MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with the Allen Mouse Brain Reference Atlas

An experimental coronal mouse brain section automatically aligned to the Allen Mouse Brain Reference Atlas

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.

Visit us at the Society for Neuroscience meeting in Washington, DC

The SfN 2017 meeting is the culmination of an exciting year of new technological achievements at MBF Bioscience. Our new version 2017 of Neurolucida, Stereo Investigator, and Neurolucida 360 features a totally re-designed interface and has been an overwhelming success with our customers. We’ve also expanded the stereology family with Stereo Investigator Cleared Tissue edition and Stereo Investigator Whole Slide Imaging edition. And we have received wide enthusiasm for our new optogenetics stand for WormLab, our worm tracking software.

Come see our innovative new system that includes a high-speed, 4-channel laser confocal scanner for fast confocal whole slide imaging in both 2D and 3D. It is creating a new paradigm for big data image acquisition and analysis. You simply will not believe the slide scanning speed we will be demonstrating for confocal imaging.

Curious about new technologies for microvasculature analysis? Come and discover Vesselucida.

Tired of using a printed brain atlas and wish there was an easier way to identify the brain anatomy on your sections? Imagine technology that can automatically identify the anatomical region on your sections by just clicking on it! Come see our new automatic brain mapping technology that matches serial sections of mouse brain to the Allen Brain Atlas.

Visit us at booth #1637 to see the latest advancements in quantitative neuroscience research and learn how our “End-To-End” solutions for Image Acquisition – Image Management – Image Analyses will revolutionize the way you make your next discovery.

If you’ve visited our booth at SfN before, you know how busy we can be.  If you’d like to schedule an appointment to reserve the time to meet with us that works best for you, just use this online form.  Or just stop by to see us for a personalized demonstration of any of our software or imaging systems.

We are looking forward to seeing you there!

Researchers cited MBF Bioscience systems in 32 papers between 08/11/2017 and 08/18/2017

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Bazzigaluppi, P., Beckett, T. L., Koletar, M. M., Lai, A. Y., Joo, I. L., Brown, M. E., . . . Stefanovic, B. (2017). Early stage attenuation of phase amplitude coupling in the hippocampus and medial prefrontal cortex in a transgenic rat model of AD. Journal of Neurochemistry, n/a-n/a. doi: 10.1111/jnc.14136.

Bull, C., Cooper, C., Lindahl, V., Fitting, S., Persson, A. I., Grandér, R., . . . Blomgren, K. (2017). Exercise in Adulthood after Irradiation of the Juvenile Brain Ameliorates Long-Term Depletion of Oligodendroglial Cells. Radiation Research, 0(0), null. doi: 10.1667/rr14737.1.

Edler, M. K., Sherwood, C. C., Meindl, R. S., Hopkins, W. D., Ely, J. J., Erwin, J. M., . . . Raghanti, M. A. (2017). Aged chimpanzees exhibit pathologic hallmarks of Alzheimer’s disease. Neurobiology of Aging. doi: http://dx.doi.org/10.1016/j.neurobiolaging.2017.07.006.

Fernandez, G. M., & Savage, L. M. (2017). Adolescent binge ethanol exposure alters specific forebrain cholinergic cell populations and leads to selective functional deficits in the prefrontal cortex. Neuroscience. doi: https://doi.org/10.1016/j.neuroscience.2017.08.013.

Hong, J., Wang, L., Zhang, T., Zhang, B., & Chen, L. (2017). Sigma-1 receptor knockout increases α-synuclein aggregation and phosphorylation with loss of dopaminergic neurons in substantia nigra. Neurobiology of Aging. doi: https://doi.org/10.1016/j.neurobiolaging.2017.08.007.

Li, W.-Y., Wang, Y., Zhai, F.-G., Sun, P., Cheng, Y.-X., Deng, L.-X., & Wang, Z.-Y. (2017). AAV-KLF7 Promotes Descending Propriospinal Neuron Axonal Plasticity after Spinal Cord Injury. Neural Plasticity, 2017.

