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

Researchers cited MBF systems in 18 papers during the week of 12/12/2016

Stereo Investigator:journal images sm

Alberico, S. L., Kim, Y.-C., Lence, T., & Narayanan, N. S. (2016). Axial levodopa-induced dyskinesias and neuronal activity in the dorsal striatum. Neuroscience. doi: http://dx.doi.org/10.1016/j.neuroscience.2016.11.046.

Forgione, N., Chamankhah, M., & Fehlings, M. (2016). A Mouse Model of Bilateral Cervical Contusion-Compression Spinal Cord Injury. Journal of Neurotrauma. doi: 10.1089/neu.2016.4708.

Gasser, E., Johannssen, H. C., Rülicke, T., Zeilhofer, H. U., & Stoffel, M. (2016). Foxa1 is essential for development and functional integrity of the subthalamic nucleus. Scientific Reports, 6, 38611. doi: 10.1038/srep38611

Ghosh, A., Tyson, T., George, S., Hildebrandt, E. N., Steiner, J. A., Madaj, Z., . . . Brundin, P. (2016). Mitochondrial pyruvate carrier regulates autophagy, inflammation, and neurodegeneration in experimental models of Parkinson’s disease. [10.1126/scitranslmed.aag2210]. Science translational medicine, 8(368), 368ra174.

Jacinto, L. R., Mata, R., Novais, A., Marques, F., & Sousa, N. (2016). The habenula as a critical node in chronic stress-related anxiety. Experimental Neurology. doi: http://dx.doi.org/10.1016/j.expneurol.2016.12.003.

Jobe, E. M., Gao, Y., Eisinger, B. E., Mladucky, J. K., Giuliani, C. C., Kelnhofer, L. E., & Zhao, X. (2016). Methyl-CpG binding protein MBD1 regulates neuronal lineage commitment through maintaining adult neural stem cell identity. [10.1523/JNEUROSCI.1075-16.2016]. The Journal of Neuroscience.

Mandolesi, G., De Vito, F., Musella, A., Gentile, A., Bullitta, S., Fresegna, D., . . . Mori, F. (2016). miR-142-3p is a key regulator of IL-1β-dependent synaptopathy in neuroinflammation. Journal of Neuroscience, 0851-0816.

Continue reading “Researchers cited MBF systems in 18 papers during the week of 12/12/2016” »

Researchers cited MBF systems in 16 papers between 11/1/2016 and 11/11/2016

Stereo Investigator: journal images sm

Bode, C., Richter, F., Spröte, C., Brigadski, T., Bauer, A., Fietz, S., . . . Richter, A. (2017). Altered postnatal maturation of striatal GABAergic interneurons in a phenotypic animal model of dystonia. Experimental Neurology, 287, Part 1, 44-53. doi: http://dx.doi.org/10.1016/j.expneurol.2016.10.013.

Calvez, J., de Ávila, C., Guèvremont, G., & Timofeeva, E. (2016). Sex-specific effects of chronic administration of relaxin-3 on food intake, body weight and hypothalamo-pituitary-gonadal axis in rats. Journal of Neuroendocrinology, n/a-n/a. doi: 10.1111/jne.12439.

Haight, J. L., Fuller, Z. L., Fraser, K. M., & Flagel, S. B. (2016). A food-predictive cue attributed with incentive salience engages subcortical afferents and efferents of the paraventricular nucleus of the thalamus. Neuroscience. doi: http://dx.doi.org/10.1016/j.neuroscience.2016.10.043.

He, H., Guo, W.-W., Xu, R.-R., Chen, X.-Q., Zhang, N., Wu, X., & Wang, X.-M. (2016). Alkaloids from piper longum protect dopaminergic neurons against inflammation-mediated damage induced by intranigral injection of lipopolysaccharide. BMC Complementary and Alternative Medicine, 16(1), 412. doi: 10.1186/s12906-016-1392-6.

