Key Updates

• Offline Licensing Update
  To ensure uninterrupted use of Neurolucida® 360 on systems without internet access, reactivation is now required.

• Activation Process:
• • To obtain a new offline Activation Key, please fill out this webform.
  • Once submitted, detailed instructions for completing the offline authorization process will be provided.

• Support Documentation:
  Step-by-step instructions for offline activation are available in the Neurolucida 360 User Guide for your convenience.

New Features and Enhancements

• Enhanced Vessel Tracing: Improvements to the vessel tracing options in the 2D window for better precision.
• Streamlined Continuous Tracing: Automove now repositions focus seamlessly when using Continuous tracing.
• Puncta Setup Updates: Color channel selection now begins at number 1, simplifying the setup process.
• 2D and 3D Synchronization: Improved synchronization for contours delineated across both dimensions.
• Image Organization: Image file paths are now displayed in the Image Organizer for easier management.
• Dynamic Movie Adjustments: You can now change image-display settings for image slices and partial projections during a movie.
• 3D Scale Bar Display: Movies can now feature a 3D scale bar for added clarity.
• Movie Mode Interface Enhancements: Other improvements have been implemented to make recording and playback more intuitive.

For additional support or questions, please contact our customer support team at support@mbfbioscience.com.

The post Neurolucida 360 Software Update: Version 2024.2.2 appeared first on MBF Bioscience.

The authors obtained post-mortem human brain samples from the Brodmann area 28 (BA28) entorhinal cortex (EC) of subjects exhibiting a range of Alzheimer’s disease (AD) pathology and categorized into 3 groups based on cognition and AD pathology: normal cognition, noAD pathology; normal cognition with moderate to severe AD pathology, and definite AD cases. Synaptosome fractions were characterized biochemically, and proteomic profiles were determined using liquid chromatography coupled to mass spectrometry. Weighted gene co-expression network analysis was used to generate a protein co-expression network and identify protein modules (co-expressed proteins) that were present in the different cognition/AD pathology categories.

In parallel, tissue samples from the same brain area were fixed and processed for dendrite imaging using Golgi-Cox staining. Dendritic segments of pyramidal neurons from layers 2 and 3 of BA28 from each category of cognition/AD pathology were imaged with a 60X/1.40 NA oil-immersion objective using a brightfield microscope. The resulting 3D image stacks were opened in Neurolucida 360 and dendrite and dendritic spine morphologies were reconstructed using semi-automatic and automatic functions. Spines were automatically classified as stubby, mushroom, or filopodia. Volumetric measurements of the spine, as well as the density of each spine type per dendrite length were extracted with Neurolucida Explorer.

Figure: Overview of workflow. Synaptosomes were isolated from postmortem human BA28 entorhinal cortex (EC) and subjected to liquid chromatography tandem mass spectrometry-based proteomics. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to generate a network of protein co-expression modules. BA28 EC samples were also Golgi stained and z-stacks of dendritic segments were imaged and digitally reconstructed to obtain measurements of dendritic spine density and morphology. Module eigenprotein values were correlated with dendritic spine metrics. The hub protein of a module significantly correlated with a dendritic spine metric would be selected for functional validation by CRISPR activation in rat primary hippocampal neurons.

The authors then correlated dendritic spine measurements with module eigenprotein expression from the proteomic analysis to integrate the two data categories. Among the results, one particular protein module stood out; it was consistently present in both AD and non-AD tissue, and was positively correlated with thin dendritic spine length, especially thin spines. Twinfilin2, the hub protein within this module, has a well-established role in modulating the cytoskeleton, specifically the protein actin. When the authors looked at neurons from rats grown in culture with different amounts of TWF2, they found those with more TWF2 grew longer thin-spines. This was the only type of spine affected by TWF2, demonstrating what the authors call a remarkable specificity regarding the ability of their cross-platform analysis to identify the functions of proteins.

Looking ahead, the researchers have identified many proteins organized in modules with hub-proteins, some that are expressed equally in AD and non-AD cases, and some that are not. They are in a good position to determine which of these hub proteins merit further study using functional analyses.

The comprehensive workflow employed by the researchers opens up new possibilities for unraveling the mysteries of neuronal function and holds immense potential for advancing our knowledge of diverse neurological conditions. As we delve deeper into the complex world of neuroscience, the connection between technology and scientific inquiry continues to illuminate the path towards groundbreaking discoveries.

