NeuroInfo®

The New Standard for Brain-Wide Registration and Quantification
MBF Bioscience > NeuroInfo®

Developed in collaboration with top neuroscientists at leading research institutions. Validated in peer-reviewed publication for expert-level accuracy across laboratories and imaging modalities. Used in 200+ peer-reviewed studies at MIT, NIH, Harvard, Stanford, and leading laboratories worldwide. Supports mouse, rat, and zebrafish —
primarily used for brain-wide analysis in mice. No programmer required.

Product Overview

NeuroInfo turns brain images into atlas-registered, quantitative maps. It works on cleared whole brains from light sheet microscopy, on hemispheres, on partial volumes, on serial sections from slide scanners, on micro-CT — one application, one workflow, whatever imaging modality and whatever portion of the brain your science requires. Free open-source tools exist for pieces of this problem, and many of them sort of work — if you have a computational biologist on staff willing to stitch them together, tune them per dataset, and maintain the pipeline as versions drift. NeuroInfo is the alternative: deep-learning cell detection, non-linear registration to standard reference atlases, and region-by-region quantitative reports across hundreds of brain structures, run by the same graduate student who prepared the tissue.

 

NeuroInfo is used for brain-wide analysis across mouse, rat, and zebrafish, with the great majority of studies in mice. It is the tool behind brain-wide screening of cell locations in behavioral studies, circuit mapping projects, drug-response cohorts, and comparative anatomy across strains and conditions — at the NIH, at leading research institutions on four continents, and in published studies in Nature, Cell Reports, Nature Neuroscience, Journal of Neuroscience, and dozens of other peer-reviewed journals.

Key Benefits

Go from Raw Images to Quantitative Results, Instantly

NeuroInfo automates whole-brain analysis of cell populations and biochemical markers, generating quantitative reports across hundreds of brain regions. Powered by advanced deep learning, it eliminates the need for manual cell counting and hand-drawn anatomical boundaries.

Seamlessly align your experimental data with standardized digital brain atlases for fast, accurate, and reproducible analysis. Developed in collaboration with the Allen Institute for Brain Science, NeuroInfo ensures anatomical precision and consistency across studies.

Anchor Your Data in a Standardized Anatomical Context

NeuroInfo registers brain images to expertly validated atlases developed by leading neuroanatomists. Anchoring your data to these coordinate frameworks enables reliable comparisons across samples, time points, and research groups.

NeuroInfo supports a growing library of atlases:

The gold standard in mouse neuroanatomy. Register mouse brain volumes to this open-access, expertly curated atlas from the Allen Institute. Conduct region-specific studies of structure, function, and cell populations across the entire mouse brain.

A high-resolution reference for rat brain research. Standardize your rat brain analysis with automated registration to the Waxholm Space atlas (Sprague Dawley). Ensure consistent anatomical comparisons across samples and studies.

The first comprehensive 3D atlas of the adult zebrafish brain. It is ideal for labs studying neural circuits, behavioral genetics, or pharmacological effects. Automate zebrafish brain segmentation and analysis using AZBA:

      •  203 annotated brain regions
      • Data from 17 adult male and female zebrafish
      • 10 molecular markers for neurons, glia, and neurotransmitters

A powerful set of developmental mouse brain atlases that contain multiple embryonic and postnatal timepoints and reference brain modalities.

      • devCCF: Covers embryonic and postnatal stages with structures aligned to the Allen Mouse Brain CCF.
      • epDev: Tracks postnatal changes in GABAergic, microglial, and cortical cell populations.

  • Custom Atlas Integration

Work with almost any species that has a 3D digital atlas. NeuroInfo’s open, documented atlas architecture makes it easy to integrate your own digital atlases and use preferred coordinate systems for custom workflows.

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 11 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

Download NeuroInfo brochure here.

