The file format is used in our products for neuroscience research for important applications such as digital neuron tracing, brain mapping and stereological analyses. MBF Bioscience products, including Neurolucida, Neurolucida 360, Stereo Investigator, Vesselucida 360, and NeuroInfo use this neuromorphological file format.

This file format has evolved over several decades through input and requests from many scientists who’ve been using our products. The current format is truly a collaborative effort between MBF and our users.

“We are very pleased to have received this endorsement from the INCF. It recognizes our ongoing efforts in supporting open and FAIR neuroscience, and our commitment to supporting neuroscience researchers. We’ve established rigorous standards and processes for the file format so that it can be confidently used by the entire research community”, said Jack Glaser, President of MBF Bioscience.

What does this mean for researchers who use MBF products? It expands opportunities for data sharing between individual researchers, laboratories, and within larger collaborative research initiatives. Also, it will be easier for third-party software tools to be developed and maintained that extend the usefulness of the data generated by MBF products.

The official INCF announcement stated, “The committee is pleased to see an open format from a commercial entity go through the endorsement process, and applaud MBF Bioscience for taking this very important step in support of open and FAIR neuroscience. The committee considers the governance process for MBF Bioscience’s neuromorphological file format to be well elaborated, with a sufficient mechanism for the user community to request format updates.”

MBF Bioscience and the INCF will work together to further improve the FAIRness of the standard, including implementation of the governance policy and modification of the standard’s license from the CC-BY-ND-NC to a CC-BY-ND.

The standard number is INCFSN-22-01.

Read the review report, with community feedback in comments: https://f1000research.com/documents/10-712

Read the full INCF endorsement here: https://www.incf.org/blog/incf-endorses-mbf-neuromorphological-file-format

Read a recent publication on the format:

A.E. Sullivan, S. J. Tappan, P. J. Angstman, A. Rodriguez, G. C. Thomas, D. M. Hoppes, M. A. Abdul-Karim, M. L. Heal & Jack R. Glaser. A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling. Neuroinform (2021). https://doi.org/10.1007/s12021-021-09530-x

The post INCF endorses the MBF Bioscience neuromorphological file format appeared first on MBF Bioscience.

Representative maps of resistance networks from feed artery to terminal

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.

In this study, researchers used Vesselucida from MBF Bioscience to characterize changes in skeletal microvasculature throughout a mouse model of muscle injury. 3D reconstructions of injured and recovering vessels in whole-mount preparations of the gluteus maximus muscle at various time points reveal the chronological degeneration and remodeling of the vascular network before and after injury.

“Using Vesselucida, we were able to assess changes in resistance network architecture during muscle regeneration for the first time,” said Dr. Nicole Jacobsen. “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.”

When quantifying segments and overall length of capillaries in Vesselucida, Dr. Jacobsen and her team binned the data based on vessel diameter to consider changes in vasculature of varying sizes. This revealed injury and recovery-related morphological changes in capillaries (five to ten micrometers in diameter), but not in arterioles and venules.

This study is unique in demonstrating significant microvasculature damage and repair in a model of acute injury using thick tissue sections. In previous studies, thin sections have been used selectively to show cross-sections of capillaries with a measurement bias based on their proximity to muscle-cell intersects (Jacobsen, et. al. 2021).

This work demonstrates the unique power of using Vesselucida to trace capillaries and other vessels in thick sections, while avoiding the bias inherent in thin section measurements, to more accurately characterize vascular networks.

Jacobsen NL, Norton CE, Shaw RL, Cornelison D, Segal SS. Myofibre injury induces capillary disruption and regeneration of disorganized microvascular networks. J Physiol. 2021 Nov 11. doi: 10.1113/JP282292.

The post Vesselucida Helps Researchers Quantify Post-Injury Capillary Damage and Regeneration appeared first on MBF Bioscience.

Cells need oxygen to survive, but during a heart attack, blood flow is restricted and cardiac cells can’t get the oxygen they need to stay alive. A new therapy, developed by researchers at the Coulombe Lab at Brown University may be able to provide the heart with the support it needs to recover after a heart attack, according to a study published in the journal Biomaterials.

Using Vesselucida 360 and Vesselucida Explorer to quantify blood vessels in the rat heart, the research team, led by Dr. Fabiola Munarin, observed improved cardiac function and saw evidence of revascularization 30 days after implanting engineered tissue into injured rat hearts. Critical elements in the implanted tissue included heart muscle cells derived from human pluripotent stem cells and alginate microspheres loaded with angiogenic growth factors (VEGF, bFGF, and Sonic Hedgehog).