Reference:

Walker, C. K., Greathouse, K. M., Tuscher, J. J., Dammer, E. B., Weber, A. J., Liu, E., Curtis, K. A., Boros, B. D., Freeman, C. D., Seo, J. V., Ramdas, R., Hurst, C., Duong, D. M., Gearing, M., Murchison, C. F., Day, J. J., Seyfried, N. T., & Herskowitz, J. H. (2023). Cross-platform synaptic network analysis of human entorhinal cortex identifies TWF2 as a modulator of dendritic spine length. The Journal of Neuroscience. https://doi.org/10.1523/jneurosci.2102-22.2023

The post From Proteins to Dendritic Spines: Neurolucida 360 Plays a Crucial Role in Advancing Neuroscience appeared first on MBF Bioscience.

The field of applied mathematics known as “topological data analysis” uses topological methods to uncover patterns in large, high-dimensional datasets that might otherwise go unnoticed. In a collaborative effort led by the Blue Brain Project, directed by Dr. Henry Markram, researchers used topological data analysis to develop an objective method of classifying pyramidal cells based on their morphology.

The morphology and behavior of neurons can vary widely, and developing methods for classifying and differentiating between different types of cells has proven advantageous for scientific research. However, investigators tend to devise their own methods, which often results in contradictory classifications of the same tissue between researchers, and even repeat trials of the same tissue with the same investigator can produce contradictory results (DeFelipe et al, 2013). To avoid investigator biases, the Blue Brain scientists used the Topological Morphology Descriptor (TMD) algorithm to analyze pyramidal cells reconstructed with Neurolucida 360. The aim of the TMD algorithm is to produce a simplified representation of the cell morphology based on the topological descriptors of the cell’s shape rather than visual inspection and feature selection (Kanari et al, 2018). Using the algorithm, they made the same differentiations between cell types that experts had made previously, but they also observed two types of pyramidal cells typically identified by experts, which were not able to be differentiated by the topological data available, suggesting that these cell types either represent opposite ends of a continuum of expression, or that experts are noticing topological features that were not captured by this version of the algorithm.

Three PC types/subtypes in Layer 2. (A) Exemplar reconstructed morphologies of PC dendrites: the apical dendrite is presented in purple and the basal dendrites in red. (B) Polar plot analysis of dendritic branches (apical in purple, basal in red). Tufted PCs are oriented towards the pia and the inverted PCs in the opposite direction as they project towards the white matter. (C) The Topological Morphology Descriptor (TMD) of apical dendrites characterizes the spatial distribution of branches with respect to the radial distance from the neuronal soma. The average persistence images (per type of PC) illustrate the average dendritic arbor density around the soma.

This study represents an important step towards objective classification of cells, and there is broad potential for expanding on this work. One challenge the authors discuss is the volume of data available for developing and validating a TMD algorithm—some cell types simply haven’t been observed and digitally reconstructed as often as the pyramidal cells studied here. However, the analytical potential of the TMD lies in its broad applicability. Since it operates on 3D tree-like structures, any neuron digitally reconstructed in 3D can in theory be analyzed by the TMD algorithm. The authors leave us with an open invitation to work with and expand the TMD algorithm.

In a very recent publication (Gillespie et al, 2022) researchers have noted that the US Brain Initiative Cell Census Network, Human Cell Atlas, Blue Brain Project, and others are generating vast amounts of data and characterizing large numbers of neurons throughout the nervous system. They have proposed Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types.

At MBF Bioscience we’re also working to establish consensus within the neuroscience community, and have published a full specification of our neuromorphological file format used to store these 3D digital reconstructions. We invite the global community to make use of this format for storing their own digital reconstructions.

And if you’re interested in learning more about obtaining detailed reconstructions of cells in your samples with Neurolucida 360, request a free demonstration of Neurolucida 360 from our team of experts.

References:

DeFelipe, J., López-Cruz, P., Benavides-Piccione, R. et al. New insights into the classification and nomenclature of cortical GABAergic interneurons. Nat Rev Neurosci 14, 202–216 (2013). https://doi.org/10.1038/nrn3444

Gillespie, T.H., Tripathy, S.J., Sy, M.F. et al. The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. Neuroinform (2022). https://doi.org/10.1007/s12021-022-09566-7

Kanari, L., Dłotko, P., Scolamiero, M. et al. A Topological Representation of Branching Neuronal Morphologies. Neuroinform 16, 3–13 (2018). https://doi.org/10.1007/s12021-017-9341-1

Lida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess, Henry Markram, Objective Morphological Classification of Neocortical Pyramidal Cells, Cerebral Cortex, Volume 29, Issue 4, April 2019, Pages 1719–1735, https://doi.org/10.1093/cercor/bhy339

The post Blue Brain scientists develop pyramidal cell classification system using neurons reconstructed with Neurolucida 360 appeared first on MBF Bioscience.

