Vesselucida 360

Vesselucida® 360

Quantify Microvasculature Accurately and Efficiently

Vesselucida 360 is revolutionary software designed to quickly segment and fully reconstruct vessels and microvasculature in 3D to obtain reliable data about the length, connections, and complexity of vessels and microvessels. The breakthrough software’s quantitative analysis capabilties are designed to empower researchers studying cancer, diabetes, strokes, and other conditions that affect microvasculature.


  • Changes in vasculature due to traumatic brain injury or stroke
  • Changes in blood vessels of the retina due to diabetes (diabetic retinopathy)
  • New blood vessels due to a cancerous tumor (angiogenesis)

See how Vesselucida 360 revolutionizes microvasculature reconstruction and analysis!

    No Bottom Padding

    Move at the Speed of Neuroscience with the Latest Version of Vesselucida 360

    We’ve re-engineered image and data handling within MBF Bioscience software solutions from the ground up to maximize your computer hardware investment. No matter the image data size, from lightsheet microscopes, confocal microscopes, or slide scanners, you are now able to work efficiently, and without delay.

    Image load times in Vesselucida 360 is up to 5000x faster in the 3D environment and 250x faster in the 2D environment, so now your research can move as fast as you do.

    With our new intelligent image loading, maximized concurrent usage of CPU cores, multiple levels of data caching, and efficient use of RAM and GPU resources, you can now display and reconstruct your images faster than ever before to you make your scientific discoveries.

    Introduction to: Vesselucida 360



    Vesselucida 360 efficiently, accurately, and automatically reconstructs microvasculature in 3D. Watch the video to see how fast, easy, and accurate our software is!


    A Comprehensive Solution to Analyze Microvasculature

    Vesselucida works with 3D images from a wide array of imaging techniques, even large 3D images of intact tissue specimens. Once your reconstruction is complete, you can obtain a comprehensive morphological profile.

    • Fully reconstruct microvascular structures in 3D accurately and fast
    • Built-in quantitative analyses means no need for programming skills or the creation of supplementary scripts (e.g., MatLab)
    • Metrics for comprehensive morphological analyses: Segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more
    • Consult with our staff scientists to determine the best course of action to make sense of your data

    Customer Reviews

    "After examining different vessel quantification tools for use with neovessel formation in the heart, we chose to use Vesselucida 360 because it offered us flexibility in viewing and adjusting vessel geometries in 3D to accurately represent our microCT dataset. Also, the quantitative parameter extrapolation is excellent."
    Dr. Kareen Coulombe
    Brown University
    "Vesselucida enables us to visualize and quantify microvascular networks in a way that has not been done before. The ability to render 3D maps is integral to analysis of network structure, remodeling and blood flow distribution."
    Dr. Nicole Jacobsen
    University of Missouri
    "Mapping microvascular networks are opening the door on novel aspects of microvascular perfusion. At this preliminary stage we are able to identify a fundamentally new perspective on oxygen transport. Very exciting to be developing this with you guys."
    Prof. Steven Segal, Ph.D.
    University of Missouri
    "The support team at MBF Bioscience has been great to work with. As a beta test site for Vesselucida, we are in constant communication. Their staff is professional & responsive to the problems we have identified & our requests for specific applications."
    Rebecca Shaw, Research Specialist
    University of Missouri
    Using Vesselucida, we were able to assess changes in resistance network architecture during muscle regeneration for the first time. We were limited by other imaging methods due to the network size and location of arteriolar networks within skeletal muscle. Vesselucida uniquely enabled us to reconstruct and analyze intact arteriolar networks in 3 dimensions with micrometer resolution over distances spanning millimeters to centimeters.
    Dr. Nicole Jacobsen
    University of Missouri

    Automatically Reconstruct Vasculature

    The sophisticated software algorithms in Vesselucida 360 were developed specifically to take into account vascular loops. 

    Compare with Ground-Truth Data

    Vesselucida 360 also includes a full suite of tools to manually trace and edit your reconstruction to create a ground-truth representation of your vascular data. You can also fine-tune and correct the automatic reconstructions in cases of particularly challenging image data.

    Case Studies

    Case Study: Several research affiliations, including MBF Bioscience

    A team of researchers observed chronic neurovascular damage in a rat model of mTBI. Ten-months after rats were exposed to a series of blasts, the researchers captured micro-CT images of the rat brains. Vesselucida 360 analyzed the data in these micro-CT scans and automatically reconstructed the vascular networks in 3D. For more efficient visualization, the software color-coded individual vessels. The analysis revealed decreases in neurovascular length, total surface area, and total volume as compared to controls. It also showed a disorganization of the neat radial patterns that blood vessels in healthy brains are normally arranged in.

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    Case Study: Brown University

    Researchers in the Coulombe Lab at Brown University, may be able to provide hearts with the support they need to recover after a heart attack. Using Vesselucida 360 and Vesselucida Explorer to trace and quantify blood vessels in rat hearts, they observed a more robust vascular network in rats that received engineered tissue implants.

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    Case Study: University of Missouri, Columbia

    In a study published in the Journal of Physiology, researchers at the University of Missouri, Columbia, describe short- and long-term capillary damage and recovery after acute skeletal muscle injury. The researchers observed that two to three days after injury, surviving microvessel fragments began to sprout new capillaries, and that five days post-injury new functional capillary networks formed.