By embedding this combination of heart cells and loaded alginate microspheres into the implanted tissue, the scientists were able to support the heart’s vascular network by delivering growth factors to the injured muscle. These growth factors worked with host cells to stimulate regeneration in the injured heart.

After implanting the engineered tissue, the researchers monitored the rats’ heart function over the next four weeks. They observed improvements in rats that had received tissue containing alginate microspheres loaded with angiogenic growth factors versus control groups, which had received either sham implants, only heart cells, or heart cells and unloaded alginate microspheres.

Thirty days after implantation, the research team sectioned 23 hearts. They made 3D reconstructions of four of them, after clearing and imaging with a florescence microscope. They then turned to Vesselucida 360 and Vesselucida Explorer to quantify vascular growth.

Image source: https://doi.org/10.1016/j.biomaterials.2020.120033

“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,” explained Dr. Kareen Coulombe.

Tracing the blood vessels in the four 3D heart reconstructions with Vesselucida 360, and then using Vesselucida Explorer for automated analysis, revealed an increase in vascular network density, vessel length, branching, and a wider distribution of blood vessel diameters. They also observed reduced tortuosity, or distortion of the vessel pathways — a sign that blood could travel more freely to the heart.

“Our results show for the first time the beneficial effects of integrating cardiac engineered tissues with a localized angiogenic therapy. With this combined therapy, we are able to induce the formation of new functional and perfused vessels in the implanted cardiac tissue, the revascularization of the ischemic heart, and the improvement of whole heart function.” (Munarin, et al 2020)

Munarin F, Kant RJ, Rupert CE, Khoo A, Coulombe KLK, Engineered human myocardium with local release of angiogenic proteins improves vascularization and cardiac function in injured rat hearts, Biomaterials (2020), doi: https://doi.org/10.1016/j.biomaterials.2020.120033.

The post New Therapy May Aid Heart Repair After Heart Attack appeared first on MBF Bioscience.

In their study of a mouse model of mTBI that mimics the blast exposure associated with human mild TBI, a research team, that includes MBF Bioscience Scientific Director Dr. Susan Tappan, say that low-level blast exposure disrupts the way cells interact with each other within the brain’s neurovascular unit.

Fig:1 Chronic vascular pathology in blast-exposed rats revealed by micro-CT scanning. Two control and two blast-exposed rats were transcardially perfused with the Brite Vu contrast agent at 10 months after blast exposure. Brains were scanned at a resolution of 7.5 μm using equispaced angles of view around 360°, and 3D reconstructions were prepared with Bruker’s CTVox 3D visualization software. a-d MIP images of volume-rendered brain vasculature from two control (a, b) and two blast-exposed (c, d) rats revealed diffuse thinning of the brain vasculature in the blast-exposed rats. Scale bar, 2 mm. e-h Trace sagittal reconstructions used for the automated quantitation from control (e-f) and blastexposed rats (g-h) o-p Higher magnification views of the regions outlined by the boxes in panels (f) and (h). Scale bars, 1 mm for (e-h), and 0.6mm for (o-p). i-n Reconstructions of coronal optical sections from the brains of control (i, k) and blast-exposed (j, l) animals. Panels (i) and (j) correspond approximately to coordinates interaural 12.24–9.48 mm and panels (k) and (l) correspond approximately to coordinates interaural 6.94–3.24 mm. Lateral views of (i) and (j) are shown in (m) and (n), respectively. Vessels were color coded to allow visualization of individual vessels automatically traced by the Vesselucida 360 software. Note the general loss of radial organization in the blast-exposed shown in panel (j). Scale bar, 1 mm for (i-n)

Aiming to mimic an event often experienced by soldiers and military personnel in war-torn regions, the scientists exposed rats to a series of three blasts — one blast per day, over three consecutive days. Though the rats developed behaviors typical to chronic PTSD, their neuronal pathology, at least at the light and electron microscopy levels remained unchanged, according to the study. However, when the researchers examined the rat brains on a vascular level, they found evidence of chronic damage.

One molecular change they observed was a decrease in vascular-associated glial fibrillary acidic protein (GFAP) levels in brain vascular fractions six-weeks after blast exposure. These low levels of GFAP tipped the researchers off to the possibility that gliovascular and neurovascular interactions were being disrupted in mTBI brains.

