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.

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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
64-bit Windows 10 operating system
8-core processor (16 threads)
Solid state drive(s)
64 GB of system memory
Graphics card with 8 GB texture memory or more: This is required for the 3D environment, but is optional for working only in 2D. Graphics cards from NVIDIA and AMD have been tested with MBF Bioscience software.
Minimum Hardware Requirements (not recommended)
64-bit Windows 10 operating system
4 core processor (8 threads)
16 GB memory
Graphics card with 2 GB texture memory or more: This is the minimum needed for the 3D environment, but is adequate for working only in 2D.
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 a total of 64 GB
Replace hard disk drives (HDDs) with solid-state drives (SSDs), preferably non-volatile memory express (NVMe) drives
Increase system memory to a total of 96–128 GB
If you're working with solids/3D images, upgrade graphics card (GPU) to one with 8-12 GB texture memory
Upgrade to a processor with 14+ cores (28+ threads)
Increase system memory to a total of 128-256 GB
Upgrade to a processor with to 28+ cores (56+ threads)
Increase system memory to a total of 256–512 GB

Case Study
A GPS for the brain and so much more
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Murra, D., K. L. Hilde, et al. (2023). "Patterns of Neural Activation During an Initial Social Stress Encounter are Predictive of Future Susceptibility or Resilience: A FosTRAP2 Study." bioRxiv: 2023.2003.2010.532130.

Niraula, S., J. J. Doderer, et al. (2023). "Excitation-inhibition imbalance disrupts visual familiarity in amyloid and non-pathology conditions." Cell Reports 42(1): 111946.

Boitet, M., H. Eun, et al. (2022). "Non-invasive In Vivo Brain Astrogenesis and Astrogliosis Quantification Using a Far-red E2-Crimson Transgenic Reporter Mouse." Molecular Neurobiology.

Xue, Y., Z. Gursky, et al. (2022). "Sustained glymphatic transport and impaired drainage to the nasal cavity observed in multiciliated cell ciliopathies with hydrocephalus." Fluids and Barriers of the CNS 19(1): 20.

Terstege, D. J., D. O. Oboh, et al. (2022). "FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images." eneuro: ENEURO.0325-0321.2022.

Eastwood, B. S., B. M. Hooks, et al. (2019). "Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections." Journal of Comparative Neurology 527(13): 2170-2178.

Gergues, M. M., K. J. Han, et al. (2020). "Circuit and molecular architecture of a ventral hippocampal network." Nature Neuroscience 23(11): 1444-1452.

Otomo, K., J. Perkins, et al. (2020). "In vivo patch-clamp recordings reveal distinct subthreshold signatures and threshold dynamics of midbrain dopamine neurons." Nature Communications 11(1): 6286.

Tappan, S. J., B. S. Eastwood, et al. (2019). "Automatic navigation system for the mouse brain." Journal of Comparative Neurology 527(13): 2200-2211.

Ma, J., J. du Hoffmann, et al. (2021). "Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors." Nature Neuroscience 24(10): 1429-1440.

Eastwood, B. S., Hooks, B. M., Paletzki, R. F., O'Connor, N. J., Glaser, J. R., & Gerfen, C. R. (2019). Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections. Journal of Comparative Neurology, 0(0). doi: 10.1002/cne.24602.

Naskar, S., Qi, J., Pereira, F., Gerfen, C. R., & Lee, S. (2021). Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs. Cell Reports, 34(8), 108774. doi:

Download NeuroInfo product sheet here.

NeuroInfo® Version 2022.1.1
Released April 2022

New Features and Enhancements

  • Re-engineered BrainMaker workflow includes numerous enhancements, including a new Contact sheet that makes reordering sections easier
  • Additional image formats are now supported
  • Image selection will match between the BrainMaker workflow and the Image Organizer


View Full Version History Here.

Who Is Using NeuroInfo?

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

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