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    Comprehensive Quantitative Analyses

    Our rigorously tested analyses provide accurate and robust results that you and others can trust in publications.

    Use Vesselucida Explorer, Vesselucida 360 companion analysis software, to perform sophisticated analyses that help answer your research questions.

    We provide dozens of analyses that analyze and graph hundreds of metrics and parameters, including: 

    • Structure
    • Distribution
    • Orientation
    • Colocalization

    Our New Machine Learning Algorithms Allow you to Make New Discoveries

    Puncta detection in the 3D environment allows you to detect anything from cells to punctate subcellular structures. The feature includes the ability to utilize machine learning to generate more accurate reconstructions. The machine learning detection mechanism employs specific models of object size and appearance that accept or reject locations in your image that meet general detection parameters. Only objects that meet the requirements of the specialized machine learning model are further considered for detection and reconstruction, leading to a more accurate selection of puncta of interest.

    Image courtesy: Campbell-Thompson, M., Butterworth, E., Carty, K., Nasif, L., & Peñaloza, J. (2021). Human Islet Microvasculature Analysis (Version 5) [Data set]. Blackfynn Discover.

    Our New High-Tech Imaging Engine Allow you to make your Scientific Discoveries Flow with Ease. These Include:




    The subvolume function enables seamless, dynamic tracing on systematically selected focus sites of 2D and 3D image stacks within the 3D environment.

    No Padding


    Color channel specification allows you to select one or multiple channels to view, hide, and reconstruct your images by associating traced structures with specific color channels in the 3D environment to facilitate multiplexed analyses.

    Image courtesy: Campbell-Thompson, M., Butterworth, E., Carty, K., Nasif, L., & Peñaloza, J. (2021). Human Islet Microvasculature Analysis (Version 5) [Data set]. Blackfynn Discover.

    Real-Time Interactive 3D Visualization

    As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable for effective data interpretation. 

    Our software includes a highly versatile 3D visualization environment suitable to most microscopy images with state-of-the-art functionalities to support your analysis and publication needs.

    No Bottom Padding
    • Visualize large, complex 3D images (including multichannel images) and reconstructions
    • 2D and 3D image data from two-photon, confocal, brightfield or light sheet microscopy
    • 3D volume, image slicing, and simultaneous views
    • Multiple projections: XY, YZ, XZ, alpha, minimum, and maximum
    • Transparency, rendering (wireframe, centerline, surface, texture) and other display options for image and traces that can be adjusted on the fly
    • Create dynamic movies
    • Export options including exporting 3D graphics to third-party applications
    • Loads complex surfaces in seconds
    • Works with the most advanced “gaming class” graphics cards to deliver high performance visualization at an affordable price
    • Support almost all file formats
    No Top Padding

    Compatible with Most Microscopy File Formats

    • Brightfield
    • Two-photon
    • Confocal 
    • Fluorescence
    • Light sheet
    • Slide scanners
    • MicroCT

    Our File Format is Now Open and FAIR to Allow Collaboration Between the Scientific Community

    Vesselucida 360 supports the collaborative goals of Open Science through the practice of data openness, integrity, and reproducibility, by using MBF Bioscience’s published digital reconstruction data file format, the Neuromorphological File Specification (NFS).

    The data elements in this NFS format were specifically implemented to ensure the files are Findable, Accessible, Interoperable, and Reusable (FAIR). Abiding by these data standards and providing microscopy image and experimental data provenance enhances the ease of repurposing this data. Encoded in the well-recognized and readable format, the modeling elements specify microscopic neuroanatomies in a calibrated 3D coordinate system with appropriate units.

    These Vesselucida 360 files can also easily be viewed and parsed in a variety of software, e.g. MATLAB and Python. To learn more about the key elements of the file format and their relevant structural advantages, view our manuscript, A comprehensive, FAIR file format for neuroanatomical structure modeling.

    What are the Differences Between Vesselucida and Vesselucida 360?


     To learn more about Vesselucida Microscope Edition click here.

    Designed by Scientists for Scientists

    Developed with support from the National Institute of Mental Health (NIMH), Vesselucida 360 was specifically designed for researchers focused on conditions affecting microvasculature. Our scientists regularly consult with our customers to gain a better understanding of their needs and incorporate their suggestions into the design of Vesselucida 360. Our staff scientists are available to help you determine the best course of action to make the most sense of your data.

    Professional Technical Support

    When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

    Contract Services for Vessel Reconstruction

    Our Vessel Reconstruction services gives your lab the ability to have industry-leading experts create a 3D reconstruction of microvasculature, for your research MBF Labs will reconstruct your microvasculature giving you a breadth of quantitative including  length, volume, connections, and the complexity of the micro vessels. By providing us with slides or images, our experts at MBF Labs are able to quantify changes in vasculature derived from traumatic brain injury, stroke, changes in blood vessels of the retina due to diabetes, new blood vessels due to a cancerous tumor.

    Request More Information

    MBF Bioscience Forum

    Get answers to your most pressing research and technical questions from MBF scientists and fellow researchers.


    Visit MBF Bioscience Forum



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

    We can also custom develop for you

    MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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