The devCCF developmental mouse atlas includes embryonic and postnatal developmental brain structures parallel to the Allen Mouse Brain Atlas CCF. The epDev developmental mouse atlas includes postnatal 3D mappings of GABAergic, microglial, and cortical cell types.  

NeuroInfo has an open, documented atlas architecture that allows researchers to utilize other digital atlases. If you are interested in other support for other atlases, just let us know.

Please contact nate.oconnor@mbfbioscience.com for information on using these exciting developing brain resources for mapping structures and cell populations in NeuroInfo.

References

Developmental mouse brain common coordinate framework – PMC

epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains | bioRxiv

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas: Cell

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At MBF Bioscience, democratizing neuroscience has been part of our DNA since our founding 35 years ago when we launched Neurolucida. Our goal was to provide affordable, cutting-edge technology to neuroscience laboratories in every institution worldwide so that neuroscientists could make discoveries without having huge research budgets or having computer programmers on staff.

When we started MBF, advances in Neuroscience research were driven by individual investigators.  More and more “big science” is having a greater impact on the field.  This transition began around the turn of the century, with the discovery that there are more than 20,000 unique genes in the brain. Advances in molecular biologic, neuroanatomical, neurophysiologic and computational techniques employed by teams of researchers at research institutes or by networked labs at multiple universities have analyzed the complexity of the brain’s neural circuits comprised of thousands of unique neuron subtypes.  Amongst “big science” projects are those that produced whole brain maps of the expression of 20,000 genes, the connectome of hundreds of neuron subtypes, the axonal projections of thousands of individual neurons and the physiologic characteristics of hundreds of genetically unique neuron subtypes.  Typically, publication of these projects includes upwards of 50 authors, indicative of the effort required.  The value of these large-scale databases and data sets is the ability to extract information about specific brain circuits to understand how their function generates behavior.   This is the work still primarily driven by individual investigators, who continue to make conceptual advances in the field now aided by the resources provided by “big science”. 

One of our long-time users, Dr. Charles Gerfen, has been involved in several “big science” projects, including the GENSAT project at NIMH/NINDS with Dr. Nat Heintz at Rockefeller University that generated 300 Cre-expressing transgenic mouse lines, the Allen Institute’s Mouse Connectome study that mapped the projections of neuron subtypes from 1000 brain areas, and the HHMI Janelia Mouse Light Project that traced the axonal projections of 900 individual cortical neurons.  With teams of researchers these projects each mapped the distribution and connections of diverse subtypes of neurons into a standard whole brain atlas to provide a searchable “google map-like” database of brain circuits. 

With advice from Dr. Gerfen, MBF developed a new software platform called NeuroInfo, that incorporates functions to allow individual researchers to map their neuroanatomical data into a standard atlas framework.  NeuroInfo is becoming a widely used platform for individual researchers to use a “big science” approach to study their specific biologic questions of interest to understand how neural circuits are related to neurologic and mental disorders. 

At MBF Bioscience, we’re committed to providing the best products and value to neuroscientists in labs of all sizes. We’re focused on making our products something that labs can rely on for years to come at a reasonable cost with great support. We’re proud of our own accomplishments and how we’ve adapted and evolved over the years to bring the most advanced technology at affordable prices to labs around the world.

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The file format is used in our products for neuroscience research for important applications such as digital neuron tracing, brain mapping and stereological analyses. MBF Bioscience products, including Neurolucida, Neurolucida 360, Stereo Investigator, Vesselucida 360, and NeuroInfo use this neuromorphological file format.

This file format has evolved over several decades through input and requests from many scientists who’ve been using our products. The current format is truly a collaborative effort between MBF and our users.

“We are very pleased to have received this endorsement from the INCF. It recognizes our ongoing efforts in supporting open and FAIR neuroscience, and our commitment to supporting neuroscience researchers. We’ve established rigorous standards and processes for the file format so that it can be confidently used by the entire research community”, said Jack Glaser, President of MBF Bioscience.