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.

Some inflammation is normal in a healthy mammalian brain. But as the brain ages, processes can break down, leading to chronic neuroinflammation. This can develop into Alzheimer’s disease, dementia, and other neurodegenerative diseases.

Scientists at Prof. Gerald Muench’s lab, at Western Sydney University say that curcumin, a substance in the spice turmeric, has the potential to lower inflammation in the brain.

In two recent studies, the researchers, led by Dr. Erika Gyengesi, used Stereo Investigator and Neurolucida 360 to reconstruct and quantify glial cells in the brains of mice after feeding them two different curcumin formulations.

“MBF Bioscience’s software helped us immensely to differentiate and follow the changes caused by chronic microglia activation in various areas of the brain during aging, but also to quantify the effects of different modified curcumin products, which otherwise would have been impossible,” said Dr. Gyengesi.

In a study published February, 2020 in Scientific Reports: “Effects of a solid lipid curcumin particle formulation on chronic activation of microglia and astroglia in the GFAP-IL6 mouse model,” (Ullah et al, 2020), the researchers describe positive results after feeding GFAP-IL6 mice — a mouse model of chronic neuroinflammation — 500 ppm of Longvida® Optimised Curcumin (LC) over a course of six months.

Effect of MC on the morphological characteristics of microglial cells in the hippocampus. (A) Morphological assessment of reactive and non-reactive microglia in the hippocampus. (B–H) Microglia in the inflamed mice have significantly larger soma area, soma perimeter and processes compared with the WT mice. High dose MC significantly reduced soma area and soma perimeter compared with GFAP-IL6 mice. However, the same high dose MC significantly increased the number of nodes compared with the GFAP-Il6 mice. It has no effect on the convex area, convex perimeter, dendritic length and number of processes. Significance = *p < 0.05, **p < 0.001, ***p < 0.0001, ****p < 0.0001.

Stereological analysis of the mouse brains revealed lower levels of activated microglia in the hippocampus (26 percent less) and in the cerebellum (48 percent less) in GFAP-IL6 mice that were fed the curcumin diet, compared to GFAP-IL6 mice fed a normal diet. They also quantified astrocytes — another cell type activated in response to neuroinflammation, finding decreased levels in the hippocampus (30 percent less). TSPO+ cells — another marker of brain inflammation, decreased as well (by 24 percent in the hippocampus and 31 percent in the cerebellum) in the experimental mice compared to controls.

Dr. Gyengesi and her team then checked to see what effect the curcumin formulation had on cell morphology. Using Neurolucida 360 they reconstructed 16 to 20 astrocytes in the hippocampus of each brain of the four different cohorts (wild type normal-fed, wild type LC-fed, GFAP-IL6 normal-fed, GFAP-IL6 LC fed).

They found that in GFAP-IL6 mice, LC decreased “dendritic length of microglia and the convex area, convex perimeter, dendritic length, nodes and number of processes of astrocytes in the hippocampus.” The curcumin formulation also decreased the unusually enlarged soma area and perimeter of neurons in the cerebellum. Increased pre- and postsynaptic protein levels and improved balance were observed as well in LC-fed GFAP-IL6 mice.

In another study, published by the group earlier this year, in the journal Frontiers in Neuroscience, “Evaluation of Phytosomal Curcumin as an Anti-inflammatory Agent for Chronic Glial Activation in the GFAP-IL6 Mouse Model” (Ullah et al, 2020), the researchers tested a different curcumin formulation. This time, they fed GFAP-IL6 mice a soy-lecithin based phytosomal curcumin formulation (Meriva® curcumin).

After feeding the GFAP-IL6 mice three doses of Meriva curcumin over a period of just four weeks, they saw promising results. They quantified lower numbers of activated microglia in the hippocampus (26.2 percent less) and in the cerebellum (48 percent less) compared to those in the population of GFAP-IL6 mice, which was fed a normal diet. Lower levels of GFAP+ astrocytes were also observed in this group.

As in the previous study, the scientists witnessed morphological differences in the mice fed the curcumin diet, including a decrease in the size of the already enlarged soma.