Continue reading “Researchers cited MBF Bioscience systems in 32 papers between 08/11/2017 and 08/18/2017” »

MBF Bioscience and the Journal of Neuroscience Research to award NeuroArt contest winners with placement on the journal’s covers

Diversity of Enteric Glial Cells – April NeuroArt Juror’s Choice Winner
Marissa Puzan, Boston University

MBF Bioscience and the Journal of Neuroscience Research announced today that beginning this month, the Juror’s Choice winner in the NeuroArt image contest will be featured on the cover of the Journal of Neuroscience Research. Winners also have the opportunity to publish an editorial article or a research paper in the journal. A Juror’s Choice Award winner is chosen each month by an interdisciplinary panel of neuroscientists and artists.

“Partnering with the Journal of Neuroscience Research to offer this award fits perfectly with the mission of NeuroArt, which is to recognize and foster appreciation for the visual beauty and the aesthetic qualities of Neuroscience,” said Jack Glaser, President of MBF Bioscience.

The NeuroArt image contest is a creative outlet where neuroscientists and neuroscience enthusiasts can share their views of the brain and learn from each other  ̶  a sentiment that resonated with Dr. Eric Prager, Editor-in-Chief of the Journal of Neuroscience Research. “It seemed timely to feature these images on the cover of Journal of Neuroscience Research as the journal enters an era focusing on transparency in research,” said Dr. Prager. “The works of art will provide artistic interpretations and representations of neuroscience and the brain, which we, the audience, can internalize and interpret from our own perspectives. In research, we also strive for each article to provide the elements necessary for other researchers to reexamine from their own perspectives. It was a natural fit.”

Even if you don’t have an image to submit to the contest, you can still participate by voting for your favorite image. The image with the most votes at the end of the month wins the People’s Choice Award and $250 towards the purchase of MBF Bioscience products.

To enter this month’s contest, or vote for an image, go to neuroart.com

Over 80 images have been submitted to the contest since it started February 1, 2017, and there have been 12 winning images. Here’s what some NeuroArt participants have to say about the contest:

“It’s a great opportunity to share some very interesting images I’ve taken.”

“Fun, creative outlet and a place to share images with colleagues.”

“I learned something new about neuroscience. I saw something that I did not expect to be beautiful in an image.”

Researchers cited MBF Bioscience systems in 12 papers during the week of 07/10/2017

Stereo Investigator:

Abdurakhmanova, S., Chary, K., Kettunen, M., Sierra, A., & Panula, P. (2017). Behavioral and stereological characterization of Hdc KO mice: relation to Tourette syndrome. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24279. http://dx.doi.org/10.1002/cne.24279

Filice, F., Celio, M. R., Babalian, A., Blum, W., & Szabolcsi, V. (2017). Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24276. http://dx.doi.org/10.1002/cne.24276

Han, S.-W., Kim, Y.-C., & Narayanan, N. S. (2017). Projection targets of medial frontal D1DR-expressing neurons. Neuroscience Letters. doi: http://dx.doi.org/10.1016/j.neulet.2017.06.057http://www.sciencedirect.com/science/article/pii/S0304394017305487

Lee, J. Q., Sutherland, R. J., & McDonald, R. J. (2017). Hippocampal damage causes retrograde but not anterograde memory loss for context fear discrimination in rats. Hippocampus, n/a-n/a. doi: 10.1002/hipo.22759. http://dx.doi.org/10.1002/hipo.22759

Ma, E. L., Smith, A. D., Desai, N., Cheung, L., Hanscom, M., Stoica, B. A., . . . Faden, A. I. (2017). Bidirectional brain-gut interactions and chronic pathological changes after traumatic brain injury in mice. Brain, Behavior, and Immunity. doi: http://dx.doi.org/10.1016/j.bbi.2017.06.018http://www.sciencedirect.com/science/article/pii/S0889159117302076

