INCF endorses the MBF Bioscience neuromorphological file format
We are pleased to announce that the International Neuroinformatics Coordinating Facility (INCF) has endorsed the MBF Bioscience neuromorphological file format as
Neurolucida®
Neuron tracing & analysis directly on the microscope. The gold standard for neuron tracing.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
- Create quantifiable reconstructions using automated neuron tracing tools
- Trace directly on a microscope without the need for acquiring large image files
- Get started quickly with the intuitive, easy-to-use Neurolucida interface
- Seamlessly controls dedicated microscope hardware for efficient neuroanatomical data and image acquisition using brightfield, darkfield and multi-channel florescence
The Neurolucida system is widely recognized by neuroscientists as the gold standard for neuron tracing and 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 |
| Processor | 4-core |
| CPU RAM | 16 GB |
| GPU RAM | >6 GB |
| Recommended System Requirements | |
| Operating System | Windows 10, 64-bit |
| Processor | 8-core |
| CPU RAM | 64 GB |
| GPU RAM | >8 GB |
| Storage | Solid state drive(s) |
| File Input Options | |
| Supported image file formats | CZI, HDF5, H5, IMS, JP2, JPG, JPEG, JPF, MJC, JPX, LIF, LSM, ND2, OIB, OIF, TIF, TIFF, SVS |
| Output Specifications | |
| Data output formats | XML*, ASC, DAT |
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| * Our XML data file format, the Neuromorphological File Specification (NFS), is endorsed as a standard by the INCF. |
| Image file output formats | JP2, JPX, TIFF, SVG |
| Movie export format | MP4 |
| Hardware Compatibility | ||
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Computer controlled microscopes | Leica supported microscopes:
| Zeiss supported microscopes:
Nikon supported microscopes
Olympus BX and IX Series:
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| Manual microscopes | Most models after 2002 of Zeiss, Olympus, Nikon, Leica | |
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Structured illumination |
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| Filter wheels and shutters | Zeiss, Olympus, Leica, Nikon, LEP, Prior, Sutter | |
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Color video cameras |
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Monochrome video cameras |
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| Light sources |
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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
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Researchers Observe Altered Neuropathology in CTE Brains
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Scientists Discover New “Rosehip” Neuron in Human Brain
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NeuroMorpho.Org Releases Nearly 10,000 New Neuron Reconstructions and Neurolucida leads the way
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Exercise changes astrocytes and eases symptoms of neurodegenerative disorders
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Uncovering the role of microglia in fetal alcohol spectrum disorders
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Scientists Observe Differences Between Brains of Stressed and Unstressed Rats After Fear Conditioning
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Hippocampal Neurons Change After Melatonin Injection
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Dendritic Spine Loss Reported in Schizophrenia and Bipolar Disorder
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Two 2014 Nobel Laureates Used Neurolucida to Create 3D Reconstructions of Neurons That Help Rats and Humans Navigate the World
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Anorexia Accelerates the Development of the Rat Hippocampus
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Scientists Use Neurolucida to Create 3D Reconstructions of Placental Villous Trees
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New Neurons Erase Memories
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Brain Cleans Itself During Sleep; Scientists Image Cerebral Fluid Flow With Neurolucida
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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
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Ohio State Neuroscientists Use Neurolucida to Analyze Brain Cells in Sexually Active Hamsters
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Japanese Researchers Develop New Optical Clearing Agent; Neurolucida Used For 3D Imaging in Study
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Drug for Treating Asthma Improves Cognitive Function in Down Syndrome Mouse Model
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Neurolucida Helps Ohio State Scientists Study Melatonin’s Effects on Brain Plasticity in Mice
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Researchers at the University of Michigan Analyze Spine Density in Addiction-Prone Rats with Neurolucida
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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
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Scientists Use Neurolucida in Study Describing New Cell Population in Juvenile CA3 Hippocampus
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Scientists in Japan Identify Two Brain Circuits Involved in Image Recognition; Neurolucida Plays Part
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UVA Scientists Use Neurolucida in Study Identifying Two New Circuits in Rat Neocortex
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Neurolucida Helps Scientists Map Rett Syndrome’s Brain Dysfunction in Mouse Model
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Scientists Map Diaphragm’s Motor Nerve and Arteriolar Networks With Neurolucida
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Neuroscientists in Germany Outline Protocol for Best Accuracy in Neuron Reconstruction, including Use of Neurolucida
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Gene Therapy May Be Answer to Effective Parkinson’s Treatment; Neurolucida Plays Role in Study
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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
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UVM Scientists Use Neurolucida and Stereo Investigator to Study Neurons in the Avian Iris
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French Scientists Use Neurolucida to Study Plasticity in Adult Neurons
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Neurolucida Helps Florida Researchers Reconstruct a Region of the Rat Brain
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In the Forest of the Mind
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Columbia Scientists Map Neocortical Circuit Connectivity with Neurolucida
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Scientists use Neurolucida Reconstructions to Analyze Dendritic Trees
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Bethesda Scientists Use Neurolucida to Map Memories in the Brain
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Neurolucida Helps Look at Whether Dendrites Can Tell Inputs Apart
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It’s Not You, It’s Your Hormones. Scientists Study Estrogen’s Role in Stress.