Another clue that neurovascular connections were compromised was the disappearance of a series of several neuronal intermediate filament (IF) proteins. The disappearance of these proteins, which are important signals of healthy brain function, led the researchers to delve deeper into the brain’s vascular unit.

To quantify the rats’ cerebral vasculature, the research team used Vesselucida 360 to analyze micro-CT images of the rat brains 10 months after blast exposure. Using data from the micro-CT scans, Vesselucida 360 automatically reconstructed the vascular networks in 3D, color coding individual vessels for more efficient visualization. With these reconstructions, the researchers observed a decrease in total brain vascular length (about 50 percent), a decrease in total surface area (over 50 percent), and a decrease in total volume (about 60 percent) in rats who suffered from blast-induced mTBI as compared to the control group.

Their reconstructions also revealed that mTBI brains showed a major disruption of the neatly organized, radial patterns typical of blood vessels in a healthy brain.

Interestingly, GFAP and IF protein levels returned to normal after eight months, but despite this recovery, chronic vascular abnormalities remained — an observation consistent with prior studies.

“These findings suggest that normalization of GFAP and IF protein levels in isolated vascular fractions, while likely signaling the tightening of gliovascular and neurovascular connections, does not translate into a resolution of the vascular pathology.”

Gama Sosa, M.A., De Gasperi, R., Perez Garcia, G.S., Perez, G.M., Searcy, C., Vargas, D., Spencer, A., Janssen, P.L., Tschiffely, A.E., McCarron, R.M., Ache, B., Manoharan, R., Janssen, W.G., Tappan, S.J., Hanson, R.W., Gandy, S., Hof, P.R., Ahlers, S.T., and Elder G.A., Low-level blast exposure disrupts gliovascular and neurovascular connections and induces a chronic vascular pathology in rat brain, Acta Neuropathologica Communications (2019) doi.org/10.1186/s40478-018-0647-5

https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-018-0647-5

The post Scientists use Vesselucida 360 to quantify brain vasculature in mTBI model appeared first on MBF Bioscience.

Specifically designed to recognize the intricacies of the vascular system, Vesselucida features sophisticated algorithms that quickly and accurately create 3D reconstructions of images and tissue specimens. Built-in analyses provide data on segments and node counts, frequency of anastomoses, as well as metrics on vessel surface and volume.

Automatic reconstruction of vascular structure labeled with tomato lectin
Image courtesy Dr. Stan Watson, University of Michigan, USA

Vesselucida 360 also features a full suite of tools, which lets researchers manually trace and edit 3D reconstructions to fine-tune particularly complex image data. Companion analysis software, Vesselucida Explorer performs sophisticated data analysis for scientists seeking answers to their most challenging research questions.

“For the first time, researchers studying microvasculature and how it is affected by illnesses, injuries and treatments for those afflictions, have a tool specifically designed for these studies,” says Jack Glaser, President of MBF Bioscience. “We believe Vesselucida will have a significant impact in advancing scientific research in this field.”

For a comprehensive evaluation on how Vesselucida 360 can meet your research needs, we invite you to consult with one of our MBF Bioscience staff scientists.

Visit https://www.mbfbioscience.com/vesselucida360 for more information about Vesselucida 360.

About MBF Bioscience:

MBF Bioscience creates quantitative imaging and visualization software for stereology, neuron reconstruction, vascular analysis, c. elegans behavior analysis and medical education, integrated with the world’s leading microscope systems, to empower research. Our development team and staff scientists are actively engaged with leading bioscience researchers, constantly working to refine our products based on state-of-the-art scientific advances in the field.

Founded as MicroBrightField, Inc. in 1988, we changed our name to MBF Bioscience in 2005 to reflect the expansion of our products and services to new microscopy techniques in all fields of biological research and education. While we continue to specialize in neuroscience research, our products are also used extensively in the research fields of stem cells, lung, kidney, cardiac, cancer, and toxicology.

MBF Bioscience has grown into a global business, with offices in North America, Europe, Japan, and South Korea, and a dealer network active on five continents.

Our commitment to innovative products and unrivaled customer support has gained high praise from distinguished scientists who use our products all over the world. Our flagship products Stereo Investigator and Neurolucida are the most widely-used analysis systems for stereology and neuron reconstruction.

The post MBF Bioscience’s New Software Vesselucida 360 Reconstructs Microvascular Networks in 3D appeared first on MBF Bioscience.