Mahar, I., Labonte, B., Yogendran, S., Isingrini, E., Perret, L., Davoli, M. A., . . . Mechawar, N. (2017). Disrupted hippocampal neuregulin-1/ErbB3 signaling and dentate gyrus granule cell alterations in suicide. [Original Article]. Transl Psychiatry, 7, e1161. doi: 10.1038/tp.2017.132. http://dx.doi.org/10.1038/tp.2017.132

Shyng, C., Nelvagal, H. R., Dearborn, J. T., Tyynelä, J., Schmidt, R. E., Sands, M. S., & Cooper, J. D. (2017). Synergistic effects of treating the spinal cord and brain in CLN1 disease. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1701832114. http://www.pnas.org/content/early/2017/06/27/1701832114.abstract

Venezia, S., Refolo, V., Polissidis, A., Stefanis, L., Wenning, G. K., & Stefanova, N. (2017). Toll-like receptor 4 stimulation with monophosphoryl lipid A ameliorates motor deficits and nigral neurodegeneration triggered by extraneuronal α-synucleinopathy. [journal article]. Molecular Neurodegeneration, 12(1), 52. doi: 10.1186/s13024-017-0195-7. http://dx.doi.org/10.1186/s13024-017-0195-7

Neurolucida:

Morecraft, R. J., Binneboese, A., Stilwell-Morecraft, K. S., & Ge, J. (2017). Localization of Orofacial Representation in the Corona Radiata, Internal Capsule and Cerebral Peduncle in Macaca mulatta. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24275. http://dx.doi.org/10.1002/cne.24275

Santello, M., Bisco, A., Nevian, N. E., Lacivita, E., Leopoldo, M., & Nevian, T. (2017). The brain-penetrant 5-HT7 receptor agonist LP-211 reduces the sensory and affective components of neuropathic pain. Neurobiology of Disease. doi: http://dx.doi.org/10.1016/j.nbd.2017.07.005http://www.sciencedirect.com/science/article/pii/S0969996117301584

Scott, B. H., Saleem, K. S., Kikuchi, Y., Fukushima, M., Mishkin, M., & Saunders, R. C. (2017). Thalamic connections of the core auditory cortex and rostral supratemporal plane in the macaque monkey. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24283. http://dx.doi.org/10.1002/cne.24283

Biolucida:

Sakano, H., Zorio, D. A. R., Wang, X., Ting, Y. S., Noble, W. S., MacCoss, M. J., . . . Wang, Y. (2017). Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24281. http://dx.doi.org/10.1002/cne.24281

Researchers cited MBF systems in 29 papers between 6/30/2017 to 7/14/2017

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Abdurakhmanova, S., Chary, K., Kettunen, M., Sierra, A., & Panula, P. (2017). Behavioral and stereological characterization of Hdc KO mice: relation to Tourette syndrome. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24279.

Arathoon, L. R., Gleave, J. A., Trinh, D., Lizal, K. E., Giguère, N., Barber, J. H. M., . . . Nash, J. E. (2017). Sirtuin 3 rescues neurons through the stabilisation of mitochondrial biogenetics in the virally-expressing mutant α-synuclein rat model of parkinsonism. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.06.009.

Chen, L., Wang, X., Lin, Z.-X., Dai, J.-G., Huang, Y.-F., & Zhao, Y.-N. (2017). Preventive Effects of Ginseng Total Saponins on Chronic Corticosterone-Induced Impairment in Astrocyte Structural Plasticity and Hippocampal Atrophy. Phytotherapy Research, n/a-n/a. doi: 10.1002/ptr.5859.

Collette, J. C., Choubey, L., & Smith, K. M. (2017). ­Glial and stem cell expression of murine Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system. PeerJ, 5, e3519. doi: 10.7717/peerj.3519.

Filice, F., Celio, M. R., Babalian, A., Blum, W., & Szabolcsi, V. (2017). Parvalbumin-expressing ependymal cells in rostral lateral ventricle wall adhesions contribute to aging-related ventricle stenosis in mice. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24276.

