Automatically reconstruct microvascular networks
MBF Bioscience > Vesselucida®360

Product Overview

Vesselucida 360 is designed to accurately segment and fully reconstruct vessels and microvasculature in 3D. Vesselucida 360 works on vessels in any species from a variety of labeling and microscopy techniques, as well as with micro-CT. Obtain reliable data about vascular length, connections, loops, and complexity of vessels and microvessels from small or large 3D images.  


Vesselucida 360 software includes breakthrough quantitative analysis capabilities that empower researchers studying neurodegeneration, TBI, stroke, angiogenesis in cancer, diabetic retinopathy, and other conditions that affect microvasculature.

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Key Benefits

Model and quantify blood vessels from any organ and any species

Characterizing and understanding the vasculature in the brain and other organs is fundamental to identifying disease mechanisms that can ultimately uncover new treatment opportunities.  With Vesselucida 360, you can quantitatively characterize vascular architecture in healthy tissue and analyze changes due to injury, age, and/or disease states.

We engineered Vesselucida 360 to provide the research community with a comprehensive solution for quantification of microvasculature structures. With an intuitive 3D environment, automatic detection and modelling of vessels from 3D microscopy image data is not only possible, but fast and easy. Robust tools for viewing and editing both reconstructions and 3D image data enable users to validate and revise reconstructions if needed.

Vesselucida 360 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)


Input Specifications

Supported image file formats



Output Specifications

Model data output formats



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

Image file output formats


Movie export format


Case Study: University of Missouri
Vesselucida Helps Researchers Quantify Post-Injury Capillary Damage and Regeneration
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Case Study: Brown University 
New Therapy May Aid Heart Repair After Heart Attack
>> Learn More

Case Study:  Icahn School of Medicine at Mount Sinai
Scientists use Vesselucida 360 to quantify brain vasculature in mTBI model
>> Learn More

Jaffey, D. M., L. Chesney, et al. (2021). "Stomach serosal arteries distinguish gastric regions of the rat." Journal of Anatomy 239(4): 903-912.

Gama Sosa, M. A., R. De Gasperi, et al. (2019). "Low-level blast exposure disrupts gliovascular and neurovascular connections and induces a chronic vascular pathology in rat brain." Acta Neuropathologica Communications 7(1): 6.

Sullivan, A. E., S. J. Tappan, et al. (2021). "A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling." Neuroinformatics.

Gama Sosa, M. A., R. De Gasperi, et al. (2021). "Low-level blast exposure induces chronic vascular remodeling, perivascular astrocytic degeneration and vascular-associated neuroinflammation." Acta Neuropathologica Communications 9(1): 167.

Yao, Y., A. B. n. Taub, et al. (2021). "Identification of the suprachiasmatic nucleus venous portal system in the mammalian brain." Nature Communications 12(1): 5643.

Button, E. B., Boyce, G. K., Wilkinson, A., Stukas, S., Hayat, A., Fan, J., . . . Wellington, C. L. (2019). ApoA-I deficiency increases cortical amyloid deposition, cerebral amyloid angiopathy, cortical and hippocampal astrogliosis, and amyloid-associated astrocyte reactivity in APP/PS1 mice. Alzheimer's Research & Therapy, 11(1), 44. doi: 10.1186/s13195-019-0497-9.

Munarin, F., Kant, R. J., Rupert, C. E., Khoo, A., & Coulombe, K. L. K. (2020). Engineered human myocardium with local release of angiogenic proteins improves vascularization and cardiac function in injured rat hearts. Biomaterials, 120033. doi:

Rountree, I., Polucha, C., Coulombe, K. L. K., & Munarin, F. (2021). Assessing the angiogenic efficacy of pleiotrophin released from injectable heparin-alginate gels. Tissue Engineering Part A. doi: 10.1089/ten.TEA.2020.0335.

Download our product sheet here.

Who Is Using Vesselucida 360?

Vesselucida 360 is used across the globe by the most prestigious laboratories. 

Cited in Peer Reviewed Scientific Publications

Vesselucida 360’s utility is underscored by the number of references it receives in the worlds most important scientific publications.

Frequently Asked Questions (FAQ)

What’s the difference between tracing vessels using Vesselucida 360 and tracing neuronal structures using Neurolucida 360?

Vesselucida 360 is designed to work with characteristics unique to vessels, which are represented with a graph structure that include loops, rather than neurons which are non-looping branching objects.  Unlike Neurolucida 360, the tracing algorithms and data structure in Vesselucida 360 were specifically developed to model vascular loops. Companion software, Vesselucida Explorer, enables researchers to quantify the frequency and morphology of such anastomoses.

How can I quantify the vessel models created in Vesselucida 360?

With the companion analysis Vesselucida Explorer software, available for free with your Vesselucida 360 purchase, you can perform detailed morphometric analyses of your reconstructions. Obtain quantitative data from a plethora of network, segment, spatial, and puncta analyses with a few clicks. In addition, Vesselucida Explorer can generate graphical displays (e.g., convex hull) to visualize your quantitative data in intuitive ways–and generate figures for publications and presentations.

What are the differences between Vesselucida and Vesselucida 360?

Vesselucida 360 can automatically or semi-automatically reconstruct vasculature and anatomies from images and image stacks acquired using a variety of microscopy types. In contrast, Vesselucida includes microscope-control capability and manual tracing tools to reconstruct vessels in tissue specimen slides directly from a research microscope.

Are there tools for creating high-quality movies and images for publications?

Yes, you can create dynamic, high-resolution MP4 videos of your tracing and image data. You can export images or vector graphics from the main Vesselucida 360 window (2D) or take snapshots in the 3D environment.

Does Vesselucida 360 have any image post-processing tools?

Yes, Vesselucida 360 includes an image filter, specifically designed for vasculature data, that helps make vessels (and other hollow structures) appear solid. The vessel-filter first identifies the boundaries of labeled structures, then synthesizes a cross-section of even intensity based on a model adjusted to fit the input data. An evenly labeled foreground is generated to prepare the output image for automatic digital reconstruction.


I have so many images to process with Vesselucida 360 – can I generate data in batches?

Yes, Vesselucida 360 has sophisticated batch tracing tools. Identify automatic detection parameters that suit your data well, then easily apply the settings to multiple files with very limited user interaction.

To further expand your data throughput, you can batch-apply image filters, batch trace to create your reconstructions, then follow up with batch analyses using Vesselucida Explorer.


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.
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  • 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 both a free expert demonstration and a free trial copy of Vesselucida 360. During your demonstration you’ll have the opportunity to discuss your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, vessel tracing, and image processing.


During your free trial, use the tips and suggestions from a free, expert evaluation and find out how easy Vesselucida 360 is to use and how quickly you can obtain useful data.

Related Products

Vesselucida® Explorer

The analytical software companion for Vesselucida 360 designed to perform extensive morphometric analysis.


Reconstruct and analyze microvascular networks.

Neurolucida® 360

The most advanced software for automatic 3D neuron reconstruction.


Ground-breaking light sheet microscope system for cleared specimens.