Jin, T., Nicholls, F. J., Crum, W. R., Ghuman, H., Badylak, S. F., & Modo, M. (2017). Diamagnetic chemical exchange saturation transfer (diaCEST) affords magnetic resonance imaging of extracellular matrix hydrogel implantation in a rat model of stroke. Biomaterials, 113, 176-190. doi: http://dx.doi.org/10.1016/j.biomaterials.2016.10.043.

Kyyriäinen, J., Ekolle Ndode-Ekane, X., & Pitkänen, A. (2016). Dynamics of PDGFRβ expression in different cell types after brain injury. Glia, n/a-n/a. doi: 10.1002/glia.23094.

Continue reading “Researchers cited MBF systems in 16 papers between 11/1/2016 and 11/11/2016” »

Researchers cited MBF systems in 15 papers during the week of 10/24/2016

Stereo Investigator:journal images sm

Casaca-Carreira, J., Temel, Y., Larrakoetxea, I., & Jahanshahi, A. (2016). Distribution and Penetration of Intracerebroventricularly Administered 2′OMePS Oligonucleotide in the Mouse Brain. Nucleic Acid Therapeutics. doi: 10.1089/nat.2016.0642.

Guatteo, E., Rizzo, F. R., Federici, M., Cordella, A., Ledonne, A., Latini, L., . . . Mercuri, N. B. (2017). Functional alterations of the dopaminergic and glutamatergic systems in spontaneous α-synuclein overexpressing rats. Experimental Neurology, 287, Part 1, 21-33.

Gupta, R., Saini, S., Sharma, S., Jacob, T. G., & Roy, T. S. (2017). Morphology of the Human Pancreas During Development and Aging. In P. C. Rath, R. Sharma & S. Prasad (Eds.), Topics in Biomedical Gerontology (pp. 67-89). Singapore: Springer Singapore.

Hook, M., Woller, S., Bancroft, E., Aceves, M., Funk, M. K., Hartman, J., & Garraway, S. M. (2016). Neurobiological effects of Morphine following Spinal Cord Injury. Journal of Neurotrauma. doi: 10.1089/neu.2016.4507. http://dx.doi.org/10.1089/neu.2016.4507

Schaeffer, E. L., Catanozi, S., West, M. J., & Gattaz, W. F. (2016). Stereological investigation of the CA1 pyramidal cell layer in untreated and lithium-treated 3xTg-AD and wild-type mice. Annals of Anatomy – Anatomischer Anzeiger. doi: http://dx.doi.org/10.1016/j.aanat.2016.10.002.

Continue reading “Researchers cited MBF systems in 15 papers during the week of 10/24/2016” »

Researchers cited MBF systems in 14 papers during the week of 10/17/2016

Stereo Investigator:journal images sm

Bacigaluppi, M., Russo, G. L., Peruzzotti-Jametti, L., Rossi, S., Sandrone, S., Butti, E., . . . Martino, G. (2016). Neural Stem Cell Transplantation Induces Stroke Recovery by Upregulating Glutamate Transporter GLT-1 in Astrocytes.  The Journal of Neuroscience, 36(41), 10529.

Beck, M. H., Haumesser, J. K., Kühn, J., Altschüler, J., Kühn, A. A., & van Riesen, C. (2016). Short- and long-term dopamine depletion causes enhanced beta oscillations in the cortico-basal ganglia loop of parkinsonian rats. Experimental Neurology, 286, 124-136. doi: http://dx.doi.org/10.1016/j.expneurol.2016.10.005.

Huang, C.-W., Chen, Y.-W., Lin, Y.-R., Chen, P.-H., Chou, M.-H., Lee, L.-J., . . . Chen, S.-L. (2016). Conditional Knockout of Breast Carcinoma Amplified Sequence 2 (BCAS2) in Mouse Forebrain Causes Dendritic Malformation via β-catenin.  Scientific Reports, 6, 34927. doi: 10.1038/srep34927

Sack, M., Lenz, J. N., Jakovcevski, M., Biedermann, S. V., Falfán-Melgoza, C., Deussing, J., . . . Auer, M. K. (2016). Early effects of a high-caloric diet and physical exercise on brain volumetry and behavior: a combined MRI and histology study in mice. Brain Imaging and Behavior, 1-12. doi: 10.1007/s11682-016-9638-y.