Finkelstein, D. I., Billings, J. L., Adlard, P. A., Ayton, S., Sedjahtera, A., Masters, C. L., . . . Cherny, R. A. (2017). The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson’s disease. Acta Neuropathologica Communications, 5(1), 53. doi: 10.1186/s40478-017-0456-2.

Han, S.-W., Kim, Y.-C., & Narayanan, N. S. (2017). Projection targets of medial frontal D1DR-expressing neurons. Neuroscience Letters. doi: http://dx.doi.org/10.1016/j.neulet.2017.06.057.

Lee, J. Q., Sutherland, R. J., & McDonald, R. J. (2017). Hippocampal damage causes retrograde but not anterograde memory loss for context fear discrimination in rats. Hippocampus, n/a-n/a. doi: 10.1002/hipo.22759.

Continue reading “Researchers cited MBF systems in 29 papers between 6/30/2017 to 7/14/2017” »

Researchers cited MBF systems in 8 papers during the week of 06/19/2017

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Kaur, C., Pal, I., Saini, S., Jacob, T. G., Nag, T. C., Thakar, A., . . . Roy, T. S. (2017). Comparison of unbiased stereological estimation of total number of cresyl violet stained neurons and parvalbumin positive neurons in the adult human spiral ganglion. Journal of Chemical Neuroanatomy. doi: https://doi.org/10.1016/j.jchemneu.2017.06.004.

Mani, B. K., Osborne-Lawrence, S., Mequinion, M., Lawrence, S., Gautron, L., Andrews, Z. B., & Zigman, J. M. (2017). The role of ghrelin-responsive mediobasal hypothalamic neurons in mediating feeding responses to fasting. Molecular Metabolism. doi: 10.1016/j.molmet.2017.06.011. http://dx.doi.org/10.1016/j.molmet.2017.06.011

Martinez, E. M., Young, A. L., Patankar, Y. R., Berwin, B. L., Wang, L., von Herrmann, K. M., . . . Havrda, M. C. (2017). Nlrp3 is required for inflammatory changes and nigral cell loss resulting from chronic intragastric rotenone exposure in mice. Toxicological Sciences. https://academic.oup.com/toxsci/article-abstract/doi/10.1093/toxsci/kfx1…

Po, K. K.-t., Leung, J. W.-h., Chan, J. N.-m., Fung, T. K.-h., Sánchez-Vidaña, D. I., Sin, E. L.-l., . . . Siu, A. M.-h. (2017). Protective effect of Lycium Barbarum polysaccharides on dextromethorphan-induced mood impairment and neurogenesis suppression. Brain Research Bulletin, 134, 10-17. doi: https://doi.org/10.1016/j.brainresbull.2017.06.014.  Continue reading “Researchers cited MBF systems in 8 papers during the week of 06/19/2017” »

Researchers cited MBF systems in 25 papers between 6/10/2017 and 6/16/2017

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Arawaka, S., Sato, H., Sasaki, A., Koyama, S., & Kato, T. (2017). Mechanisms underlying extensive Ser129-phosphorylation in α-synuclein aggregates. Acta Neuropathologica Communications, 5(1), 48.

Birkl, C., Carassiti, D., Hussain, F., Langkammer, C., Enzinger, C., Fazekas, F., . . . Ropele, S. (2017). Assessment of ferritin content in multiple sclerosis brains using temperature-induced R*2 changes. Magnetic Resonance in Medicine, n/a-n/a. doi: 10.1002/mrm.26780.

Boudewyn, L. C., Sikora, J., Kuchar, L., Ledvinova, J., Grishchuk, Y., Wang, S. L., . . . Walkley, S. U. (2017). N-butyl-deoxynojirimycin delays motor deficits, cerebellar microgliosis, and Purkinje cell loss in a mouse model of mucolipidosis type IV. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.06.003.

Chaves, P. P., Valdoria, C. M., Amorim, M. C. P., & Vasconcelos, R. O. (2017). Ontogenetic development of the inner ear saccule and utricle in the Lusitanian toadfish: Potential implications for auditory sensitivity. Hearing Research. doi: https://doi.org/10.1016/j.heares.2017.06.008.