“Using Neurolucida and Stereo Investigator, we have demonstrated that various curcumin formulations with increased bioavailablity have the capability to attenuate chronic inflammatory pathology, by not only reducing activated glial numbers but also reversing their activated morphological state,” said Dr. Gyengesi.

Citations:

Ullah F, Asgarov R, Venigalla M, Liang H, Niedermayer G, Münch G, Gyengesi E. Effects of a solid lipid curcumin particle formulation on chronic activation of microglia and astroglia in the GFAP-IL6 mouse model. Sci Rep. 2020;10(1):2365. Published 2020 Feb 11. doi:10.1038/s41598-020-58838-2 https://pubmed.ncbi.nlm.nih.gov/32047191/

Ullah F, Liang H, Niedermayer G, Münch G, Gyengesi E. Evaluation of Phytosomal Curcumin as an Anti-inflammatory Agent for Chronic Glial Activation in the GFAP-IL6 Mouse Model. Front Neurosci. 2020;14:170. Published 2020 Mar 12. doi:10.3389/fnins.2020.00170 https://pubmed.ncbi.nlm.nih.gov/32226360/

The post Curcumin Lowers Neuroinflammation in Mouse Model appeared first on MBF Bioscience.

Amyloid plaques and tau tangles are the hallmarks of Alzheimer’s disease (AD) pathology, but synapse loss is what causes cognitive decline, scientists say. In a paper published in Science Signaling, researchers at the Herskowitz Lab, at the University of Alabama at Birmingham, used Neurolucida 360 to analyze spine density and dendritic length in hAPP mice — a mouse model of AD. Their findings describe a treatment that could protect against synapse loss and prevent the onset of dementia in patients at risk for Alzheimer’s disease.

Targeting LIMK1 to Protect Against Dendritic Damage

In their study, the scientists targeted LIMK1, an enzyme that regulates the size and density of dendritic spines. Previous studies have shown that in animal models of AD, LIMK1 activity is increased, causing synaptic hyperactivity and dendritic damage. After confirming this phenomenon, the research team set out to find a way to inhibit LIMK1, which lies downstream of two other important players in dementia pathology — the Rho-associated kinases known as ROCK1 and ROCK2.

Representative maximum-intensity high-resolution confocal microscope images of dye-filled dendrites, from CA1 hippocampal neurons in mice, after deconvolution and corresponding 3D digital reconstruction models of dendrites. Scale bar, 5 μm. Colors in digital reconstructions correspond to dendritic protrusion classes: blue, thin spines; orange, stubby spines; green, mushroom spines; and yellow, dendritic filopodia.

Previous studies have shown that severe side effects including fatally low blood pressure are associated with the inhibition of ROCK1 and ROCK2, so the researchers looked further down the signaling pathway to the LIMK1 point, potentially discovering a truly valid target in the fight to prevent dementia onset.

Since LIMK1 has also been a target in cancer treatment, the researchers turned to SR7826, an experimental drug currently in development to treat cancer patients. They found that administering SR7826 suppressed LIMK1 activity and protected dendritic morphology against the damage commonly seen in a brain afflicted with dementia. By reconstructing the mouse neurons with Neurolucida 360, they observed increased dendritic spine length and density in the experimental group, compared to controls.

Using Neurolucida 360 to Analyze Dendritic Spine Morphology

Herskowitz and his team have used Neurolucida 360 in previous studies, and used the software extensively throughout the current study to image and quantify dendritic morphology.

“Neurolucida 360 is a remarkable system that has provided us with tools to study dendritic architecture in cultured neurons, rodent models, and humans, with outstanding precision and detail,” said principal investigator Jeremy Herskowitz, Ph.D.

Their first step was to confirm that increased ROCK1 or ROCK2 activity caused detrimental structural effects on dendritic spines. To do this, they analyzed rat hippocampal neurons that had been transfected with either green fluorescent protein (GFP), an actin-binding peptide, ROCK1, or ROCK2. Controls were transfected with empty vectors.

Using Neurolucida 360, they digitally generated neuron reconstructions and quantified dendritic spine length and density in all of the experimental groups. Neurons expressing ROCK1 showed significantly reduced spine length compared to vector or GFP controls, while neurons expressing ROCK2 showed significantly reduced spine density.

They then used Neurolucida 360 to determine that two different mechanisms dictate the distinct impacts ROCK1 and ROCK2 have on dendritic structure — ROCK1 kinase activity regulates spine length through myosin-actin pathways, whereas ROCK2 kinase activity controls spine density through LIMK1-cofilin-actin signaling.