NeuroInfo® Version 2025.1.1
Released November 2025

  • New Map to Intermediate option is available after completing Section Registration using Atlas-constrained registration to create a brain image volume registration that can be further refined for better precision using the Register Volume tools
  • New Nonlinear Registration options added provide better results and more control of the parameters used
  • Calibration and transform information from image registration are now stored with the data file
  • Additional tools and information in the Calibration panel:
    • View information about installed atlases
    • Atlas names now include the species, version, and section spacing
    • Activate an updated or different brain atlas to modify the transforms from a previous registration
    • New warning if the atlas and/or spacing is not compatible with the experimental images
  • Improvements to the Tone Mapping filter
  • New marker density visualization surface option added to the 3D Visualization window
  • Large image and data file handling are now faster and more robust
  • Improvements and updates to the Movie mode interface have been implemented
  • The Gerfen Nissl Mouse Atlas has been updated to version 2

 

View Full Version History Here.

This is a NeuroInfo poster

Brain-wide analysis of rodent brains using standardized mouse and rat reference atlases

A novel workflow for whole-brain analysis in rodents using light sheet microscopy, brain atlases, and artificial intelligence

NeuroInfo for Light Sheet Data

NeuroInfo for Light Sheet Data — The Last Mile of Your Imaging Pipeline

 

A cleared mouse brain on a light sheet microscope gives you hundreds of gigabytes of image data. Turning that data into publishable results — atlas-registered, region-by-region cell counts, comparable across animals and conditions — is where many labs get stuck. NeuroInfo is the software that finishes the job.

 

NeuroInfo was built from the ground up to handle the realities of cleared-tissue imaging. Uneven illumination, depth-dependent intensity falloff, refractive-index artifacts at tile boundaries, stitching seams, the dynamic range that lets you see a surface dendrite and a deep cell body in the same volume — these are not afterthoughts. They are what the detection and registration algorithms were trained against.

 

 

What NeuroInfo does with your light sheet data

 

  • Non-linear 3D registration to standard reference atlases. Register whole brains, hemispheres, or partial volumes. Mouse, rat, or zebrafish. NeuroInfo uses symmetric normalization (SyN) non-linear algorithms to align your experimental volume to the reference atlas in true 3D — not a 2D slice-by-slice approximation.
  • Trained on real cleared tissue data. The registration models work on iDISCO, CLARITY, CUBIC, SHANEL, and BINAREE clearing techniques out of the box. No retraining. No per-protocol tuning.
  • Brain-wide screening for behavioral studies. Map activity-dependent labeling (c-Fos, FosTRAP) across every region in a single brain, then compare cohorts of animals against behavioral conditions. The analytical workflow behind a growing share of systems-neuroscience publications.
  • Direct pipeline from SLICE. BrightSLICE exports straight into NeuroInfo. No format conversion, no metadata loss, no reparameterization between acquisition and analysis.
  • Opens multi-terabyte datasets interactively. GPU-accelerated viewing, streaming data access, real-time maximum intensity projections — on a single workstation.
  • Tone mapping for cleared tissue. Local contrast adjustment that reveals detail in bright and dark regions of the same volume simultaneously.
  • Cell detection and tallying across hundreds of brain regions. Brain-wide quantitative output, reproducible across animals and laboratories.
  • Published, peer-reviewed validation. Expert-level registration accuracy demonstrated across multiple labs and imaging modalities.

SLICE + NeuroInfo: One Workflow, One Vendor, One Support Line

 

Most light sheet labs assemble their analysis pipeline from three or four sources: the microscope from one company, visualization software from another, atlas registration from an academic open-source project, cell detection from a fourth. Every interface between them is a potential failure point, and when something breaks, no one owns the problem.

 

Sample Cleared Tissue
Specimen
 → 
SLICE Light Sheet Imaging
Acquisition
 → 
BrightSLICE Visualize
Processing
 → 
NeuroInfo Register & Detect Cells
Analysis
 → 
Atlas Output
Result

No other company offers a similar comprehensive end-to-end light sheet acquisition and atlas-registered quantification pipeline from a single source.

NeuroInfo for Serial Sections

NeuroInfo for Serial Sections — Brain-Wide Analysis Without a Light Sheet Microscope

 

For decades, brain-wide cellular analysis meant one of two things: hand-drawing anatomical boundaries on hundreds of sections, or getting your labeling protocols to work on a cleared tissued and light sheet microscope. NeuroInfo offers a third option.


