According to Dr. Jenny, “the 3D capabilities of Neurolucida has made it possible to better understand the distribution of small motoneurons within the motor column, and the patterns of motoneuron dendrites within the spinal cord.” The researchers are interested in comparing the patterns of motoneuron dendritic trees with the known patterns of brain-spinal cord terminal connections.

“We believe a better understanding of the motor column dendritic trees relative to descending supra-spinal inputs can be used to guide rehabilitation efforts in people recovering from stroke or spinal cord injury.”(Jenny, Cheney, 2022)

 © Elsevier B.V. All rights reserved.

Over the last four decades, advances in technology such as injections of anatomical tracers into motoneurons have provided a clearer picture of the entire dendritic tree. Dendritic trees appear to extend outward from the cell body in mostly linear and radial directions before branching. In the current research, only the proximal parts of the dendritic trees were labeled with tracer, but the patterns of the proximal dendrites were similar to the patterns seen with intracellular injections of tracer. The researchers considered the direction of dendrites seen in their material to be a reasonable estimate for the direction of the more distal unlabeled dendrites.

In the current study, the researchers used Neurolucida to digitally reconstruct the neurons from the original microscopic slides from 1983 to perform a detailed 3D analysis of dendritic tree patterns. While they observed dendrites radiating in all directions, this new analysis revealed a preference for two specific directions (either toward the gray matter at the base of the dorsal horn or to the gray matter of the medial ventral horn) suggesting the possibility that motoneuron dendritic trees extend toward functional terminal regions.

The authors plan to use Neurolucida to continue re-examining the motoneuron columns analyzed in the original 1983 study, with the ultimate goal of merging their data with data from other investigations into a 3D neuron database.

Jenny AB, Cheney PD. Monkey flexor and abductor pollicis brevis motoneuron pools: Proximal dendritic trees and small motoneurons. Neuroscience Letters. Vol. 769, 2022 Jan 19. doi: 10.1016/j.neulet.2021.136429

Jenny AB, Inukai J. Principles of Motor Organization of the Monkey Cervical Spinal Cord. Journal of Neurosci. Vol. 3, No. 3, pp. 567-575, 1983 Mar. https://www.jneurosci.org/content/jneuro/3/3/567.full.pdf

The post Neurolucida helps to reveal new findings in a follow-up to a 40 year old study appeared first on MBF Bioscience.

“NeuroInfo already includes extensive analysis capabilities for mouse brain research by standardizing measurements on brain volumes to the Allen Mouse Brain Atlas. The inclusion of a rat atlas in NeuroInfo expands brain research to more complicated behavioral and disease models,” says MBF Bioscience Senior Product Manager Dr. Nathan J. O’Connor.

Image Credit: Harvey Karten, PhD

Successful neuroscience research projects in big data areas such as transcriptomics, proteomics, and connectomics rely on efficient methodologies and data reporting. NeuroInfo uses deep learning and automated image processing workflows guided by widely used standardized atlases to repeatably produce and report outcomes that can be combined and compared across animals, cohorts, and laboratories.

Learn more about NeuroInfo.

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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.

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Building on previous research (Achanta et al., 2020), which resulted in a 3D map of the rat ICNS, a new study by a team of scientists from the University of Central Florida, Thomas Jefferson University, the University of Auckland, Strateos Inc, and MBF Bioscience further explores the organization of peripheral neurons in the ICNS of the rat heart and describes variations in female and male rats.

Using MBF Bioscience’s Tissue Mapper^® software, the research team, which included Scientific Director Dr. Susan Tappan, and Research Analyst Maci Heal, comprehensively annotated, mapped, and visualized the anatomy and ICNS of female and male rat hearts in 3D.

By marking the ICNS neuron locations for each heart using Tissue Mapper, the investigators found that the pattern, distribution, and clustering of ICNS neurons across all male and female rat hearts is highly conserved and neuron clusters are organized and localized. Female hearts had fewer neurons, lower packing density, and slightly reduced distribution than male hearts.

“The team at MBF has been highly receptive to our research needs,” says Dr. Rajanikanth Vadigepalli. “They made constant adjustments and improvements to TissueMapper to enable smooth handling of large image stacks, in-depth annotation, and seamless mapping of external data sets onto a 3D map of the intrinsic cardiac nervous system. The expertise of the MBF staff was crucial to preprocess and assemble the large-scale imaging data to jumpstart the 3D map building process.”

