Advanced software 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
- 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, as well as 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, "the most widely used and versatile system to produce neuronal reconstruction is Neurolucida." (P. Aguiar, M. Souda, P. Szucs, 2013)
In addition to 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 optimize your experimental design.
The Neurolucida workstation edition allows researchers to trace and analyze neurons in previously acquired image stacks with a computer that is not connected to a microscope.
Neurolucida on a microscope
A system for neuron tracing and analysis typically includes a computer connected to a microscope. Most of what is visible through the oculars is displayed on the computer screen.
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 on an offline workstation
Pair Neurolucida with the Image Stack extension module and you will be able to acquire image stacks at a microscope, then trace and analyze neurons at a computer workstation to free up the microscope for other projects. Image stacks are also a digital resource to refer to if data needs to be double checked, and it’s a way to preserve your fluorescent tissue since images, unlike fluorescent tissue, don’t degrade, fade, or bleach.
During image stack acquisition, Neurolucida directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes. This means you can automatically capture image stacks at the microscope and analyze them on a computer with the workstation edition of Neurolucida. Image stacks can be saved to the Biolucida Cloud for easy retrieval.
Neurolucida workstation edition is also compatible with image stacks acquired with other software.
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.
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.
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.
Neurolucida has been developed with support from SBIR grants awarded by the NIMH.