Ebenezer, G. J., Liu, Y., Judge, D. P., Cunningham, K., Truelove, S., Carter, N. D., . . . Polydefkis, M. (2017). Cutaneous nerve biomarkers in transthyretin familial amyloid polyneuropathy. Annals of Neurology, n/a-n/a. doi: 10.1002/ana.24972.

Fischer, D. L., Kemp, C. J., Cole-Strauss, A., Polinski, N. K., Paumier, K. L., Lipton, J. W., . . . Sortwell, C. E. (2017). Subthalamic Nucleus Deep Brain Stimulation Employs TrkB Signaling for Neuroprotection and Functional Restoration. The Journal of Neuroscience.

Continue reading “Researchers cited MBF systems in 25 papers between 6/10/2017 and 6/16/2017” »

Researchers cited MBF systems in 25 papers between 5/27/2017 and 6/9/2017

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Bastidas, J., Athauda, G., De La Cruz, G., Chan, W.-M., Golshani, R., Berrocal, Y., . . . Pearse, D. D. (2017). Human schwann cells exhibit long-term cell survival, are not tumorigenic and promote repair when transplanted into the contused spinal cord. Glia, n/a-n/a. doi: 10.1002/glia.23161.

Claflin, D. I., Schmidt, K. D., Vallandingham, Z. D., Kraszpulski, M., & Hennessy, M. B. (2017). Influence of postnatal glucocorticoids on hippocampal-dependent learning varies with elevation patterns and administration methods. Neurobiology of Learning and Memory. doi: https://doi.org/10.1016/j.nlm.2017.05.010.

Dioli, C., Patricio, P., Trindade, R., Pinto, L. G., Silva, J. M., Morais, M., . . . Sotiropoulos, I. (2017). Tau-dependent suppression of adult neurogenesis in the stressed hippocampus.  Molecular Psychiatry. doi: 10.1038/mp.2017.103.

Giesert, F., Glasl, L., Zimprich, A., Ernst, L., Piccoli, G., Stautner, C., . . . Wurst, W. (2017). The pathogenic LRRK2 R1441C mutation induces specific deficits modeling the prodromal phase of Parkinson’s disease in the mouse. Neurobiology of Disease. doi: https://doi.org/10.1016/j.nbd.2017.05.013.

Gumusoglu, S. B., Fine, R. S., Murray, S. J., Bittle, J. L., & Stevens, H. E. (2017). The role of IL-6 in neurodevelopment after prenatal stress. Brain, Behavior, and Immunity. doi: https://doi.org/10.1016/j.bbi.2017.05.015.

Issa, J. P. M., Trawitzki, B. F., Ervolino, E., Macedo, A. P., & Lilge, L. (2017). Low-intensity laser therapy efficacy evaluation in FVB mice subjected to acute and chronic arthritis. [journal article]. Lasers in Medical Science, 1-9. doi: 10.1007/s10103-017-2235-5.

Liu, H., Rose, M. E., Ma, X., Culver, S., Dixon, C. E., & Graham, S. H. (2017). In vivo transduction of neurons with TAT-UCH-L1 protects brain against controlled cortical impact injury. Plos one, 12(5), e0178049. doi: 10.1371/journal.pone.0178049.

Continue reading “Researchers cited MBF systems in 25 papers between 5/27/2017 and 6/9/2017” »

A complete guide to imaging and analyzing spines and neurons with Neurolucida 360


Following a well-designed protocol is essential to achieving accurate and consistent results in scientific research. Now, scientists using Neurolucida 360 for dendritic spine and neuron analysis can follow a published set of guidelines to ensure optimal confocal data series for proper dendritic spine quantification and neuron reconstruction. The paper, written by MBF Bioscience scientists and researchers from the Icahn School of Medicine at Mount Sinai in New York, was published in Current Protocols in Neuroscience.

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