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Multiple Sclerosis and Schizophrenia Research May Benefit From New Findings
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University of Maryland Scientists Reconstruct Neuronal Processes in 3D with Neurolucida
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Neurolucida Helps Scientists Better Understand Sound Localization
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Using Neurolucida for Dendritic Spine Analysis
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Download Neurolucida product sheet here.
Neurolucida® Version 2024.1.2
New Features and EnhancementsReleased July 2024
- New auto-calibration feature offers hands-free correction for camera rotation and establishes lens calibration
- New Scan Repair for continuing incomplete slide scans and replacing problematic image tiles
- Added the ability to Live Zoom or zoom in on the live-camera feed
- Slide scanning workflow now includes the option to employ “Stitching” for improved alignment of adjacent images
- Added new vessel tracing tools
- Added the ability to conduct Parcentric Parfocal calibration of just a single objective
- Slide Scanning added a new filter for background subtraction
- New ability to set the rotation angle in 3D view
- Biolucida integration
- New image browser
- Improved Biolucida connection interface
- Added support for the new MBF Bioscience Vesalius Spinning disk confocal structured illumination device
- Added support for Aura Light source and the 89 North LDI
- Can now save a file containing a single color channel from a multi-color channel image
- Added support for 12-bit OME-TIFF files
View Full Version History Here.
Neurolucida: Key Features
Quantify neuronal morphology
The Neurolucida microscopy system was built by engineers working in close collaboration with neuroscience researchers to perform accurate reconstruction of neuronal structures directly from histological specimens. It is capable of over 500 quantitative morphometric analyses for structures, including:
- Metrics about dendrites, axons, nodes, synapses, and spines
- The complexity, branching and extents of neurons
- Proximity, direction and network schemas
Neurolucida: Key Features
Reconstruct neurons from a single section or from serial sections
To obtain morphometric data about neurons or structures that extend beyond a single tissue section, creating a serial section reconstruction—a digital representation of aligned serial tissue sections—is extremely useful. You can reconstruct serial sections directly at the microscope or using images captured with Neurolucida.
Neurolucida includes tools that help you create neuron and neuroanatomical volume reconstructions quickly, including a tool for automatically tracing the outline of each tissue section or cytoarchitectural boundaries within the specimen. Once the reconstruction is complete, you can trace neurons and other structures of interest in each tissue section at a higher magnification and see the bigger picture with clarity.
Neurolucida: Key Features
Acquire images, image stacks and whole-slide images
Neurolucida can serve as your microscope image acquisition system, too. With features to acquire high-quality images and z-stacks, your system can be used for much more than neuron tracing. You can also capture high-quality 2D and 3D whole-slide images (high resolution digital montages of your specimen) with the addition of the Slide-Scanning Module. Use image processing features such as background correction to insure clean, even, image quality images. Neurolucida can acquire a wide array of images, using brightfield and multi-channel fluorescence that surpass the quality of most slide scanners in a box.
Neurolucida: Key Features
Automatic cell-detection workflow
Identify labeled neurons in whole slide images using an intuitive cell detection workflow that incorporates advanced machine learning. Our deep-learning algorithms provide robust cell detection even when there are histologic and/or imaging artifacts such as edge effects, uneven illumination, and variable staining across specimens.
