The analytical companion for Vesselucida 360 designed to perform extensive morphometric analysis
MBF Bioscience > Vesselucida®Explorer

Product Overview

Vesselucida Explorer is the analytical software companion for Vesselucida and Vesselucida 360 – engineered to perform extensive morphometric analyses on microvascular models and serial section reconstructions.


Dynamically visualize and comprehensively analyze vessels, puncta, and regions in an intuitive 3D environment while making quantitative measurements. Vesselucida Explorer is highly interactive, enabling researchers to explore their data models and export quantitative metrics generated directly from the models.

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Key Benefits

Comprehensive quantitative vascular and anatomical morphometric analysis

Understanding the vascular makeup of cerebral architecture or visceral organs is an integral part of uncovering mechanisms of disease and finding new treatments.  With Vesselucida Explorer, you can quantify vascular morphology from vessel reconstruction data derived in Vesselucida 360 or Vesselucida.

Vesselucida Explorer is equipped with dozens of neuronal and regional analyses that are customizable to your specific research questions. We have removed the obstacles for rapid, high-volume, quantitative data analysis by programming all the complex morphological analyses, so you don’t have to.

Minimum System Requirements

Operating system

Windows 10, 64-bit

Input Specifications

Supported image file formats

XML, ASC, or DAT generated in Vesselucida 360 or Vesselucida

Output Specifications

Tracing export formats

Data model: XML*, ASC, DAT, NRX 

Vector: SVG 

Images: TIFF, JPEG, PNG 

Marker coordinates: TXT 


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

Case Study
Vesselucida Helps Researchers at University of Missouri to Quantify Post-Injury Capillary Damage and Regeneration
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Case Study
New Therapy May Aid Heart Repair After Heart Attack
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Case Study
Scientists at Icahn School of Medicine at Mount Sinai use Vesselucida 360 to quantify brain vasculature in mTBI model
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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 Explorer?

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

Cited in Peer Reviewed Scientific Publications

Vesselucida Explorer’s utility is underscored by the number of references it receives in the worlds most important scientific publications. See examples below: 

Frequently Asked Questions (FAQ)

Do I have to purchase Vesselucida 360 and Vesselucida Explorer separately?

Vesselucida Explorer software is complimentary to the purchase of Vesselucida or Vesselucida 360 software. Additional licenses of Vesselucida Explorer sold separately.

Can I install Vesselucida Explorer on a different computer than Vesselucida or Vesselucida 360?

Yes. Though Vesselucida Explorer can be directly launched from Vesselucida or Vesselucida 360 applications, the software can be installed separately on other computers in your lab to increase data generation and interpretation throughput.

Can I export Vesselucida Explorer-derived metrics?

With a click of a button, the tabular morphometric data generated by Vesselucida Explorer can be easily exported to Excel. For researchers who prefer to program custom analyses and operations, data can be exported as separate files for loading into other software such as Matlab, Python, or R. 

Can I request a custom analysis that isn’t already included in the Vesselucida Explorer toolset?

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. 

What are the differences between Vesselucida 360 and Vesselucida Explorer?

Vesselucida Explorer is the analytical software companion for Vesselucida and Vesselucida 360. Researchers can use Vesselucida 360 or Vesselucida to generate vessel reconstructions and anatomical models from acquired image data or directly from slides at the microscope, respectively. Then you can leave the image data and microscope behind, and employ Vesselucida Explorer to quantify the Vesselucida 360 or Vesselucida -derived models. 

Are there online resources to help me learn the software and better understand the analysis formulas in Vesselucida Explorer?

All MBF Bioscience software comes with comprehensive, context-sensitive help guides accessible online or offline. All of the analysis available in Vesselucida Explorer have been fully documented in the product user-guide.


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.
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  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
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Request an Expert Demonstration

We offer both a free demonstration and a free trial copy of Vesselucida Explorer. During your demonstration you’ll 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.


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