Neurolucida Helps Scientists Map Rett Syndrome’s Brain Dysfunction in Mouse Model


At first, all appears normal with the infant’s development. But one day, around her first birthday, she stops making eye contact, her babbling comes to an end, she wrings her hands, and holds her breath. The child will likely survive into adulthood, but with Rett syndrome, she will lead a life with severe disabilities.

The symptoms of this autism-related disorder are complex, and treatments are not available. At the Case Western Reserve University School of Medicine, in Cleveland, Dr. David Katz and his team of neuroscientists are researching the rare genetic disorder, which affects one in 10,000 mostly female children. Their recent study, published in the Journal of Neuroscience, describes a map of brain dysfunction in a mouse model of Rett syndrome, as well as a promising treatment with the drug ketamine.

Continue reading “Neurolucida Helps Scientists Map Rett Syndrome’s Brain Dysfunction in Mouse Model” »

Scientists Map Diaphragm’s Motor Nerve and Arteriolar Networks With Neurolucida


Image adapted from “Neurovascular proximity in the diaphragm muscle of adult mice,” published with permission from Dr. S. Segal

A 3D model of a mouse diaphragm appears on the monitor. Blood vessels branch out from entry points around the muscle’s periphery, engaging in a graceful choreography with the nerve fibers that radiate from its center.

Could these two networks work together to ensure healthy blood and oxygen flow to the muscle? Or do they exist independently of each other, house mates living side by side within the confines of the diaphragm? Dr. Diego Correa and Dr. Steven Segal set out to test the hypothesis that the motor innervation and blood supply of the diaphragm muscle are physically associated.

“We used Neurolucida to map entire arteriolar networks together with entire motor nerve networks of the diaphragm muscle in adult mice,” explained Dr. Segal in an email.

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Neuroscientists in Germany Outline Protocol for Best Accuracy in Neuron Reconstruction, including Use of Neurolucida

biocytinNo two neurons are exactly alike. Structure dictates function, so for scientists to fully understand the way different types of neurons work, they must first get to know their forms.

Scientists at the Institute for Neuroscience and Medicine at the Research Center Jülich in Jülich, Germany use Neurolucida to perform neuron reconstruction, the most effective method for studying neuron morphology.

In their paper “Improved biocytin labeling and neuronal 3D reconstruction,” published last year in Nature Protocols, the German team describes a distinct series of steps, which must be carried out before a truly accurate model of a neuron can be created. From brain dissection and slice preparation to fixation, staining, embedding, and 3D reconstruction, the authors clearly lay out the process.

In detailing their protocol, the team took into consideration common issues that occur with the embedding and labeling of neuronal tissue such as shrinkage, distortion, and fading. Biocytin labeling, they say, is superior to other methods because of the “extremely durable and strong staining” it achieves. According to them, the labeling method also allows for tissue to be re-examined “to test a new scientific hypothesis or to verify the findings in a different context.”

In one section of the protocol, entitled “Suggestions for 3D, light-microscopic reconstructions of neurons,” the authors describe how to perform 3D reconstructions of biocytin labeled neurons with Neurolucida. “This software allows manual reconstructions of neurons in all three dimensions and generates reconstruction data files in the Neurolucida format for a quantitative morphological analysis,” they explain.

Read “Improved biocytin labeling and neuronal 3D reconstruction” at

(Note that the image above is for illustration purposes only and was not actually used in the study described in this post.)

Marx, M., Günter, R. H., Hucko, W., Radnikow, G., & Feldmeyer, D. (2012). Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols,7(2), 394-407.

Gene Therapy May Be Answer to Effective Parkinson’s Treatment; Neurolucida Plays Role in Study


Neurotrophic factors may be the key to the cure for Parkinson’s, Huntington’s, Alzheimer’s, and other neurodegenerative disorders. Scientists have known this for over twenty years. But the question continues to loom – how does one safely and effectively deliver the neurotrophic factors to the damaged neurons? Dr. Raymond Bartus and his team at Ceregene, a biotechnology company in San Diego, have developed an innovative approach that may be the answer.

Rather than focusing on conventional methods of neurotrophic factor delivery, which have always been extremely difficult and resulted in undesirable side effects, the Ceregene researchers took a different approach. They turned to gene therapy. Instead of delivering the restorative protein to the targeted sites in the brain, the Ceregene researchers developed a way to deliver only the gene for the protein. Once in place, the gene induces local cells to make the protein on site.

