Researchers Identify Potential Treatment for Patients at Risk for Alzheimer’s Disease

Neurolucida 360 Used to Analyze Dendrites and Dendritic Spines

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.

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MBF Bioscience Announces Launch of MicroDynamix

New Software Application Quantifies Changes in Dendritic Spine Morphology Over Time

Williston, VT — December 10, 2019 — The ability to track the changes that occur in dendritic spine morphology over time is critical to many scientific studies, which is why MBF Bioscience is pleased to announce the launch of MicroDynamix. This powerful new software application helps neuroscientists acquire more information about morphological changes in the brain with impressive speed. MicroDynamix also offers the ability to visualize and quantify dendritic spine morphology over time.

After loading image data acquired at different time points from in vivo and in vitro imaging sessions, MicroDynamix automatically aligns the images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics — such as length, thickness, and overall number, for accurate quantitative comparison.

Since all images are managed within a single framework, the research process is streamlined, saving neuroscientists time in the laboratory that would otherwise be spent locating and manually finding the same spine. MicroDynamix also offers researchers the ability to view two 3D images side-by-side — an invaluable feature for tracking the changes that occur in dendritic spine morphology over time.

Over the course of an experiment, researchers have the ability to upload new images and compare the same region at different time points with MicroDynamix thanks to the software’s sophisticated algorithms. Dendrites and spines are automatically associated across images, so that the same dendrite imaged at any timepoint — two days later, two weeks later, or two months later is automatically detected and identified. The researcher is then able to very clearly view and quantify the changes in morphology that may or may not have occurred.

The software also includes customizable graphs, which give researchers the ability to present their data visually. Key metrics, such as the number and density of spines per time point; head diameter, plane angle, and luminance of individual spines; as well as the total number of spines within a specific region can all be clearly presented in tabular and graph form.

“MicroDynamix provides researchers with the unprecedented capability to get more information about changes in dendritic spines observed in repeated imaging experiments,” says MBF Bioscience President Jack Glaser. “We’re so pleased to announce the launch of this powerful new product for visualizing and quantifying spine morphology over time.”

To learn more about MicroDynamix visit 

About MBF Bioscience: MBF Bioscience creates quantitative imaging and visualization software for stereology, neuron reconstruction, vascular analysis, c. elegans behavior analysis and medical education, integrated with the world’s leading microscope systems, to empower research.

Our development team and staff scientists are actively engaged with leading bioscience researchers, constantly working to refine our products based on state-of-the-art scientific advances in the field.

Founded as MicroBrightField, Inc. in 1988, we changed our name to MBF Bioscience in 2005 to reflect the expansion of our products and services to new microscopy techniques in all fields of biological research and education. While we continue to specialize in neuroscience research, our products are also used extensively in the research fields of stem cells, lung, kidney, cardiac, cancer, and toxicology.

MBF Bioscience has grown into a global business, with offices in North America, Europe, Japan, and China, and a dealer network active on five continents. Our commitment to innovative products and unrivaled customer support has gained high praise from distinguished scientists who use our products all over the world. Our flagship products Stereo Investigator and Neurolucida are the most widely-used analysis systems for stereology and neuron reconstruction.

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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

Dendritic Spine Loss Reported in Schizophrenia and Bipolar Disorder

Golgi-stained human brain tissue from the dorsolateral prefrontal cortex.

Golgi-stained human brain tissue from the dorsolateral prefrontal cortex.

Schizophrenia and bipolar disorder are very different mental illnesses, but researchers are discovering evidence that the two disorders have some common pathologies. According to a recent study, a shared characteristic appears to be dendritic spine loss.

The researchers used Neurolucida to study pyramidal cells in human brain tissue from individuals with schizophrenia (n=14), individuals with bipolar disorder (n=9) and unaffected control participants (n=19). The pyramidal cells were located in the dorsolateral prefrontal cortex – a region that plays a key role in working memory. Bipolar patients showed significantly reduced spine density (10.5 percent) compared to control. Schizophrenic patients also showed lower spine density (6.5 percent), but this number just missed significance when compared to control patients. Individuals with both illnesses showed a lower number of spines per dendrite, as well as reduced dendritic length compared to controls.

