can provide 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