A method of mapping atlas information to a histological section image of a histological section

MBF Bioscience was just awarded a patent by the USPTO for our new brain mapping technology! This novel technology is now available in our BrainMaker and NeuroInfo software to map image data and all associated measurements into a common coordinate system so that data can be compared across animals, cohorts, and laboratories. Learn more about NeuroInfo at https://www.mbfbioscience.com/neuroinfo



A GPS for the brain and so much more

Scientists use NeuroInfo to help navigate the brain and compare findings across labs

Reproducibility has always been a primary goal in science. But the human effort involved in replicating a research study and analyzing the results, can be considerable. NeuroInfo® is a revolutionary new tool that scientists are using to register whole slide images into a standardized mouse brain atlas in an easy, automated way. Images and subsequent measurements can then be cross-referenced against findings from a myriad of other studies.


Coronal mouse brain section from the Laboratory of Systems Neuroscience of Dr. Charles Gerfen, NIMH Bethesda, Maryland

Meeting the demands of users is always a priority for MBF Bioscience, and working with customers like Dr. Charles Gerfen of the National Institute of Mental Health provided a major impetus for developing NeuroInfo into such a revolutionary product.

“The major advance,” said Dr. Gerfen, “is that we’re able to analyze projections from within and between different areas of the cerebral cortex to determine organizational principles of the cerebral cortex,” Along with Dr. Bryan M. Hooks of the University of Pittsburgh School of Medicine, Dr. Gerfen uses NeuroInfo to trace pyramidal neuron projections in Cre-driver mice (Hooks, et al 2018).

As outlined in a study published in Nature Communications, the research team first used MBF Bioscience’s BrainMaker functionality of NeuroInfo to reconstruct four Cre-recombinase driver mouse brains with sections imaged with Neurolucida. They then registered the reconstructed brains into the Allen Mouse Brain Atlas and then collectively visualized experimental data overlain with the atlas to determine exactly how the four populations of cortical pyramidal neurons they were tracking fit within the greater structure of the brain. “Essentially every pixel or image in our original images could be assigned to one of the 2500 brain structures in the Allen Atlas, said Dr. Gerfen.

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MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with the Allen Mouse Brain Reference Atlas

An experimental coronal mouse brain section automatically aligned to the Allen Mouse Brain Reference Atlas

Analyzing cellular populations within specific anatomies in brain images requires expertise in both neuroanatomy and cellular identification. This typically involves a scientist comparing experimental images with a reference atlas and manually delineating anatomical regions and marking cell populations within. NeuroInfo®, a revolutionary new technology from MBF Bioscience, enables researchers to automatically identify and delineate mouse brain regions based on the publicly available Allen Mouse Brain Reference Atlas.

“NeuroInfo has the potential to greatly improve our understanding of how mental disorders influence neuronal cell populations,” says Nathan O’Connor Ph.D., product manager at MBF Bioscience. “Because it makes identifying brain regions substantially faster and more accurate, researchers will be able to explore many more brain regions.”

“The Allen Mouse Brain Reference Atlas is a valuable tool to assist scientists in their research. We’re thrilled that MBF has chosen to integrate this resource into NeuroInfo,” stated Amy Bernard, Ph.D., Product Architect at the Allen Institute for Brain Science.

“Using this remarkable technology, neuroscientists will obtain more repeatable, objective analyses that have been possible to date. Thanks to the integration with the Allen Mouse Brain Reference Atlas, these analyses will be more standardized so that they can be compared across experiments and laboratories,” says Jack Glaser, President.

NeuroInfo can be used with MBF Bioscience’s slide scanning software and virtually all commercial whole slide scanners. The data from NeuroInfo seamlessly integrates with MBF Bioscience’s products including Neurolucida, Stereo Investigator, Biolucida, and BrainMaker.

The tools in NeuroInfo allow researchers to automatically delineate anatomies in the experimental specimens, and detect cells within these anatomies. NeuroInfo yields data that can be invaluable to better understand the organization and composition of the nervous system, and to further knowledge in neurogenomics, transcriptomics, proteomics, and connectomics.

The National Institute of Mental Health provides funding to support the development of NeuroInfo.