
Developmental Mouse Brain Atlases are now available in NeuroInfo
MBF Bioscience is excited to announce that NeuroInfo now supports two developmental mouse brain atlases from the Kim Lab. These atlases

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.
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.
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:
A powerful set of developmental mouse brain atlases that contain multiple embryonic and postnatal timepoints and reference brain modalities.
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) |
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| 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 |
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| To upgrade your system for better performance with MBF Bioscience software, we suggest that you prioritize computer hardware upgrades as follows: |
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Download NeuroInfo brochure here.
NeuroInfo® Version 2025.1.1
Released November 2025
View Full Version History Here.
NeuroInfo uses BrainMaker technology to automatically create full-resolution 3D brain (or any organ!) volumes from serial sections on whole slide images. Simply load high resolution images of serial sections acquired from a slide scanner or research microscope and then let the software do the work of automatically aligning and reconstructing them. Reconstructed brain volume offer full anatomical context at just a glance, you can identify neurons that are expressing a particular gene or visualize axonal projections of specific neurons through a brain.

Once mouse or rat brain sections are registered to a standardized atlas, it immediately becomes possible to automatically delineate brain regions in the experimental sections under study. With NeuroInfo you can choose to use a subset of brain regions you customize for your specific research, or all of the hundreds of distinct anatomically delineated regions in a given brain atlas.

Identify labeled cells in brain volumes using an intuitive AI cell detection workflow. Our deep learning algorithms are robust against histologic and imaging artifacts such as edge effects, uneven illumination, and variable staining across specimens. Detected cells can be mapped to the Allen Mouse Brain Atlas and tallied in each of its 2500 brain structures, making comparative quantitative analysis between mice from different experiments and laboratories easy and standardized.

Once mouse or rat brain sections are registered to a standardized atlas, it immediately becomes possible to automatically accumulate and compare measurements made on those sections (e.g., cell counts per brain region) across animals, cohorts, and laboratories.

NeuroInfo supports 3D registration of large light sheet imaging volumes to a common reference atlas, providing precise anatomical localization and consistent alignment across experiments.
MBF Bioscience is always working to ensure that scientific image data in a wide variety of file formats are supported. Our development team works closely with all major microscope and slide scanner vendors to make sure that our support for the latest big-data file formats is supported in NeuroInfo.

Tone mapping applies local contrast adjustments that make it easier to visualize details in both bright and dark regions of an image simultaneously. You can now explore large images with a high dynamic range between the brightest and darkest parts of the image to truly see what you’re looking for.

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.
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.
SLICE and NeuroInfo are built to work together. Data acquired on a SLICE microscope moves into NeuroInfo through a native pipeline — same metadata, same coordinate system, same support team. One phone call. One training visit. One vendor accountable for the whole workflow from specimen to quantitative map.
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 — 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.
| 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?

A specific group of striatal direct-pathway neurons becomes hyperactive during levodopa-induced dyskinesia. Enhanced excitatory inputs and heightened D1 receptor sensitivity cause excessive firing, identifying a key circuit element that drives dyskinesia.

Serial-section images aligned to a reference atlas enables accurate, brain-wide quantification of labeled neurons and axons. Using automated detection and multistage registration, this approach yields high-precision whole-brain maps from standard histology.

Single-nucleus sequencing, spatial transcriptomics, and whole-brain reconstructions reveal 76 distinct spinal-projecting neuron types. Defined by transcriptional signatures, anatomy, and physiology, these subclasses link molecular identity to specialized roles in descending motor control.

NeuroInfo uses multi-stage 3D registration to align mouse brain sections to the Allen CCF v3 with expert-level accuracy. Tested across labs and imaging modalities, it provides a fast, objective, and reproducible solution for identifying brain regions.


Movement-correlated neurons in somatosensory cortex receive stronger thalamic glutamatergic input and weaker motor cortical input than uncorrelated cells. Silencing thalamus reduces movement responses, indicating that stable movement encoding in wS1 is primarily driven by thalamic circuits.