Mount your sections on slides. Scan them on the slide scanner your institution already owns, or on your Stereo Investigator or Neurolucida system. NeuroInfo does the rest. BrainMaker technology automatically reconstructs a full-resolution 3D volume from your serial sections, registers it to a standard reference atlas, detects and counts labeled cells across every region, and produces the same atlas-registered quantitative output a light sheet workflow would — from the histology pipeline your lab already runs.

 

What NeuroInfo does with your serial section data

 

  • BrainMaker 3D reconstruction. Automatic alignment of serial sections from any slide scanner into a full-resolution 3D volume, with anatomical context restored.
  • Robust to the realities of histology. Damaged sections, torn tissue, warped mounts, pronounced cut angles, sections loaded out of order — the multi-stage registration algorithms handle all of it.
  • Coronal, sagittal, or transverse. No need to recut. NeuroInfo registers any standard cut orientation.
  • Works across species. Mouse, rat, and zebrafish, with support for developmental timepoints and custom atlases.
  • Compatible with the labels your lab already uses. Nissl, NeuroTrace, DAPI, fluorescent reporters, brightfield IHC — tested and validated across the full range of standard histological preparations.
  • Ideal for brain-wide screening of cell locations in behavioral studies. c-Fos, FosTRAP, and other activity-dependent labels mapped across every region of interest, cohort by cohort, from standard histology.
  • Automatic brain region delineation. Once registered, every section is automatically annotated with the hundreds of distinct anatomical regions from the reference atlas. Choose all of them, or a custom subset relevant to your study.
  • Deep-learning cell detection robust to staining variation. Edge effects, uneven illumination, batch-to-batch staining differences across a cohort — the AI detection handles these without per-sample retraining.
  • Cross-lab reproducible. Your cell counts, registered to the same atlas, are directly comparable to every other NeuroInfo user’s data on the same atlas — something no in-house Python pipeline can claim.

The Economics Are Simple

  NeuroInfo + Serial Sections Light Sheet Workflow
Instrument Slide scanner your institution likely owns Dedicated light sheet microscope
Added instrument cost None $99,000 – $750,000+
Sample preparation Standard histology, any lab Tissue clearing (iDISCO, CLARITY, CUBIC, etc.)
Compatible labels Brightfield IHC, fluorescence, Nissl, NeuroTrace, DAPI, and all standard stains Fluorescent only
Spatial resolution Native slide-scan resolution, section-limited Sub-micron, isotropic 3D
Best suited for Multiplex IHC, large cohorts, brightfield studies, labs without clearing infrastructure Whole intact organs, vasculature, 3D morphology
Atlas-registered quantitative output Yes (NeuroInfo) Yes (NeuroInfo)

 

 

Both workflows end in the same place: atlas-registered, brain-wide, quantitative maps that compare across animals, cohorts, and laboratories. Light sheet is the right answer when your science requires intact 3D morphology. Serial sections plus NeuroInfo is the right answer when it doesn’t.

 

This is what democratized neuroscience looks like: the analytical endpoint that used to require a core facility, delivered from the histology workflow every lab already runs.

 

Watch: Do You Really Need a Light Sheet Microscope for Brain-Wide Analysis?

Case Studies

Affordable Packages

There are flexible options for bringing NeuroInfo into your lab: choose between a perpetual license or annual subscription, with the option to add mobile licensing for flexible use across multiple workstations.

Feature Description

NeuroInfo LITE

NeuroInfo STUDIO

Assemble serial sections into 3D volumes
Dynamic, full-resolution 3D visualization
Detect cells and biochemical markers automatically
Create and publish high-quality movies
Stitch whole slide and light sheet images
Align 2D sections to brain atlas
Align 3D volumes to brain atlas
Identify and delineate anatomical regions automatically

News and Updates

Who Is Using NeuroInfo?

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

Cited in Peer Reviewed Scientific Publications

The utility of NeuroInfo is underscored by the number of references it receives in the world’s leading 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.

Testimonials

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 More Information

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

Do You Really Need a Light Sheet Microscope for Brain-Wide Analysis?

Webinar: Registering Mouse Brain Serial Sections to the Allen Atlas

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