Performs brain-wide analyses that are standardized to reference brain atlases
MBF Bioscience > NeuroInfo®

Product Overview

NeuroInfo enables whole brain investigation of circuits, neuronal populations, and biochemical marker expression using widely accepted brain atlases for anatomic reference. Visual and quantitative measurements from 2D and 3D brain images are characterized and visualized within brain region delineations from a standardized reference space.  NeuroInfo supports a variety of brain imaging techniques including; whole and semi brain volumes from cleared tissue specimens, serial section series, MRI and micro-CT imagery, and even single serial section whole slide images. Advanced AI segmentation and registration methods provide accurate results that are standardized and repeatable. NeuroInfo streamlines sophisticated computational pipelines into a single, powerful application that can be used in laboratories of every size.

NeuroInfo Video Intro-Image
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Key Benefits

NeuroInfo performs brain-wide characterization of cell populations and biochemical marker expression, and generates quantitative analysis reports on these objects within individual brain regions. Brain volumes are registered to either the Allen Mouse Brain Atlas or the Waxholm Rat Atlas so that experimental measurements can be accumulated or compared in a standardized coordinate system across animals, cohorts, and laboratories. Advanced deep learning methods mean that you can get highly accurate data automatically, and no longer need to manually click cells or draw anatomic boundaries. NeuroInfo’s use of standardized brain atlases established by the scientific community means you can leverage the work of the expert neuroanatomists that created the atlases by aligning your experimental brains with their coordinate systems.

NeuroInfo was developed in collaboration with the Allen Institute for Brain Science.

Recommended Hardware Requirements

NeuroInfo is powerful software that works with image data of any size and complexity. Because of its flexibility, our computing resource recommendations vary to balance affordability and performance required for large, multi-channel data.  
Please contact us to help you specify a computing configuration that best suits your imaging and research needs.

64-bit Windows 11 operating system
CPU with at least 18-24 cores (36-48 threads). More cores improve performance when using large data sets.
Solid state hard drive(s). Preferably non-volatile memory express (NVMe) drives.
128 GB of system memory. More memory is better for large data sets and 3D brain registration.
Graphics card with 8 GB memory or more. Graphics cards from NVIDIA and AMD have been tested with MBF Bioscience software.
Minimum Hardware Requirements (not recommended)
64-bit Windows 10 operating system
12 core processor (24 threads)
32 GB memory
Graphics card with 2 GB memory or more
Computer-Hardware Upgrade Priorities
To upgrade your system for better performance with MBF Bioscience software, we suggest that you prioritize computer hardware upgrades as follows:
      • Increase system memory to at least 128 GB.  More memory, eg 256 MB or 512 MB, improves performance when using large data sets
      • Replace hard disk drives (HDDs) with solid-state drives (SSDs), preferably non-volatile memory express (NVMe) drives
      • If you're working with 3D images and graphics, upgrade graphics card (GPU) to one with at least 8-12 GB memory

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A GPS for the brain and so much more
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Neurolucida, NeuroInfo Aids NIH GENSAT Project
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Visit our blog to read more case studies

Download NeuroInfo product sheet here.

NeuroInfo® Version 2023.2.1
Released November 2023

New Features and Enhancements

  • Added a new analysis tool for reporting experimental brain region volumes and intensities; these results can be exported to Excel
  • In the Brain Region Ontology list, subregions can be automatically selected when the region is selected
  • Markers can now be placed in the 3D visualization window
  • Improved rendering and display responsiveness for millions of markers in 3D views
  • Increased the speed of Map Experiment to Atlas for millions of markers from hours to minutes

NeuroInfo® Version 2023.1.1
Released May 2023

New Features and Enhancements

  • Image registration (alignment) to a reference brain atlas has been completely re-engineered to include new Volume Registration tools and to make registration easier to use, more dynamic, and more robust. Highlights include:
    • Using the new Register Volume process, you can align 3D volumes, either from intact, unsectioned tissue (e.g., cleared tissue) or blockface images, to a reference-brain atlas.
    • Registering 3D serial-section reconstructions to an atlas using the Register Sections set of tools has been enhanced with updated registration algorithms
    • Registration-integrated 3D visualization makes it easier to register experimental images to an atlas.
    • Atlas calibration has been incorporated into the registration process, streamlining your work.
    • New Map Atlas to Experiment tool, in combination with the updated Map Experiment to Atlas tool provides the capability to bidirectionally map experimental and atlas information.
    • New ability to assign brain regions to the left or right hemisphere
    • New ability to create and edit groups of anatomical structures of interest that can be used across experiments.
    • Updated Waxholm rat-brain atlas included
  • Faster Assemble Serial Sections (previously called the BrainMaker workflow) workflow processing to obtain 3D reconstructions from serial-section image sets.
  • Nikon ND2 and Olympus VSI image formats are now supported
  • Improved handling of multiple image formats, including CZI and some TIFF file types
  • New Pipelines ribbon houses features previously located in the Automatic section of the Registration Ribbon
  • New Batch Pipeline enables easy-to-use batch image filtering of multiple images—find it on the Pipelines ribbon
  • In the Cell detection workflow, the image source is now automatically updated based on the image modality selected


View Full Version History Here.

This is a NeuroInfo poster

Registering brain image volumes from serial sections and light sheet microscopy to standardized rodent reference atlases for quantitative analyses

Who Is Using NeuroInfo?

NeuroInfo is used across the globe by the most prestigious laboratories. 

News About NeuroInfo

Cited in Peer Reviewed Scientific Publications

NeuroInfo’s utility is underscored by the number of references it receives in the worlds most important scientific publications. See examples below: 

Frequently Asked Questions (FAQ)

Can NeuroInfo run on my typical laboratory computer?

NeuroInfo will run on most PCs running Windows 10 or later and having at least 16GB of RAM and 4GB GPU RAM. NeuroInfo will take advantage of available computer resources, so larger data sets will benefit from having more cores and memory. We’d be happy to discuss your needs with you to ensure you have the optimal computer configuration.

Can I use NeuroInfo on multiple computers in my laboratory?

Yes. NeuroInfo supports multiple software seats running under one license.

Can NeuroInfo analyze all typical section cut orientations?

NeuroInfo can register mouse and rat sections cut in coronal, sagittal, or transverse orientations.

Can NeuroInfo analyze sections that have pronounced cut angles?

Yes! The innovative registration algorithms in NeuroInfo account for cut angles that deviate significantly from canonical orientations.

What stains and markers work with Atlas registration in NeuroInfo?

NeuroInfo can register sections from a variety of stains and imaging methods and cytoarchitectural indicators, and has been tested with fluorescence microscopy (NeuroTrace and DAPI), brightfield microscopy (multiple structural visualizing stains), and MRI.

Is it possible to register damaged or warped sections?

NeuroInfo utilizes both linear and non-linear methods that can accommodate a damaged or warped sections while registering sections to an Atlas.

What brain atlases does NeuroInfo support?

Currently, NeuroInfo supports the latest versions of the Allen Mouse Brain Atlas and the Waxholm Rat Atlas

Does NeuroInfo work with any atlas?

Yes. NeuroInfo was designed to support alternate atlases, including developmental and other strains and species. Here is a description of our open atlas format.

Please contact us for guidance on including your atlas for use in NeuroInfo.


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 NeuroInfo. 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 NeuroInfo and use the tips and suggestions from the free evaluation 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

Introduction to NeuroInfo

Webinar: Registering Mouse Brain Serial Sections to the Allen Atlas

Webinar: Improved Detection of c-fos Labeled & Pyramidal Neurons with Machine Learning in NeuroInfo