Dopamine from the ventral tegmental area signals unexpected threat omission to D1-rich neurons in the basolateral amygdala. Manipulating this pathway alters extinction behavior, showing that VTA-to-BLA dopamine acts as a teaching signal that drives fear extinction memory formation.
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 |

MBF Bioscience is excited to announce that NeuroInfo now supports two developmental mouse brain atlases from the Kim Lab. These atlases

The democratization of neuroscience is a movement that aims to make neuroscience research more accessible and inclusive to everyone. This movement

We are pleased to announce that the International Neuroinformatics Coordinating Facility (INCF) has endorsed the MBF Bioscience neuromorphological file format as
NeuroInfo is used across the globe by the most prestigious laboratories.











The utility of NeuroInfo is underscored by the number of references it receives in the world’s leading scientific publications. See examples below:
Boitet, M., H. Eun, et al.
“Non-invasive In Vivo Brain Astrogenesis and Astrogliosis Quantification Using a Far-red E2-Crimson Transgenic Reporter Mouse.” Molecular Neurobiology.View Publication

Niraula, S., J. J. Doderer, et al.
“Excitation-inhibition imbalance disrupts visual familiarity in amyloid and non-pathology conditions.” Cell ReportsView Publication

Emily, P., D. Sarah, et al.
Circuit-Specific Plasticity of Callosal Inputs Underlies Cortical TakeoverView Publication

Sandra, U. O., U. G. Roman, et al.
Organization of Cortical and Thalamic Input to Inhibitory Neurons in Mouse Motor CortexView Publication

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

Gergues, M. M., K. J. Han, et al.
Circuit and molecular architecture of a ventral hippocampal network." Nature Neuroscience 23(11): 1444-1452. https://doi.org/10.1038/s41593-020-0705-8View Publication

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.
Yes. NeuroInfo supports multiple software seats running under one license.
NeuroInfo can register mouse and rat sections cut in coronal, sagittal, or transverse orientations.
Yes! The innovative registration algorithms in NeuroInfo account for cut angles that deviate significantly from canonical orientations.
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.
NeuroInfo utilizes both linear and non-linear methods that can accommodate a damaged or warped sections while registering sections to an Atlas.
Currently, NeuroInfo supports the latest versions of the Allen Mouse Brain Atlas and the Waxholm Rat 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.
I was genuinely impressed by how effortlessly I was able to start using NeuroInfo, and the registration precision is outstanding. I have trialed many different automated counting pipelines but found that the anatomical alignment within NeuroInfo was exceptionally reliable. This tool’s intuitive interface paired with such accurate output has truly streamlined our neuroanatomical analysis.

Andrea Muñoz Zamora, Ph.D. Icahn School of Medicine at Mount Sinai
"I rarely have encountered a company so committed to support and troubleshooting as MBF."

Andrew Hardaway, Ph.D. Vanderbuilt University
"The NeuroInfo software is so good. It compensates for students’ inexperience. They always lay down sections in the wrong order and have trouble recognizing the anatomy. This solves that problem."

Hermina Nedelescu, Ph.D. Scripps Research
"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 C. Veasey, MD University of Pennsylvania
"I am so happy to be a customer of your company. I always get great help related with your product or not. With the experienced members, you are the best team I've ever met. All of your staff are very kind and helpful. Thank you for your great help and support all the time."

Mazhar Özkan Marmara Üniversitesi Tıp Fakültesi, Turkey
"We’ve been very happy for many years with MBF products and the course of upgrades and improvements. Your service department is outstanding. I have gotten great help from the staff with the software and hardware."

William E. Armstrong, Ph.D. University of Tennessee

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:
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.

SLICE: a paradigm shift in light-sheet microscopy that combines high performance with unprecedented affordability and a compact device footprint.