What does this mean for researchers who use MBF products? It expands opportunities for data sharing between individual researchers, laboratories, and within larger collaborative research initiatives. Also, it will be easier for third-party software tools to be developed and maintained that extend the usefulness of the data generated by MBF products.

The official INCF announcement stated, “The committee is pleased to see an open format from a commercial entity go through the endorsement process, and applaud MBF Bioscience for taking this very important step in support of open and FAIR neuroscience. The committee considers the governance process for MBF Bioscience’s neuromorphological file format to be well elaborated, with a sufficient mechanism for the user community to request format updates.”

MBF Bioscience and the INCF will work together to further improve the FAIRness of the standard, including implementation of the governance policy and modification of the standard’s license from the CC-BY-ND-NC to a CC-BY-ND.

The standard number is INCFSN-22-01.

Read the review report, with community feedback in comments: https://f1000research.com/documents/10-712

Read the full INCF endorsement here: https://www.incf.org/blog/incf-endorses-mbf-neuromorphological-file-format

Read a recent publication on the format:

A.E. Sullivan, S. J. Tappan, P. J. Angstman, A. Rodriguez, G. C. Thomas, D. M. Hoppes, M. A. Abdul-Karim, M. L. Heal & Jack R. Glaser. A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling. Neuroinform (2021). https://doi.org/10.1007/s12021-021-09530-x

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“NeuroInfo already includes extensive analysis capabilities for mouse brain research by standardizing measurements on brain volumes to the Allen Mouse Brain Atlas. The inclusion of a rat atlas in NeuroInfo expands brain research to more complicated behavioral and disease models,” says MBF Bioscience Senior Product Manager Dr. Nathan J. O’Connor.

Image Credit: Harvey Karten, PhD

Successful neuroscience research projects in big data areas such as transcriptomics, proteomics, and connectomics rely on efficient methodologies and data reporting. NeuroInfo uses deep learning and automated image processing workflows guided by widely used standardized atlases to repeatably produce and report outcomes that can be combined and compared across animals, cohorts, and laboratories.

Learn more about NeuroInfo.

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In the webinar titled, “Improved detection of c-fos labeled and pyramidal neurons using deep machine learning in NeuroInfo,” Dr. Gerfen, joined by Dr. Brian Eastwood and Dr. Nathan O’Connor, demonstrates how NeuroInfo uses deep learning neuronal networks to successfully detect pyramidal neurons in multiple brain regions.

Dr. Gerfen nicely summarizes the starting point of the cell detection algorithm: “The way to think about it, is that it’s a topographic map of a mountain range. Things that are very bright have very high intensity levels (e.g., peaks) relative to their surrounding areas. That’s what this software picks out.”

With that criterion as a starting point, all detected objects–which can include somas, axons, dendrites, and fiber bundles–are passed into the neural network which has been trained to identify pyramidal cell bodies. According to Dr. O’Connor, over 90 thousand labeled images were used to teach NeuroInfo’s neural network how to recognize pyramidal neurons. The end result is a neural network that contains millions of parameters able to distinguish pyramidal neurons from all the other features in an image.

“We automatically adjust millions of parameters during network training,” says computational neuroscientist Dr. Eastwood. “The training process updates these parameters to improve how the neural network identifies pyramidal cells in images. During training, we know the answers. So, we use that knowledge to inform the network about true and false outcomes to update network parameters.”. Neural networks become “smarter” and more refined as they encounter more training data. The MBF Bioscience development team leverages this to create increasingly robust neural networks for detecting a variety of cell and tissue types as we work with data from laboratories.

“The networks are getting better and smarter as we provide more types of neurons from different images of brain sections into the training sets, so that the networks are able to identify not only different types of neurons but distinguish labeled neurons from histologic processing artifacts.” says Dr. Gerfen.