Continue reading “Gene Therapy May Be Answer to Effective Parkinson’s Treatment; Neurolucida Plays Role in Study” »

Neurolucida Helps Scientists in Jerusalem Study Synaptic Density in Lactating Mice

A baby cries and her mother’s maternal instincts kick in. She picks her baby up, rocks her, feeds her. Changes in a new mother’s brain compel her to act in ways that ensure her baby’s survival. Researchers at the Hebrew University of Jerusalem are working on learning more about those changes. Their recent focus is on the olfactory bulb – a region of the brain shown to ignite maternal behavior in mice.

“As a scientist and mother I wanted to study plasticity in the maternal brain,” said Hagit Kopel a co-author of the study. “Previous studies showed that olfaction is essential for the production of normal maternal behavior. Therefore, we hypothesized that there are plastic changes in the olfactory system, which accompany the transition into motherhood.”

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Dr. Henry Markram’s Team Uses Neurolucida in New Blue Brain Study

Blue Brain Project researchers have hit an important milestone in their quest to create a virtual model of the human brain. They figured out how to accurately predict the location of synapses in the neocortex; and Neurolucida played an important part.

In a paper published last week in PNAS, the research team led by Dr. Henry Markram at the Brain Mind Institute at the Ecole Polytechnique Fédérale de Lausanne (EPFL), in Lausanne, Switzerland, demonstrated that neurons grow independently of each other, forming connections in places where they accidentally collide. In other words, i is not chemicals that guide axons and dendrites along their path to form synapses.

“Neurons are growing as physically independent of each other as possible. They’re just expressing themselves, saying ‘I want this shape, this is my shape. I’m going to grow like this,’ and when they’ve all grown together, they just take what they get when they bump into each other. It’s just going to grow and rely on accidental collisions to decide where it’s going to form synapses. It’s a remarkable design principle of the brain,” Dr. Markram told EPFL News.

To achieve these results, the researchers used Neurolucida to create 3D models of neurons and form a virtual reconstruction of a cortical microcircuit. They analyzed the places where connections occurred, and found their model to be remarkably similar to the real-brain sample.

Read our previous article about the Blue Brain Project, as well as the research team’s latest paper:

S.L. Hill, Y. Wang, I. Riachi, F. Schürmann, H. Markram: Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits, PNAS, Published online before print September 18, 2012, doi: 10.1073/pnas.1202128109

UVM Scientists Use Neurolucida and Stereo Investigator to Study Neurons in the Avian Iris

During a chicken embryo’s twenty-one days of incubation, its eyes develop in astonishing ways. Muscles form, neurons branch, innervation occurs. Researchers at Dr. Rae Nishi’s lab at the University of Vermont, including two MBF Bioscience staff scientists Julie Simpson, Ph.D. and Julie Keefe, M.S. are studying the development of a chicken embryo’s nervous system. Their specific focus is on the behavior of neurons in the ciliary ganglion – a mass of nerve cells in the eye’s ciliary muscle.

Published last month in Developmental Neurology, their paper “Differential effects of RET and TRKB on axonal branching and survival of parasympathetic neurons” describes the multiple functions of several trophic factors in the development of ciliary ganglion neurons.

According to the paper, the researchers’ principal finding is that the neurotrophic factor receptors RET and TRKB work to ensure the survival of ciliary neurons and foster their axonal outgrowth as they innervate the striated muscle of the avian iris.

To come to this conclusion, the scientists first used Neurolucida to identify specific neurotrophic factors that are important in outgrowth and branching ciliary neurons. Next, they evaluated neuronal survival in the ciliary ganglion, and axonal branching in the iris after blocking neuromuscular transmission and signaling through RET and TRKB. They used Stereo Investigator with the Optical Fractionator probe to perform a design-based stereological count of the ciliary neurons.

“When the normal number of ciliary neurons is decreased by exogenous manipulations such as dTC and dnRET, axonal outgrowth increases to fill synaptic space. However, when neuromuscular transmission is blocked, the lack of activity causes the muscle to attract more axons through retrograde signaling mediated by RET, leading to a higher than normal axonal density,” the researchers said in their paper.

The study, which may be beneficial in neurodegenerative disease research,“suggests that interfering with neuromuscular transmission enhances retrograde signaling between muscle and nerve, which, in turn, promotes axonal branching, endplate formation, and neuronal survival.” (Simpson, Keefe, Nishi, 2012)

“It is always a pleasure to see hard work come to fruition in the form of a publication,” said Dr. Simpson. “I’d like to thank to Dr. Rae Nishi who was a wonderful advisor and mentor during my graduate career at the University of Vermont.”

