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.

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

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


  • Registers serial section images of any orientation to the Allen Mouse Brain Atlas
  • Delineates anatomies in the experimental anatomic space
  • Automatically detects and reports on cell number within selected anatomies
  • Corrects for distortion due to histological processing
  • Combines all image measurements to anatomies in the Allen Mouse Brain Atlas for cross-cohort, or experiment, comparisons.


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 especially pivotal for many neurogenomics, transcriptomics, proteomics and connectomics studies, yet this process is 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 NeuroInfo demonstrated that the novel technology performs remarkably well in accurately delineating regions independent on whether the sections were imaged with fluorescence or brightfield microscopy. Read more.


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.

Still Have Questions? Just Ask!

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