Tracking and analysis of dendritic spine motility in high resolution repeated imaging experiments
MBF Bioscience > MicroDynamix®

Product Overview

MicroDynamix is state-of-the art software that enables you to visualize and quantify changes in spine morphology in repeated imaging experiments. MicroDynamix automatically measures spine dynamics by quantifying changes in shape, volume, and number over time.  Simply load your in vivo 3D image data acquired at different time points. MicroDynamix will automatically align the images if they have different orientations in 3D so that you can see how neuronal structures change over time. It will reconstruct dendritic branches, detect dendritic spines, and automatically identify important change in metrics — such as spine length, luminance, classification, head diameter, neck length, and overall number, providing you with quantitative information about the changes.

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Key Benefits

Purpose built to address

MicroDynamix is specially designed to perform 4D analysis of spine dynamics and motility. With its algorithms adapted from the renowned Neurolucida 360 dendritic spine detection and neuron reconstruction capabilities, Microdynamix includes novel functionality requested by neuroscientists performing in vivo imaging of structural changes and dynamic analyses over time. Features include automatic 3D alignment and integrated analyses for dendritic spines. You can align images at different time points from in vivo imaging sessions and analyze morphologic differences in neuronal structures between any or all time points. Building on the Neurolucida 360 interface, MicroDynamix makes it easy for neuroscientists interested in performing in-depth dendritic spine analysis research.

MicroDynamix takes spine analysis a step further, though. With three ways to register and align images from different time points (automatically, manually, and with refined alignment) you have maximum control over the efficiency and accuracy in which images are associated with each other. MicroDynamix also conveniently stores all of the data from the experiment/session in a single file.

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 confer with our customers regularly, incorporating their suggestions into the design of MicroDynamix to help enable discoveries in neuroscience worldwide.

Minimum Hardware Requirements

64-bit Windows 10 or 11 operating system

Minimum PC hardware configuration: 32GB of RAM, dual core processor graphics card with 8GB of GPU memory

Most 3D microscope image stack formats are supported

Download MicroDynamix product sheet here.

Version 2024.1.1 
Released March 2024

New Features and Enhancements:

  • Updated user interface for easier navigation
  • Improved navigation through experimental timepoints, with new icons for Previous Image/Next Image and Previous Image Pair/Next Image Pair
  • You can now place markers and associate them with each other
  • New quantitative analyses including:
    • Dendritic length
    • Spine count
    • XYZ coordinates of spines
    • Marker change ratio
  • Improved data export; you can now export all analyses at once to Excel or CSV format
  • Image filters, including an in vivo specific filter, are now available through the new Batch Pipeline
  • Updated image processing and image-handling engines that greatly increase the speed of loading, viewing, and saving images
  • Easier software authorization: MicroDynamix autofills the online Authorization Request Form with information about your computer system. Just add information about you and your lab to submit the form
  • Floating licenses are now available that enable you to use Microdynamix on more than one computer


Version 2021.1.1
Released February 2021

New Features and Enhancements:


  • Display changes in each viewport are applied to the viewport that is currently active. Changes to the viewport display will remain active independent from the time point being viewed
  • Image data adjustments are retained throughout the active sessions and can be saved with the image file
  • Added the ability to turn on/off center and zoom in association mode
  • Added a new, Remove Tracings button that makes it easy to start anew without having to reload and re-align image stacks
  • Expanded the list of supported file formats
  • Simplified software authorization
  • Image data is now included within the program installer

View full version history here.

Who Is Using MicroDynamix?

MicroDynamix is used across the world by scientists doing in vivo research to quantify morphometric changes in dendritic spines over time through multiple imaging rounds. Found at: 

News About MicroDynamix

Cited in Peer Reviewed Scientific Publications

MBF’s software utility is underscored by the number of references it receives in the worlds most important scientific publications.

Frequently Asked Questions (FAQ)

Does MicroDynamix work with timelapse video data?

Currently, MicroDynamix supports 3D time-series image data, not 2D time-lapse data. Standard 3D image stacks may be acquired as is typical for 3D in vivo imaging experiments. 

Can I run MicroDynamix on my laptop? What about a typical laboratory computer?

MicroDynamix is a graphics-intensive program, which means speed and efficiency depend on both the CPU and GPU in the computer. You’ll need a computer running Windows 10 or later with at least 32GB of RAM and 8GB GPU RAM to provide enough power to start working confidently.

Is there a way to adjust pixel values in individual image channels?

The Image Adjustment panel offers full control over the histogram of the image, including the individual channels that compose the image stack. You can adjust the saturation, brightness, contrast, and even change the false coloring of the image stack to better suit your research objectives.

Is there a way to adjust image data for specimen movement during acquisition?

With integrated batch processing, MicroDynamix allows you to apply image filters to help correct for animal movement during image acquisition. In addition to image filters, with batch processing you can automatically reconstruct multiple images with the same defined reconstruction parameters at the click of a button.

What is the difference between Neurolucida 360 and MicroDynamix?

The main difference between these two programs is that MicroDynamix is designed for analyzing in vivo time series image data, specifically quantifying changes over time. With MicroDynamix, you can load and visualize multiple image stacks at once, and associate data between time points automatically. Neurolucida 360 is geared more toward working with fixed tissue specimens; although it can also be used to measure change over time, by manually comparing separate data files from different time points.

Can I use reconstructed data from MicroDynamix with other MBF Bioscience products?

Yes, the data file that MicroDynamix produces for each experiment can be saved as individual time points that can be evaluated using either Neurolucida 360 or Neurolucida Explorer, depending on the specifics. With Neurolucida 360 you can add additional structures to your reconstructed data file that aren’t yet available in MicroDynamix. With Neurolucida Explorer, you can explore deeper quantitative results from your existing data structures.


Robust Professional Support

Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing.  We’ve also developed a host of additional support services, including:

  • Forums
    We have over 25 active forums where open discussions take place.
    >> Learn More
  • On-Site/Training
    We’ve conducted over 750 remote software installations.
    >> Learn More
  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
    >> Learn More

Request an Expert Demonstration

We offer both a free demonstration and a free trial copy of MicroDynamix. During your demonstration you’ll also have the opportunity to talk to us about your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, neuron tracing, and image processing.


Free 14-day trial copy: Download of a copy of MicroDynamix and use the tips and suggestions from the free demonstration to find out how easy it is to use and how quickly you can obtain useful data.

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Recorded Webinars and Videos

Webinar: Q&A session on the quantitative analysis capabilities of Neurolucida Explorer

Introduction to: MicroDynamix