The researchers used the integrated vocabulary services within Tissue Mapper to identify unique “fiducial” anatomical landmarks in their microscopy image data, thus enriching their data with machine-readable, ontologically-persistent identifiers. This simple process, in combination with thorough anatomical annotation in MBF’s Neuromorphological File Format, allowed individual subject files to be mathematically registered to organ scaffolds (3D material common coordinate frameworks) for comparison of ICNS across subjects.

“Our findings provide a foundation for future studies that explore how the intrinsic cardiac nervous system can be modulated to alter cardiac function and treat cardiac diseases,” says Scientific Director Dr. Susan Tappan. “And while this study focuses on the intrinsic cardiac nervous system, the annotation techniques used here can be applied to other investigations of visceral organs and peripheral nerve innervations.”

Similar mapping experiments are being conducted on other organs, such as the stomach, colon, and bladder for the NIH SPARC project. 3D scaffold maps similar to the ones presented in this paper can be explored on the SPARC Portal (sparc.science).

“It is heartening to see MBF, a commercial entity, drive the development, standardization and dissemination of open data formats for complex anatomical annotation towards enabling friction-free exchange of these data sets in the scientific community,” says Dr. Vadigepalli.

Citation:

Leung, C., Robbins, S., Moss, A., Heal, M., Osanlouy, M., Christie, R., Farahani, N., Monteith, C., Chen, J., Hunter, P., Tappan, S., Vadigepalli, R., Cheng, Z. (J., & Schwaber, J. S. (2021). 3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system. IScience, 24(7), 102795. https://doi.org/10.1016/j.isci.2021.102795

The post Researchers Map and Explore the Heart’s “Little Brain” appeared first on MBF Bioscience.

A neurodegenerative disorder characterized by late-onset symptoms like depression, confusion, and memory loss, CTE is caused by repeated impacts to the brain. The disease is most often seen in athletes who play high impact sports and military veterans.

While CTE is known to be associated with abnormal aggregations of the tau protein, which is also observed in diseases like Alzheimer’s disease and traumatic brain injury, no research to date had explored how CTE affected neuron morphology.

In an attempt to get a glimpse into the neurodegenerative mechanisms at work in the CTE brain, researchers at Colorado College quantified the dendritic arborizations of supragranular pyramidal neurons in two regions of the human brain — the frontal and occipital lobes.

Using Neurolucida to reconstruct Golgi-stained neurons from these two regions in 16 human brains (11 cases with CTE and 5 control cases without the disease), a team of researchers led by Dr. Bob Jacobs, observed a general degeneration and greater variability between dendritic systems in CTE brains compared to controls.

Representative Neurolucida tracings of pyramidal neurons in the frontal and occipital lobes from control and chronic traumatic encephalopathy (CTE) groups. CTE tracings show greater variability in dendritic extent compared to control tracings.

According to the study, the dendritic systems of CTE brains showed reductions in seven different measures — dendritic volume, total dendritic length, mean segment length, dendritic segment count, dendritic spine number, and dendritic spine density, as well as dendritic diameter. In contrast to the occipital lobe, dendritic apathy and loss was more severe in the frontal lobe, where p-tau is known to aggregate, possibly acting as a mechanism associated with this pathology, according to the paper.

The researchers also observed a greater variability of morphological differences between dendritic systems in the CTE brains as compared to controls, which were more uniform in size and branching patterns. As outlined in the paper, this variability among neurons in CTE brains might be a result of a combination of the disease’s degenerative effects as well as reorganizational efforts to compensate for the damage.

“This study is the first to document changes in cortical dendritic systems in CTE subjects, which sheds light on an entirely different realm of CTE related neural alterations,” said Dr. Jacobs. “These dendritic changes are probably associated with at least some of the cognitive changes one sees in CTE as well.”

While the authors point out that dendritic degeneration is a normal process in the aging brain, they also explain that their observations of CTE brains in comparison to similarly aged non-CTE brains reveal a possible acceleration in dendritic loss when CTE is present.

Over the course of their study, the scientists traced 640 Golgi-stained neurons with Neurolucida.