Schelle, J., Häsler, L., Göpfert, J. C., Joos, T. O., Vanderstichele, H., Stoops, E., . . . Kaeser, S. A. (2016). Prevention of tau increase in cerebrospinal fluid of APP transgenic mice suggests downstream effect of BACE1 inhibition. Alzheimer’s & Dementia. doi: http://dx.doi.org/10.1016/j.jalz.2016.09.005.

Teo, J. D., Morris, M. J., & Jones, N. M. (2016). Maternal obesity increases inflammation and exacerbates damage following neonatal hypoxic-ischaemic brain injury in rats. Brain, Behavior, and Immunity. doi:http://dx.doi.org/10.1016/j.bbi.2016.10.010.

Continue reading “Researchers cited MBF systems in 14 papers during the week of 10/17/2016” »

Researchers cited MBF systems in 22 papers during the week of 10/10/2016

Stereo Investigator:journal images sm

Acosta, S. A., Tajiri, N., Sanberg, P. R., Kaneko, Y., & Borlongan, C. V. (2016). Increased Amyloid Precursor Protein and Tau Expression Manifests as Key Secondary Cell Death in Chronic Traumatic Brain Injury. Journal of Cellular Physiology, n/a-n/a. doi: 10.1002/jcp.25629.

Chan, A., Li, S., Lee, A. R., Leung, J., Yip, A., Bird, J., . . . Pompeiano, M. (2016). Activation of state-regulating neurochemical systems in newborn and embryonic chicks. Neuroscience. doi:http://dx.doi.org/10.1016/j.neuroscience.2016.09.048.

Gomez-Smith, M., Karthikeyan, S., Jeffers, M. S., Janik, R., Thomason, L. A., Stefanovic, B., & Corbett, D. (2016). A physiological characterization of the Cafeteria diet model of metabolic syndrome in the rat. Physiology and Behavior. doi: http://dx.doi.org/10.1016/j.physbeh.2016.09.029.

Lei, B., James, M. L., Liu, J., Zhou, G., Venkatraman, T. N., Lascola, C. D., . . . Wang, H. (2016). Neuroprotective pentapeptide CN-105 improves functional and histological outcomes in a murine model of intracerebral hemorrhage. Scientific Reports, 6, 34834. doi: 10.1038/srep34834.

Li, Y. Q., Cheng, Z.-C., Liu, S.-W., Aubert, I., & Wong, C. S. (2016). P53 regulates disruption of neuronal development in the adult hippocampus after irradiation.  Cell Death Discovery, 2, 16072. doi: 10.1038/cddiscovery.2016.72

Continue reading “Researchers cited MBF systems in 22 papers during the week of 10/10/2016” »

Researchers cited MBF systems in 21 papers during the week of 10/3/2016

Stereo Investigator:journal images sm

Augur, I. F., Wyckoff, A. R., Aston-Jones, G., Kalivas, P. W., & Peters, J. (2016). Chemogenetic Activation of an Extinction Neural Circuit Reduces Cue-Induced Reinstatement of Cocaine Seeking. The Journal of Neuroscience, 36(39), 10174-10180.

Bocchio, M., Fisher, S. P., Unal, G., Ellender, T. J., Vyazovskiy, V. V., & Capogna, M. (2016). Sleep and serotonin modulate paracapsular nitric oxide synthase expressing neurons of the amygdale. [10.1523/ENEURO.0177-16.2016]. eneuro.

Cope, E. C., Briones, B. A., Brockett, A. T., Martinez, S., Vigneron, P.-A., Opendak, M., . . . Gould, E. (2016). Immature neurons and radial glia, but not astrocytes or microglia, are altered in adult Cntnap2 and Shank3 mice, models of autism. [10.1523/ENEURO.0196-16.2016]. eneuro.