You can try this advanced AI method for cell detection in our NeuroInfo software. If you have any questions about deep learning in neuroscience, email us at info@mbfbioscience.com, or join the discussion at forums.mbfbioscience.com.

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Williston, VT (December 10, 2020) —NeuroInfo^® is the most advanced software for mapping brain sections, 3D volumes and cell populations into a standardized atlas reference space. 

Optimized to enable researchers to work far more efficiently, the new NeuroInfo update means faster, more efficient measurements and mapping workflows. 

The new version of NeuroInfo includes: 

• Identification and delineation of brain regions in experimental mouse-brain sections 
• Automatic cell detection using deep learning to recognize and count specific neuronal subtypes 
• Performance optimizations that result in up to 500x faster loading and viewing images; and 10x faster registration, mapping, and display of detected cells 
• Comparative quantification analyses between mice from different experiments and laboratories using a simple, standardized workflow

NeuroInfo is integrated with the Allen Mouse Brain Atlas — a full-color, annotated 3D map of the mouse brain developed specifically for the benefit of the global neuroscience research community. By combining the Allen Brain Atlas’ vast dataset with the capabilities of NeuroInfo, researchers have the unique ability to facilitate their neuroanatomical analyses as well as compare their findings with those from labs around the world. 

NeuroInfo’s ability to automate quantifying anatomical structures in the brain and correlate that with the rich data within the Allen Brain Atlas is what makes NeuroInfo such a powerful tool for researchers, says MBF Bioscience Senior Product Manager Dr. Nathan O’Connor. “NeuroInfo makes it possible for labs to standardize data across their experiments and across animal tissue. NeuroInfo makes high–powered research analyses available to almost any laboratory by automating the most labor intense parts of making brain-wide measurements across animals and laboratories.”  

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About MBF Bioscience: MBF Bioscience integrates the world’s leading microscope systems with our revolutionary quantitative imaging and visualization software to accelerate research in the fields of: stereology, neuron and microvasculature reconstruction, vascular analysis, worm tracking, brain mapping and big image data management in medical research and education. 

Since 1988, MBF Bioscience has forged a rich history of creating innovative products to empower biological researchers with the quantitative analysis tools they need to obtain accurate, unbiased results. With offices in North America, Europe, Japan, and South Korea, MBF Bioscience has helped researchers across the globe publish over 15,000 peer-reviewed papers in peer reviewed journals. MBF Bioscience partners with the NIH and distinguished scientists across the world to continue their commitment to neuroscience research with their software technology, and also in the fields of stem cells, pulmonology, oncology, and toxicology. For more information visit www.mbfbioscience.com or follow MBF Bioscience on Facebook, Twitter, and LinkedIn. 

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Media Contact:
Pasang Sherpa
Marketing Manager
1-802-288-9290/ pasang@mbfbioscience.com

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The post A method of mapping atlas information to a histological section image of a histological section appeared first on MBF Bioscience.

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.

Initially developed as a tool to help scientists automatically identify where their experimental tissue fits within specific regions of the mouse brain, NeuroInfo has evolved to encompass even more powerful methods for neuroanatomical analysis.

According to MBF Bioscience Senior Project Manager Dr. Nathan O’Connor, “scientists are using NeuroInfo most heavily to get their measurements mapped into a common coordinate system for objectively comparing and compiling results across animals, experiments, and laboratories. Rather than just a simple GPS — ‘where am I?’ tool, NeuroInfo has turned into a more powerful tool that allows automated mapping of brain-wide measures of behavior and pathology into a universal space.”

By automating the process of orientation, delineation, and quantification, the software cuts out intensive manual labor involved with traditional atlas use. It also provides a way for research teams to conduct large studies with less personnel, all while increasing repeatability and accuracy.

The key to the software’s success is a sophisticated algorithm that integrates with the Allen Mouse Brain Atlas, an extensive database of mouse brain anatomies delineated in a standardized average mouse brain [ref – https://mouse.brain-map.org/static/atlas]. Thanks to new developments within NeuroInfo, researchers can compare neuroanatomical data across mice, clearly viewing their areas of interest within the atlas and experimental data to observe how their specific data fits into the whole.