“Neurolucida was very effective for this study. The software has come a long way in the last 30 years and has become much easier to use,” said Dr. Jacobs, who, over the course of his career, has traced over 5,000 neurons across 26 different species with the help of Neurolucida.

“I would not have had a research career without the Neurolucida system and the wonderful support of MBF over the years,” he said.

The post Researchers Observe Altered Neuropathology in CTE Brains appeared first on MBF Bioscience.

Researchers used Neurolucida to reconstruct a newly discovered type of neuron found only in the human brain, according to a study published in the journal Nature Neuroscience. Known as “rosehip” neurons because of the way they resemble a rose after its petals have fallen off, these cells feature compact, bushy axonal arborizations.

Found in the first layer of the cerebral cortex, a highly complex brain region that is thought to play an important role in consciousness, “rosehip neurons” have not been seen in mice or other laboratory animals, and scientists suggest that they may exist only in humans. Classified as inhibitory neurons, these brain cells form synapses with pyramidal neurons in layer 3 of the cerebral cortex, according to the study.

Led by Dr. Ed Lein, of the Allen Institute for Brain Science, and Dr. Gábor Tamás, a neuroscientist at the University of Szeged in Szeged, Hungary, the research team used Neurolucida to reconstruct rosehip neurons in 3D. Their reconstructions revealed that these cells display morphological characteristics that differ significantly from other types of cells found in this region of the brain.

Scientists used Neurolucida and Neurolucida Explorer to reconstruct and analyze a rosehip neuron. Image Credit: Tamas Lab, University of Szeged

Using Neurolucida Explorer to quantitatively analyze their cell reconstructions, the researchers observed similar numbers of primary dendrites in both rosehip neurons and basket cells, but fewer compared to neurogliaform cells. Meanwhile, they calculated similar total dendritic length and frequency of dendritic nodes in rosehip neurons and neurogliaform cells, but recorded differences in basket cells.

Also, their analysis revealed that the axonal branching of rosehip neurons was more robust than any other type of cell observed in this brain region, with the volume of axonal terminations, or boutons, measuring four times larger than NGFC boutons.

Furthermore, the researchers say that the rosehip neuron has a molecular marker signature of (GAD1+CCK+, CNR1–SST–CALB2–PVALB–), a signature not seen in the mouse cortex.

According to the paper, the researchers still have much to learn about the function of rosehip neurons in the human brain. Because they observed rosehip neurons connecting to their partner neurons – pyramidal neurons, in very specific places, they hypothesize that rosehip neurons might be controlling the flow of information in a distinctive way.

One next step will be to see if postmortem brains from patients with neuropsychiatric disorders display rosehip neurons with alterations, to begin investigating whether or not these newly discovered cells play a role in mental illness.

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Jennie L. Close, Diez-Fuertes F, Ding SL, Faragó N, Kocsis AK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G (2018) Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type. Nature Neuroscience doi.org/10.1038/s41593-018-0205-2

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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.

Image Courtesy: Bob Jacobs, Ph.D. , Colorado College

With the release of its new version on November 28, NeuroMorpho.org adds 9,987 new images to its archive, bringing its impressive collection of digitally reconstructed neurons to 80,012.

Scientists used MBF Bioscience’s software, Neurolucida and Neurolucida 360, to reconstruct the majority of these cells. In fact, 64 times more neurons were reconstructed with MBF Bioscience software than those imaged by our closest commercial competitor – that’s 42,121 reconstructions compared to 656. This metric demonstrates that Neurolucida and Neurolucida 360 are truly the gold standards for neuron reconstruction.

Featuring contributions from hundreds of laboratories from around the globe, NeuroMorpho.Org is the world’s leading database of publicly accessible 3D neuronal reconstructions and associated metadata. From the dragonfly to the humpback whale, researchers have access to accurate and verified data from an array of different organisms. Arranged by animal species, brain region, cell type, or contributing laboratory, each file contains specific details about the cell’s morphology such as age, developmental stage, soma volume, and number of branches – all of which are searchable.

Recently, NeuroMorpho.Org hit the 8 million download mark, with researchers in 166 different countries accessing this valuable resource, and more than one thousand published articles referencing its data

The post NeuroMorpho.Org Releases Nearly 10,000 New Neuron Reconstructions and Neurolucida leads the way appeared first on MBF Bioscience.