Dela Cruz, J. A. D., Coke, T., & Bodnar, R. J. (2016). Simultaneous Detection of c-Fos Activation from Mesolimbic and Mesocortical Dopamine Reward Sites Following Naive Sugar and Fat Ingestion in Rats. (114), e53897. doi: doi:10.3791/53897.

Dixon, K. J., Mier, J., Gajavelli, S., Turbic, A., Bullock, R., Turnley, A. M., & Liebl, D. J. (2016). EphrinB3 restricts endogenous neural stem cell migration after traumatic brain injury. Stem Cell Research. doi:http://dx.doi.org/10.1016/j.scr.2016.09.029.

Fahimi, A., Baktir, M. A., Moghadam, S., Mojabi, F. S., Sumanth, K., McNerney, M. W., . . . Salehi, A. (2016). Physical exercise induces structural alterations in the hippocampal astrocytes: exploring the role of BDNF-TrkB signaling. Brain Structure and Function, 1-12. doi: 10.1007/s00429-016-1308-8.

Fernandez-Gonzalez, P., Benavides-Piccione, R., Leguey, I., Bielza, C., Larrañaga, P., & DeFelipe, J. (2016). Dendritic-branching angles of pyramidal neurons of the human cerebral cortex. Brain Structure and Function, 1-13. doi: 10.1007/s00429-016-1311-0.  Continue reading “Researchers cited MBF systems in 21 papers during the week of 10/3/2016” »

Researchers cited MBF systems in 17 papers during the week of 9/26/2016

Stereo Investigator:journal images sm

Biedermann, S. V., Auer, M. K., Bindila, L., Ende, G., Lutz, B., Weber-Fahr, W., . . . Fuss, J. (2016). Restricted vs. unrestricted wheel running in mice: Effects on brain, behavior and endocannabinoids. Hormones and Behavior, 86, 45-54. doi: http://dx.doi.org/10.1016/j.yhbeh.2016.09.007.

Choi, E. Y., Tanimura, Y., Vage, P. R., Yates, E. H., & Haber, S. N. (2016). Convergence of prefrontal and parietal anatomical projections in a connectional hub in the striatum. Neuroimage. doi:http://dx.doi.org/10.1016/j.neuroimage.2016.09.037.

García-Cabezas, M. Á., & Barbas, H. (2016). Anterior Cingulate Pathways May Affect Emotions Through Orbitofrontal Cortex. Cerebral Cortex. doi: 10.1093/cercor/bhw284.

Gomez, A. M., Stevens, J. A. A., Mané-Damas, M., Molenaar, P., Duimel, H., Verheyen, F., . . . Martinez-Martinez, P. (2016). Silencing of Dok-7 in Adult Rat Muscle Increases Susceptibility to Passive Transfer Myasthenia Gravis. The American journal of pathology, 186(10), 2559-2568. doi: http://dx.doi.org/10.1016/j.ajpath.2016.05.025.

Halici, Z., Polat, B., Cadirci, E., Topcu, A., Karakus, E., Kose, D., . . . Bayir, Y. (2016). Inhibiting renin angiotensin system in rate limiting step by aliskiren as a new approach for preventing indomethacin induced gastric ulcers. Chemico-Biological Interactions, 258, 266-275. doi: http://dx.doi.org/10.1016/j.cbi.2016.09.011.

Continue reading “Researchers cited MBF systems in 17 papers during the week of 9/26/2016” »

Researchers cited MBF systems in 12 papers during the week of 9/19/2016

Stereo Investigator:journal images sm

Charvet, C. J., Hof, P. R., Raghanti, M. A., van der Kouwe, A. J., Sherwood, C. C., & Takahashi, E. (2016). Combining diffusion MR tractography with stereology highlights increased cross-cortical integration in primates. Journal of Comparative Neurology, n/a-n/a. doi: 10.1002/cne.24115.

