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.

NeuroInfo Overview



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

NeuroInfo, Align Data to the Allen Mouse Brain Atlas, Whole Brain Reconstruction, Cell Detection


  • 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 measurments 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 sophisticated detection algorithm is 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.  


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!

We offer both a free evaluation and a free trial copy of NeuroInfo. During your trial, 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.

Request a free trial

Free evaluation: Submit some of your image data and let us evaluate how NeuroInfo can match your research experiment.

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.

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.

Customer Reviews

"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 Veasey, M.D.
University of Pennsylvania
"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

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