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. 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 works on vessels in any species from a variety of labeling and microscopy techniques such as:

  • Immunofluorescence
  • Immunohistochemistry
  • Animal models with fluorescent reporters
  • Lectin perfusion
  • Brightfield
  • Widefield fluorescence
  • Confocal
  • Light sheet
  • 2-Photon, Multi-Photon
  • Micro-CT
  • Whole brain or organ
  • Cleared tissue
  • Sectioned tissue
  • Cultures
  • Expanded tissue


Vesselucida 360 has been developed with support from the National Institute of Mental Health (NIMH)

Recommended Hardware Requirements

Vesselucida 360 is a powerful software that can work with a wide range of image data of vastly different levels of size and complexity. Because of its flexibility, our recommendations for system configurations vary to balance the affordability of lower computing power for smaller data sets to more expensive high-end workstations for large, multi-channel data.
Please contact us to consult with our technical specialists for a more precise recommendation specific to your data needs.

64-bit Windows 11 operating system
CPU with 8 cores (16 threads) or more. More cores improve performance when using large data sets (>1 GB).
Solid state hard drive(s). Preferably, non-volatile memory express (NVMe) drives.
64 GB of system memory or more. More memory is better for large data sets, especially for image handling and reconstruction in the 3D environment.
Graphics card with 8 GB memory or more. Most graphics cards from NVIDIA and AMD have been tested with MBF Bioscience software.
Minimum Hardware Requirements
64-bit Windows 10 operating system
8 core processor (16 threads)
32 GB memory
Graphics card with 6 GB memory or more: This is the minimum needed for the 3D environment, but is adequate for working only in 2D.
Computer-Hardware Upgrade Priorities
To upgrade your system for better performance with MBF Bioscience software, we suggest that you prioritize computer hardware upgrades as follows:
      • Increase system memory to at least 128 GB. More memory improves performance when using large data sets
      • Replace hard disk drives (HDDs) with solid-state drives (SSDs), preferably non-volatile memory express (NVMe) drives
      • If you're working with 3D images and graphics, upgrade graphics card (GPU) to one with at least 8-12 GB memory

Vesselucida Helps Researchers Quantify Post-Injury Capillary Damage and Regeneration
>> Learn More

New Therapy May Aid Heart Repair After Heart Attack
>> Learn More

Scientists use Vesselucida 360 to quantify brain vasculature in mTBI model
>> Learn More


Visit our blog to read more case studies

Download Vesselucida 360 product sheet here.

Vesselucida® 360 Version 2022.1.1
Released December 2022

New Features and Enhancements:

  • New Batch Pipeline enables easy-to-use batch processing for image filtering, and automatic detection
    and reconstruction of vessels and puncta
  • New ability to save your 3D settings automatic vessel and puncta detection/reconstruction for use in the
    Batch Pipeline
  • New Pipelines ribbon now houses features previously located in the Automatic section of the Trace
  • Improved & expanded image support
  • New automatic, smart image-optimization preference for low-signal images available
  • Improvements to puncta detections, including recognition of manually traced vessels/puncta in other
    color channels for proximity-based puncta detection.
  • The subvolume tool is now restricted by the bounds of the image
  • In the Cell detection workflow, the image source is automatically updated based on the image modality
  • Image montage can now assemble image tiles of varying x/y sizes


SPARC Users:

  • SPARC vocabulary term lists displayed as ontological trees


View Full Version History Here.

This is a Vesselucida 360 Poster

Automated reconstruction of vasculature in cleared, intact brain specimens

Automatically reconstruct arteries, veins, and capillaries with Vesselucida 360

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Who Is Using Vesselucida 360?​

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

News About Vesselucida 360

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.
    >> 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.
    >> 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.

ClearScope® - The Light Sheet Theta Microscope

Ground-breaking light sheet microscope system for cleared specimens.

Recorded Webinars and Videos

Webinar: Reconstructing Neuron and Vessel Morphology in Cleared Tissue

Webinar: Reconstructing Vasculature & Obtaining Data using Vesselucida 360 and Vesselucida Explorer

Introduction to: Vesselucida 360