To obtain these results, researchers analyzed 15 Golgi-stained pyramidal cells in each tissue sample. They used Neurolucida to reconstruct the longest dendrite on the pyramidal cells and to mark spines. After the researchers finished reconstructing the cells, Neurolucida provided them with important data about the dendrites and spines.

Continue reading “Dendritic Spine Loss Reported in Schizophrenia and Bipolar Disorder” »

Using Neurolucida for Dendritic Spine Analysis

Dendritic Spines

by Julie Simpson, Ph.D.

Neurolucida is used for reconstruction and morphometric analysis of neurons and anatomical regions of interest. Neurolucida can also be used for quantitative and qualitative analysis of dendritic spines. Spines are small, often bulbous protrusions that emerge from the dendritic shaft. They are the main site of excitatory synapses in the brain [1], and they range in length from 0.001 to 1mm and range in diameter from 0.5 to 2mms [2, 3]. Alterations in spine number and shape have been implicated in learning and memory, long-term potentiation, and synaptic efficacy [1-3]. Abnormalities in dendritic spine number and shape have been observed in pathological conditions such as Alzheimer’s disease, Parkinson’s disease, epilepsy, and trauma [2, 3]. The aging brain also exhibits a decrease in dendritic spines on cortical pyramidal neurons, leading to a decline in cognitive function, learning, and memory [2].

In Neurolucida there are currently two methods used to trace spines for quantitative analysis. The first method involves tracing spines as the neuron is reconstructed either directly from a tissue slide using a microscope and motorized stage or from an image stack. If spines are traced on an image stack, the 3D rendering of the image stack plus the tracing can be viewed using the 3D Solid Modeling module. This rendering allows the user to validate the placement of spines and the neuronal processes. In the other method, spines can be added after the entire neuron has been reconstructed using Neurolucida editing tools. Once the neuronal reconstruction is complete, morphometric analysis of the neuronal processes and dendritic spines is done in Neurolucida Explorer.

Neurolucida Explorer offers a number of quantitative spine measurements under Branched Structure Analysis. The first analysis is ‘neuron summary’, which lists the total number of spines placed. The second is ‘segment-dendrite analysis’ which lists the number of spines per tree or segment. This number can then be used to calculate spine density per tree. The next analysis, ‘spine report’, lists the spine number and density per branch order. The final analysis, ‘spine details,’ lists the spine length (distance from spine base to tip), area, volume (assumes the spine is cylindrical), distance of the spine from the origin of the neuronal process, and the X,Y,Z coordinates at the base of the spine.

Version 9.0 of Neurolucida improves on the previous versions’ process of classifying spine morphology. Before, the user manually marked the spines with markers named for each spine type, and marker totals indicated the number of each type of spine indentified in the trace. In the new version, users have the ability to efficiently classify spines according to five classes: thin, stubby, mushroom, branched, and filopodia. The quantitative spine analyses that are available have expanded to include spine morphology, and spine detection, tracing, and editing are more effective and user-friendly.

1. Zito, K. and V.N. Murthy, Dendritic spines. Curr Biol, 2002. 12(1): p. R5.

2. Calabrese, B., M.S. Wilson, and S. Halpain, Development and regulation of dendritic spine synapses. Physiology (Bethesda), 2006. 21: p. 38-47.

3. Lee, K.J., et al., Morphological changes in dendritic spines of Purkinje cells associated with motor learning. Neurobiol Learn Mem, 2007. 88(4): p. 445-50.

Julie Simpson is a staff scientist at MBF Bioscience.

{Confocal image of dendritic spines featured above, courtesy of Jakub Jedynak}

First published in The Scope, fall 2008.

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