Further experiments used Neurolucida 360 to analyze dendrites of neurons injected with both amyloid-β oligomers and a virus expressing ROCK1- or ROCK2-targeted RNA. This allowed the scientists to discern that ROCK2, and not ROCK1, works with Aß oligomers to induce spine degeneration.

“Treatment of hAPP mice with a LIMK1 inhibitor rescued Aβ-induced hippocampal spine loss and morphologic aberrations. Our data suggest that therapeutically targeting LIMK1 may provide dendritic spine resilience to Aβ and therefore may benefit cognitively normal patients that are at high risk for developing dementia. (2019, Henderson et al)

Henderson, BW., Greathouse, KM., Ramdas, R., Walker, CK., Rao, TC., Bach, SV., Curtis, KA., Day, JJ., Mattheyses, AL., Herskowitz, JH. 2019. Pharmacologic inhibition of LIMK1 provides dendritic spine resilience against β-amyloid. Science Signaling Vol. 12, Issue 587 DOI: 10.1126/scisignal.aaw9318 (https://stke.sciencemag.org/content/12/587/eaaw9318)

The post Researchers Identify Potential Treatment for Patients at Risk for Alzheimer’s Disease appeared first on MBF Bioscience.

Today, the journal Science published a paper authored by a research team led by Dr. Ed Boyden of MIT and Nobel Prize recipient Dr. Eric Betzig of Janelia Research Campus. Among the authors are MBF Bioscience Scientific Director Dr. Susan Tappan and Senior Software Engineer Alfredo Rodriguez. In the paper, the researchers introduce new analyses for neural circuits at nanoscale resolutions.

Combining microscopy methods that create high resolution 3D images from whole brains and tissue that have been made physically larger, the researchers imaged a mouse cortex and fruit fly brain in their study “Cortical column and whole-brain imaging of neural circuits with molecular contrast and nanoscale resolution (Gao et al, 2019).”

By creating enhanced processing and analysis tools in MBF Bioscience’s Stereo Investigator and Neurolucida 360 software, Dr. Tappan and Mr. Rodriguez analyzed these images to obtain comprehensive morphometrics of delicate dendritic spines at a greater accuracy than ever before.

GAO ET AL./SCIENCE 2019

“We combined expansion microscopy and lattice light sheet microscopy (ExLLSM) to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain, including synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly neuropil domain.” (Gao et al, 2019)

While several forms of microscopy exist that have the ability to image subcellular neural elements, scientists say that each of these methods is lacking in one way or another. According to the paper, the combination of expansion microscopy with lattice-light sheet microscopy gives the most effective results, while considerably decreasing the time spent carrying out the experiment.

“I believe this type of imaging represents a major milestone in terms of the accuracy that can be achieved in dendritic spine morphometry from light microscopy,” Mr. Rodriguez said.

In their part of the study, Dr. Tappan and Mr. Rodriguez first confirmed that physically increasing the size of the tissue did not cause damage to the internal structure, by analyzing 1,500 dendritic spines in seven layers of the mouse cortex that had undergone expansion. The larger spine heads and necks observed in layers four and five (closest to the somata) compared to layers two, three, and six, were consistent with measurements achieved in earlier studies.

“Confirming that dendritic spine morphometry results are in agreement with previously published scientific literature is essential to demonstrate that the expansion microscopy technique doesn’t alter the tissue in damaging ways,” explained Dr. Tappan. “This demonstrates the utility of the technique for permitting accurate measurements of these very small features.”

In order to ensure the technology would be capable of analyzing these extremely high-resolution images with accuracy, MBF Bioscience enhanced Neurolucida 360 so that the software would take advantage of the increased resolution rendered by the ExLLSM data. With the upgraded technology, Dr. Tappan and Mr. Rodriguez were able to more accurately reconstruct dendritic spines and obtain new morphometric values, such as spine neck diameter, for the first time. The enhanced software also gave them the ability to observe and measure the entire neck of the dendritic spine, identify each point where the spine attaches to its dendrite, and measure the extent of the head and neck along the spine backbone. While these measurements had been computed before, Mr. Rodriguez explained that the technology’s ability to offer such a high resolution allowed for more accurate results.

To address the possibility that such high-resolution data might result in intracellular structures appearing granular, the developers integrated appropriate imaging filters into Neurolucida 360 to smooth the labeled dendritic structures prior to 3D reconstruction.