Simpson, J., Keefe, J. and Nishi, R. (2012), Differential effects of ret and TRKB on axonal branching and survival of parasympathetic neurons. Devel Neurobio. doi: 10.1002/dneu.22036

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{Public domain illustration depicting ciliary muscle via Wikipedia.}

Neurolucida Helps Florida Researchers Reconstruct a Region of the Rat Brain

by Dan Peruzzi, PhD

A rat uses its whiskers to get information about its environment. As it scurries along the subway tracks, or burrows into a dumpster, its whiskers send signals to ascending parts of its brain that let it know for example, whether it is safe to jump over that gap or not.

Scientists at the Max Planck Florida Institute are studying the functional responses of neurons in the rat vibrissal cortex. Using a “pipeline” method, developed to use data obtained from animals to recreate parts of the brain “in silico” (1), they have constructed a 3D model of a vibrissal cortical column. The scientists used Neurolucida® to trace neurons so they could be classified according to dendritic morphology and cell body location.

In their paper (2) “Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex,” the scientists classified nine cell types in the barrel cortex, a region of the vibrissal area of the rodent somatosensory cortex. They used these cell-types and parameters such as 3D cell location and quantity, spine and bouton densities, and definitions of pre and post-synaptic partners, to assemble an anatomically realistic network that included synapses at points where boutons and spines overlapped.  Continue reading “Neurolucida Helps Florida Researchers Reconstruct a Region of the Rat Brain” »

In the Forest of the Mind

Using Neurolucida, microscopy, and mice genetically engineered to express a random amount of red, yellow, and blue fluorescent proteins, Okinawa Institute of Science and Technology researcher Hermina Nedelescu has created a fascinating and hypnotic movie of neurons. Nedelescu and colleagues at the Institute’s Computational Neuroscience Unit used Neurolucida and its Virtual Tissue 3D Extension Module and Montaging tools to acquire and stitch together multiple images of Purkinje cells—large neurons  that form elongated branching structures called “dendritic trees”—into a recording showing each tree from different angles and visual locations. As you move around and through the video, the traced cells, highlighted by the “Brainbow” coloring, show the complexity of the structures and location and how the Purkinje cells relate to each other.

Visit the  OIST Computational Neuroscience Unit page for more information on their work.

Movie by Hermina Nedelescu of the OIST Computational Neuroscience Unit (Erik De Schutter, Principal Investigator), in collaboration with Alanna Watt of McGill University, Canada, and Hermann Cuntz of Goethe University, Germany.

This article was edited to add mention of the Montaging tool.

Columbia Scientists Map Neocortical Circuit Connectivity with Neurolucida

A willowy pair of pyramidal cells engage in an intricate dance with a dense mass of basket cells on the cover of the September 14, 2011 issue of the Journal of Neuroscience.

This exquisite image illustrates recent work by Columbia University researchers Dr. Adam M. Packer and Dr. Rafael Yuste, who used Neurolucida to study circuit connectivity in the mammalian neocortex.

According to the paper “Successfully filled and stained neurons were reconstructed using Neurolucida software (MicroBrightField). The neurons were viewed with a 100× oil objective on an Olympus IX71 inverted light microscope or an Olympus BX51 upright light microscope. The Neurolucida program projected the microscope image onto a computer drawing tablet. The neuron’s processes were traced manually while the program recorded the coordinates of the tracing to create a digital, three-dimensional reconstruction. The x- and y-axes formed the horizontal plane of the slice, while the z-axis was the depth. The user defined an initial reference point for each tracing. The z-coordinate was then determined by adjustment of the focus. In addition to the neuron, the pia and white matter were drawn. Axon and dendrite densities were calculated from the Neurolucida reconstruction using the TREES toolbox (Cuntz et al., 2010). The densities were calculated with voxels 5 μm on each side.” (Packer, Yuste, 2011)

Read the open access article in The Journal of Neuroscience.

Packer, Yuste. “Dense, Unspecific Connectivity of Neocortical Parvalbumin-Positive Interneurons: A Canonical Microcircuit for Inhibition?” The Journal of Neuroscience, 14 September 2011, 31(37):13260-13271; doi:10.1523/JNEUROSCI.3131-11.2011