Neurolucida: Key Features
Work with images from other sources
Neurolucida also supports importing image stacks and whole-slide images acquired using other systems. Working with whole-slide images enables you to create and analyze neuron tracings and reconstructions on any computer, even those not connected to a microscope.
Neurolucida: Key Features
Powerful quantitative analyses
Neurolucida Explorer, the companion software included with Neurolucida, includes dozens of quantitative morphometric analyses that you can run on reconstructions and brain maps created using Neurolucida. Reconstruct and visualize your specimen with Neurolucida, then use Neurolucida Explorer to obtain quantitative data that extend your results. Developed in concert with neuroscientists using our products, Neurolucida Explorer can be used to analyze thousands of parameters. It includes an easy-to-use batch processing function and can export results that are compatible with other software such as Excel, Matlab, Python, and R.
Who Is Using Neurolucida?
Neurolucida is used across the globe by the most prestigious laboratories.
News About Neurolucida
Neurolucida helps to reveal new findings in a follow-up to a 40 year old study
When we flex our thumb or point our finger, axons carry impulses from the brain to neurons in the spinal cord,
Researchers Observe Altered Neuropathology in CTE Brains
Researchers at Colorado College may have identified a new neuropathological hallmark of Chronic Traumatic Encephalopathy (CTE). Their findings, published in the
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.
Ament, S. A., M. Cortes-Gutierrez, et al.
A single-cell genomic atlas for maturation of the human cerebellum during early childhoodView Publication
Timonidis, N., M. Rubio-Teves, et al.
Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference SpaceView Publication
Jeon, K.-I., A. Kumar, et al.
Blocking Mitochondrial Pyruvate Transport Alters Corneal Myofibroblast Phenotype: A New Target for Treating FibrosisView Publication
Tetsushi, N., F. Satoshi, et al.
Microglia are dispensable for developmental dendrite pruning of mitral cells in miceView Publication
Qin, Y., X.-Y. Zhang, et al.
Downregulation of mGluR1-mediated signaling underlying autistic-like core symptoms in Shank1 P1812L-knock-in miceView Publication
Nevue, A. A., B. M. Zemel, et al.
Cell type specializations of the vocal-motor cortex in songbirdsView Publication
Hernandez-Reynoso, A. G., B. S. Sturgill, et al.
The effect of a Mn(III)tetrakis(4-benzoic acid) porphyrin (MnTBAP) coating on the chronic recording performance of planar silicon intracortical microelectrode arraysView Publication
Rasmussen, V. F., A. Schmeichel, et al.
Sweat gland nerve fiber density and association with sudomotor function, symptoms, and risk factors in adolescents with type 1 diabetesView Publication
Beers, D., D. Goniotaki, et al.
Barcodes distinguishing morphology of neuronal tauopathyView Publication
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.
Testimonials
"We are enjoying using your fantastic software and it is making a difference to our work."
"Our system worked almost every day for the last eight years with no major failure (we published more than 15 papers using Neurolucida). A terrific machine!"
"I have been using Neurolucida for over 20 years now. It sets the standard for what a tracing program should be able to do, and the ease of use has continually increased over the years. I have undergraduates using the program within a week. Moreover, the support MBF Bioscience provides is unmatched--they are the best."
"We have been tracing dendrites for almost 30 years, using a variety of home-grown and commercial systems. We have used Neurolucida for almost 15 of those years now, and it is by far the most powerful, reliable, flexible, and easy to learn and use system of all that we’ve worked with. Neurolucida is clearly the product of people who thoroughly understand and appreciate quantitative neuroanatomy. This system has been absolutely indispensable to our research, resulting in over 25 publications. I can’t imagine our science without Neurolucida! Furthermore, the support provided by MBF has been simply outstanding, including program modifications, hardware support and development, troubleshooting, you name it - and always provided quickly, cheerfully, and knowledgeably. Nobody does it better!"
"I'm a huge fan Neurolucida's cell tracing and auto-detection features, which greatly assisted me in characterizing the morphology of abnormal neurons. Neurolucida is easily learned, intuitive, and was clearly designed by scientists."
"I have also been using Neurolucida for over 20 years with over 50 publications that have relied at least in part on the software. The product is marvelous and the support is the best of any software product I own. The work we do would be next to impossible without Neurolucida. The software is so intuitive that even high school students can do basic tracing almost immediately."
Robust Professional Support
Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron tracing and 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.
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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.