While the research team at MBF Bioscience focused on dendritic spine analysis in the mouse cortex, the study also describes a host of other analyses in this brain region, including the quantification of lysosomes and mitochondria, synaptic proteins, and the analysis of axon myelination patterns. In addition, the researchers imaged an entire fruit fly brain and traced neurons projecting into the part of the brain responsible for sleep, navigation, and visual memory. They also analyzed the axonal branches of olfactory projection neurons, observing differences in number and size of boutons — the tiny vesicles at axon terminals — in five different fruit fly brains. Finally, they measured distances between synapses, calculating density differences in various regions of the brain.

“It’s an exciting example of how big data is transforming science in unprecedented ways and it’s amazing to be right there at the forefront of it all,” said Dr. Tappan. “At MBF Bioscience, we are committed to innovating our methods and analyses to keep pace with the driving forces of scientific research.”

R.Gao, S. M. Asano, S. Upadhyayula, I. Pisarev, D. E. Milkie, T. Liu, V. Singh, A. Graves, G. H. Huynh, Y. Zhao, J. Bogovic, J. Colonell, C. M. Ott, C. Zugates, S. Tappan, A. Rodriguez, K. R. Mosaliganti, S. Sheu, H. A. Pasolli, S. Pang, C. S. Xu, S. G. Megason, H. Hess, J. Lippincott-Schwartz, A. Hantman, G. M. Rubin, T. Kirchhausen, S. Saalfeld, Y. Aso, E.S. Boyden, E. Betzig. “Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution.” Science. Published online January 17, 2019. doi: 10.1126/science.aau8302

The post MBF Bioscience research team contributes novel dendritic spine analysis in study published in Science appeared first on MBF Bioscience.

MBF Bioscience Williston, VT – January 9, 2019 – MBF Bioscience is pleased to announce our participation in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program. Funded by the National Institutes of Health (NIH), this extensive research initiative is a vast collaborative effort, which aims to deepen the understanding of how the peripheral nervous system impacts internal organ function.

“We are honored to be working in collaboration with over 40 research teams in the United States and around the world who are making revolutionary discoveries about how the network of nerves located outside the brain and spinal cord affect organs such as the heart, stomach, and bladder, and what role these nerves play in diseases like hypertension and type II diabetes as well as gastrointestinal and inflammatory disorders,” says Jack Glaser, President of MBF Bioscience.

To facilitate this important research, MBF Bioscience will provide the collaborating research scientists with both software and support. Specifically, we will provide image segmentation tools developed to handle large and diverse amounts of scientific image data. Software applications such as Neurolucida 360^® and Tissue Maker™ will enable researchers to image and analyze nerves, tissues, and entire organs in 2D and 3D.

“Representing the innervation patterns accurately and robustly is an essential contribution to the generation of representative models that can be used for simulations.  We are working with our partners at the University of Auckland, under the direction of Professor Peter Hunter, to create these models for each organ system that will be an enduring resource for scientists for years to come,” says Susan Tappan, Scientific Director at MBF Bioscience.

Researchers involved in the SPARC program are making important advances in health and medicine, which may lead to the development of new therapies for managing an array of illnesses and disorders. Some examples of research areas include subcutaneous nerve stimulation for arrhythmia control, sensory neuromodulation of the esophagus, and mapping of the neural circuitry of bone marrow. We are thrilled about this opportunity to work in partnership with such an impressive array of research teams on this ground-breaking project.

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, and constantly work to refine our products based on state-of-the-art scientific advances.

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 pulmonary, cardiac, kidney, cancer, stem cell, and toxicology research.

Our commitment to innovative products and unrivaled customer support has gained high praise from distinguished scientists all over the world and resulted in MBF expanding into a global business with offices in North America, Europe, Japan, and South Korea. Our flagship products, Stereo Investigator^® and Neurolucida^®, are the most widely-used analysis systems of their kind.

About SPARC

Stimulating Peripheral Activity to Relieve Conditions (SPARC) is a National Institutes of Health (NIH) program that focuses on understanding peripheral nerves — nerves that connect the brain and spinal cord to the rest of the body — and how their electrical signals control internal organ function. Methods and medical devices that modulate these nerve signals are a potentially powerful way to treat many diseases and conditions, such as hypertension, heart failure, gastrointestinal disorders, type II diabetes, inflammatory disorders, and more.

The post MBF Bioscience receives NIH funding to support innovative research program on the peripheral nervous system 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.

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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