Intelligent Brain-Wide Cellular Screening with Anatomic Specificity

NeuroInfo performs brain-wide analyses of cells and biochemical markers, and automatically categorizes them in neuroanatomical regions. Uses advanced deep learning methods - no more manually clicking cells or hand drawing anatomic boundaries.

Video abstract on The Journal of Comparative Neurology article "Automatic navigation system for the mouse brain" by Tappan et al.

Automatically Delineate Regions in the Brain

Automatically Register Histological Sections and Associated Data to the Allen Mouse Brain Atlas

With NeuroInfo, researchers can automatically identify and delineate brain regions within experimental mouse brain sections. NeuroInfo replaces the tedious manual process of neuroanatomical identification; no more paging through a reference atlas to match experimental images, and manually delineating anatomies in images. NeuroInfo integrates MBF’s renowned expertise in developing productive laboratory tools for neuroscientists, with the preeminent resource of the Allen Mouse Brain Atlas, allowing for accurate research with greater ease.

Customer Reviews

"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 provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
Wilma Van De Berg, Ph.D.
VU University Medical Center - Neuroscience Campus Amsterdam
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
Bogdan A. Stoica, M.D.
University of Maryland

Introduction to: NeuroInfo



NeuroInfo assists researchers by enhancing their studies. Watch the video to see how fast, easy, and accurate our software is!


A rendering of a whole brain volume registered and compiled at full resolution by NeuroInfo from coronal mouse brains sections imaged at 10x. Images courtesy of Dr. Nuo Li and Dr. Alyse Thomas (Baylor College of Medicine) and Dr. Charles Gerfen (NIMH).

Mapping Neuroanatomical Structures Labeled in Histologic Sections to a Whole Brain Standardized Atlas Coordinate System


  • Aligns whole slide images of experimental tissue sections to the Allen Brain Atlas
  • Delineates anatomical regions in experimental sections
  • Detects cells within the anatomical regions
  • Aggregates measurements from within anatomical regions
  • Maps all image measurements to anatomies in a standardized atlas space so that results can be compared across animals, experiments, and laboratories
  • Support almost all file formats


Automatic Cell Detection and Mapping

Identify labeled neurons in whole slide images using an intuitive 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.  

Rat Brain Analysis



Researchers studying structure and function in rat brains can now use NeuroInfo to analyze and register their brain volumes to the Waxholm Rat Brain Atlas Version 4—an open access volumetric atlas of the Sprague Dawley rat brain. Read more.


Why use NeuroInfo?

Identification and delineation of brain regions in histologic mouse brain sections is pivotal for many neurogenomics, transcriptomics, proteomics and connectomics studies. Yet, this process is usually manual and prone to observer error and bias. NeuroInfo automatically navigates an investigator through the complex microscopic anatomy of histologic sections of mouse brains, eliminating much of the user's potential for error.

NeuroInfo was Validated in a Recent Peer-Reviewed Publication

Extensive validation studies of identifying anatomies in NeuroInfo demonstrated that this novel technology performs remarkably well in accurately automatically delineating regions for fluorescent and brightfield microscopic imaging methods. A publication detailing this research and validation is available here:

Tappan, SJ, Eastwood, BS, O'Connor, N, et al. Automatic navigation system for the mouse brain. J Comp Neurol. 2019; 527: 2200– 2211.

Further reading on the research behind the technologies in BrainMaker, NeuroInfo, and our brain-wide screening approach is available in these peer reviewed research papers:

Eastwood, BS, Hooks, BM, Paletzki, RF, O'Connor, NJ, Glaser, JR, Gerfen, CR. Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections. J Comp Neurol. 2019; 527: 2170– 2178.

Hooks, B.M., Papale, A.E., Paletzki, R.F. et al. Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area. Nat Commun 9, 3549 (2018) doi:10.1038/s41467-018-05780-7


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

NeuroInfo Changes the Way We Look at the Nervous System

NeuroInfo yields repeatable, objective anatomic data that is invaluable for understanding the organization and composition of the nervous system, which will further knowledge in the fields of neurogenomics, transcriptomics, proteomics, and connectomics.  


NeuroInfo's Atlas Calibration Tool

NeuroInfo’s unique calibration tool allows the registration of sections cut in any orientation (coronal, sagittal or horizontal). It also accomodates for differences in histological processing between laboratories so that it is applicable to the work performed in many laboratories. 


Works with specimens imaged with:

  • Brightfield
  • Widefield fluorescence 
  • Confocal


Try it Out!

During your demonstration, you'll 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.

Request an Expert Demonstration

NeuroInfo has been developed with support from the National Institute of Mental Health's Small Business Innovation Research program


Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

MBF Bioscience Forum

Get answers to your most pressing research and technical questions from MBF scientists and fellow researchers.


Visit MBF Bioscience Forum



Webinar: Reconstructing Whole Mouse Brain Volume from Serial Sections to Registration in Allen Atlas
Reconstruction of Whole Mouse Brain Volumes from Serial Sections for Registration to the Allen Atlas
Webinar: Performing Brain-Wide Measurements and Mapping them NeuroInfo and BrainMaker
Webinar: Performing Brain-Wide Measurements and Mapping them NeuroInfo and BrainMaker
Charting a Course for Brain Mapping — SfN Global Connectome Virtual Event
Charting a Course for Brain Mapping — SfN Global Connectome Virtual Event
Webinar: Registering Mouse Brain Serial Sections to the Allen Atlas
Webinar: Registering Mouse Brain Serial Sections to the Allen Atlas
Webinar: Improved Detection of c-fos Labeled & Pyramidal Neurons with Machine Learning in NeuroInfo
Improved Detection of c-fos Labeled & Pyramidal Neurons with Machine Learning in NeuroInfo

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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