Analyzing cellular populations within specific anatomies in brain images requires expertise in both neuroanatomy and cellular identification. This typically involves a scientist comparing experimental images with a reference atlas and manually delineating anatomical regions and marking cell populations within. NeuroInfo^®, a revolutionary new technology from MBF Bioscience, enables researchers to automatically identify and delineate mouse brain regions based on the publicly available Allen Mouse Brain Reference Atlas.

“NeuroInfo has the potential to greatly improve our understanding of how mental disorders influence neuronal cell populations,” says Nathan O’Connor Ph.D., product manager at MBF Bioscience. “Because it makes identifying brain regions substantially faster and more accurate, researchers will be able to explore many more brain regions.”

“The Allen Mouse Brain Reference Atlas is a valuable tool to assist scientists in their research. We’re thrilled that MBF has chosen to integrate this resource into NeuroInfo,” stated Amy Bernard, Ph.D., Product Architect at the Allen Institute for Brain Science.

“Using this remarkable technology, neuroscientists will obtain more repeatable, objective analyses that have been possible to date. Thanks to the integration with the Allen Mouse Brain Reference Atlas, these analyses will be more standardized so that they can be compared across experiments and laboratories,” says Jack Glaser, President.

NeuroInfo can be used with MBF Bioscience’s slide scanning software and virtually all commercial whole slide scanners. The data from NeuroInfo seamlessly integrates with MBF Bioscience’s products including Neurolucida, Stereo Investigator, Biolucida, and BrainMaker.

The tools in NeuroInfo allow researchers to automatically delineate anatomies in the experimental specimens, and detect cells within these anatomies. NeuroInfo yields data that can be invaluable to better understand the organization and composition of the nervous system, and to further knowledge in neurogenomics, transcriptomics, proteomics, and connectomics.

The National Institute of Mental Health provides funding to support the development of NeuroInfo.

The post MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with the Allen Mouse Brain Reference Atlas appeared first on MBF Bioscience.

The four protocols describe best practices for imaging and analyzing dendritic spines and entire neurons. Clearly laid out procedures specify necessary materials, image acquisition techniques, and analysis procedures with Neurolucida 360.

Imaging technique is crucial to obtaining unbiased, reproducible results. Clear, crisp images captured with an appropriate z-interval will make analysis with Neurolucida 360 easier and more accurate. Throughout the paper, the authors emphasize the importance of image scaling parameters and unbiased sampling for achieving repeatable results. They also discuss the benefits of correcting optical distortion, especially in the Z-plane, with deconvolution to acquire clear images – a process critical to getting the most accurate representation of dendrites and spines.

Dendritic spine analysis is traditionally performed through tedious, time-consuming manual techniques. According to the paper, this has spawned a growing interest in a more efficient solution for spine quantification and morphological analysis like the one Neurolucida 360 provides. A software platform for automatic neuron reconstruction and spine detection in a 3D environment, Neurolucida 360 offers a variety of benefits, including:

• Fast and accurate spine detection and neuron reconstruction
• Accurate spine classification and length quantification using a five-point segment that more accurately models the spine backbone.
• 3 user-guided and automatic algorithms to accurately model neurons visualized with multiple methodologies and imaging techniques.
• A large number of metrics, including volume, length, and surface area.

“We believe that the new quantitative software package, Neurolucida 360, provides the neuroscience research community with the ability to perform higher throughput automated 3D quantitative light microscopy spine analysis under standardized conditions to accelerate the characterization of dendritic spines with greater objectivity and reliability,” (Dickstein, et al. 2016)

The full paper can be found here.

An infographic quickly outlines Protocol 1: Imaging of fluorescently labeled dendritic segments. Use this as a quick reference tool in your lab (right-click on it to save as an image):

Dickstein, D.L., Dickstein, D.R., Janssen, W.G.M., Hof, P.R., Glaser, J.R., Rodriguez, A., O’Connor, N., Angstman, P., and Tappan, S.J. 2016. Automatic dendritic spine quantification from confocal data with Neurolucida 360. Curr. Protoc. Neurosci. 77:1.27.1-1.27.21. doi: 10.1002/cpns.16

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