Coon, E. A., Schmeichel, A. M., Parisi, J. E., Cykowski, M. D., Low, P. A., & Benarroch, E. E. (2016). Medullary neuronal loss is not associated with α-synuclein burden in multiple system atrophy. Movement Disorders, n/a-n/a. doi: 10.1002/mds.26798.

Filichia, E., Hoffer, B., Qi, X., & Luo, Y. (2016). Inhibition of Drp1 mitochondrial translocation provides neural protection in dopaminergic system in a Parkinson’s disease model induced by MPTP. [Article]. Scientific Reports, 6, 32656. doi: 10.1038/srep32656

Hodges, J. L., Yu, X., Gilmore, A., Bennett, H., Tjia, M., Perna, J. F., . . . Zuo, Y. (2016). Astrocytic Contributions to Synaptic and Learning Abnormalities in a Mouse Model of Fragile X Syndrome. Biological Psychiatry. doi:http://dx.doi.org/10.1016/j.biopsych.2016.08.036.

Komnig, D., Schulz, J. B., Reich, A., & Falkenburger, B. H. (2016). Mice lacking Faim2 show increased cell death in the MPTP mouse model of Parkinson Disease. Journal of Neurochemistry, n/a-n/a. doi: 10.1111/jnc.13847.

Continue reading “Researchers cited MBF systems in 12 papers during the week of 9/19/2016” »

Stereological Study Reveals Neuron and Glia Proliferation in Hippocampus of Lithium-Treated Mice

Dentate gyruspilot

The optical fractionator probe was used to quantify the number of neurons and glia in the dentate gyrus

Doctors have used lithium to treat patients with bipolar disorder since the 1970s. Known for its efficacy in stabilizing patients’ moods by regulating manic episodes, lithium is also associated with a decreased risk of suicide. But while this naturally occurring element is the most widely prescribed medication for those suffering from bipolar disorder, scientists still have much to learn about how lithium physically affects the brain.

A recent study published in the journal Bipolar Disorders adds to the growing body of evidence that says lithium contributes to cell proliferation in parts of the brain. Conducted by scientists at the University of Mississippi and the VU University Medical Center in Amsterdam, the study revealed an increased number of neurons and glia, and increased astrocyte density in the dentate gyrus of lithium-treated mice versus controls treated with a placebo.

Using the optical fractionator probe in Stereo Investigator, the researchers quantified the number of Nissl stained neurons and glial cells, and calculated astrocyte density. The results showed twenty-five percent more neurons and twenty-one percent more glia in the denate gyrus of lithium-treated mice. They also performed a stereological examination of another brain region – the medial prefrontal cortex (mPFC), but did not witness significant differences between lithium-treated and control mice in this area.

“In this study, particular cortical regions, ie. the fascia dentata in the hippocampus and the mPFC in the cerebral cortex needed to be selected in histological sections of the mice brains,” explained Dr. Harry B.M. Uylings, “therefore the stereological counting procedure applied was the best one. Stereo Investigator greatly assisted in the counting of cells, and the software’s excel data-output was especially beneficial.”

According to the paper, the findings present a more detailed picture of lithium-induced alterations in the dentate gyrus cellular phenotype than previously available, and provide the first evidence for lithium-induced increases in glia and astrocytes.

The authors also explain that while cell number increased in the dentate gyrus of lithium-treated mice, the region’s overall volume as well as that of the greater hippocampus was unaffected by the element. The volume of the dentate gyrus and the hippocampus as a whole was measured with the Cavalieri method in Stereo Investigator.  The researchers describe the dissociation between cell proliferation and volume as “an interesting observation that warrants further investigation.”

Rajkowska, G., Clarke, G., Mahajan, G., Licht, C.M., van de Werd, H.J., Yuan, P., Stockmeier, C.A., Maji, H.K., Uylings, H.B., Differential effect of lithium on cell number in the hippocampus and prefrontal cortex in adult mice: a stereological study. Bipolar Disord. 2016 Feb;18(1):41-51. doi: 10.1111/bdi.12364.