Elucidating and Analyzing Dendritic Spine Changes

MicroDynamix is a state-of-the art dendritic spine analysis software application that enables you to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo imaging sessions, MicroDynamix automatically aligns the images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics — such as length, luminance, classification, head diameter, neck length, and overall number for accurate comparison between dendritic spines.

Watch the video below to learn more on how MicroDynamix is revolutionizing dendritic spine analysis!

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Customer Reviews

"MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
Wilma Van De Berg, Ph.D.
VU University Medical Center - Neuroscience Campus Amsterdam
"MBF Bioscience is extremely responsive to the needs of scientists and is genuinely interested in helping all of us in science do the best job we can."
Sigrid Veasey, M.D.
University of Pennsylvania
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
Bogdan A. Stoica, M.D.
University of Maryland


MicroDynamix Builds on the Strengths of our Revolutionary Software, Neurolucida 360

With user-controls, set up, and build all remaining familiar, MicroDynamix is an easy transition for researchers coming from Neurolucida 360 looking to conduct in-depth dendritic spine analysis research. MicroDynamix takes spine analysis a step further, though.

MicroDynamix expands Neurolucida 360’s dendritic spine detection and reconstruction providing novel functionality for dynamic analyses. With new features such as automatic alignment and integrated analysis for dendritic spines, users are now able to automatically align images at different time points from in vivo imaging sessions and analyze time differences between any or all points.



Integrated Data Analysis


  • Rapidly produce quantifiable, morphometric data for comparisons across all time-points. 
  • Track the dynamics of 3D dendritic spines, including persistence, growth, loss, and transience. 
  • Illuminate key changes easily with publication-quality, customizable graphs and multiple charting options. 
  • Analyze morphometric changes comparing:
• Number and density of spines per time point
• Head diameter, plane angle, luminance intensity 
• Total extent of spine


MicroDynamix Makes Registration and Alignment Easy

With three ways to register and align images from different time points: Automatically, Manually, and with Refined alignment, users have increased control over the efficiency and accuracy in which their images are being associated with each other. MicroDynamix also makes life easy by keeping the entirety of the data from the experiment/session in one single file. Researchers can then: 

  • Access their data in one single file location. 
  • View all the images and data from the previous session.
  • Update over time: Add more images as your experiment continues over time and keep analyzing as you go.    



Instantaneous Quantitative Change Analysis Over Time – Know More, Faster

No matter the time-span, MicroDynamix makes it easier to for neuroscientists to obtain more accurate and critical 4D dynamic analyses from in vivo images than ever before by automatically associating spines and dendrites across 3D images.

  • All images in your study are automatically aligned and managed within a single framework. 
  • Designed to work with any 3D image type, including in vivo.

  • View multiple 3D images from the same location and view any 2 images from your study for side-by-side comparison.
  • Automatically reconstruct the dendrites and spines in each image. Once detected in different time points the same spine is automatically identified for you.


Real-time Interactive Visualization

As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable to effective data interpretation.

Our software includes a highly versatile 3D visualization environment suitable to most microscopy images with state-of-the-art functionalities to support your analysis and publication needs.

  • Visualize large, complex 3D images (including multichannel images) and reconstructions
  • 3D image data from two-photon, confocal, brightfield or light sheet microscopy
  • 3D volume, image slicing, and simultaneous views
  • Transparency, rendering (wireframe, centerline, surface, texture) and other display options for image and traces that can be adjusted on the fly
  • Loads complex surfaces in seconds
  • Works with the most advanced “gaming class” graphics cards to deliver high performance at an affordable price
  • Supports almost all file formats



Designed by Neuroscientists for Neuroscientists

Developed with support from the National Institute of Mental Health (NIMH), MicroDynamix was specifically conceived for the neuroscience community by neuroscientists who understand the challenges and breadth of neuroscience research. We are constantly pushing the technological boundaries of our software to support your needs in addressing cutting-edge research questions. Our scientists are regularly in dialogue with our customers, incorporating their suggestions into the design of MicroDynamix to aid discoveries in neuroscience worldwide.

MicroDynamix is an invaluable tool to advance connectomics and handle the “big data” necessary to map neural pathways at the level of synaptic connections comprehensively. It can also be automated to perform repeated neuronal analyses.

Consult with our staff neuroscientists to determine the best course of action to make sense of your data.


How can MicroDynamix help you?

  • Easy to use, intuitive work flows guide you through the process.  
  • Fast and accurate results via integrated analysis tools.
  • Easily handles big image data with speed and agility utilizing our advanced 3D imaging engine.
  • Run analyses that exactly match your research questions
  • A ready to use solution with no need for programming skills or the creation of supplementary scripts (e.g., MatLab)
  • Use the stains and visualization techniques that fit your research paradigm including Golgi, expansion microscopy, CLARITY, iDISCO, uDISCO, confocal, two-photon.
  • Work with equipment in your facility, We support .jpx, .tif(monochrome images), and .lsm.
  • Consult with our expert neuroscientists to get recommendations on the best means to analyze your experimental data.

Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

Contract Services for Dendritic Spine Analysis

Our dendritic spine analysis services gives your lab the ability to have industry-leading experts create a 3D digital reconstruction of an individual or multiple neuron's trees, branches, and dendritic spines, for your research. MBF Labs will reconstruct your neurons giving you a breadth of quantitative information. The process is simple and practical. Provide us with slides or images, and MBF Labs experts do the rest.

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Watch a Webinar About MicroDynamix

Webinar: Overview of MBF Bioscience's MicroDynamix Software
Overview of MBF Bioscience's MicroDynamix Software

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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