As explained in the paper, “Automatic navigation system for the mouse brain” (Tappan, et al 2019), NeuroInfo works much like a GPS, automatically navigating an investigator through the microscopic anatomy of histologic mouse brain sections. Once a slide is uploaded, the system registers and analyzes the data, then creates a digital overlay that clearly delineates the various brain regions contained within the section. As more and more labs integrate NeuroInfo into their research, the database grows, and researchers have more opportunities to enrich their studies.
After carrying out extensive validation studies, the research and development team, led by MBF Bioscience Scientific Director Dr. Susan Tappan, MBF Bioscience Imaging Scientist Dr. Brian Eastwood, and MBF Bioscience Senior Product Manager Dr. Nathan O’Connor, determined that the new technology identifies corresponding regions with remarkable accuracy. It also eliminates much of the manual labor that was previously required to identify the various brain regions in experimental sections.

“This novel automatic navigation system may fundamentally change the way researchers investigate sections of mouse brains under a light microscope, similar to the way surgical navigation systems have influenced neurosurgery over the past three decades (Mezger, Jendrewski and Bartels, 2013). Specifically, the approach presented here enhances the validity, reliability and reproducibility of studies that depend on the exact identification of distinct regions in the mouse brain, enables navigation through the complex anatomy of the mouse brain without requiring prior in-depth training in neuroanatomy, offers investigators the potential to analyze many more brain regions than is currently possible, and provides investigators with the means to directly correlate their experimental specimens with a number of reference tools such as GENSAT or the Allen Mouse Brain Connectivity Atlas (Oh et al., 2014),” Tappan, et al. 2019.

Citations:

Hooks BM, Papale AE, Paletzki RF, Feroze MW, Eastwood BS, Couey JJ, Winnubst J, Chandrashekar J, Gerfen CR (2018). “Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area.” Nature Communications; doi: 10.1038/s41467-018-05780-7. https://www.nature.com/articles/s41467-018-05780-7

Tappan S, Eastwood BS, O’Connor N, Wang Q, Ng L, Feng D, Hooks B, Gerfen CR, Hof PR, Schmitz S, Glaser JR (2019). “Automatic navigation system for the mouse brain.” Journal of Comparative Neurology; 527(13):2200-2211. doi: 10.1002/cne.24635
https://www.ncbi.nlm.nih.gov/pubmed/30635922

Eastwood BS, Hooks BM, Paletzki RF, O’Connor NJ, Glaser JR, Gerfen CR (2018). “Whole Mouse Brain Reconstruction and Registration to a Reference Atlas with Standard Histochemical Processing of Coronal Sections.” Journal of Comparative Neurology; DOI: 10.1002/cne.24602
https://onlinelibrary.wiley.com/doi/abs/10.1002/cne.24602

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October 23, 2018 – Huron Digital Pathology and MBF Bioscience are proud to announce their partnership to offer customized models of Huron’s TissueScope whole slide scanners integrated with MBF’s Stereo Investigator^® – Whole Slide Edition, NeuroInfo^®, Biolucida^®, and BrainMaker^® software. The partnership gives researchers new tools to visualize and analyze tissue specimens throughout entire organs, large and small, at high-resolution.

“Combining our analysis software with Huron’s whole slide scanners means that researchers can get the most advanced systems for large-scale, repeatable whole slide imaging workflows,” says Jack Glaser, President of MBF Bioscience. “We are pleased to partner with Huron Digital Pathology to provide Huron/MBF whole slide research systems. As the recognized leader in the fields of stereology, brain mapping, and neuron tracing, we are proud to offer systems with such a distinguished company as Huron. This partnership will now allow researchers to effectively work with microscopic specimens that range in size from mice brains to human brains. It is invaluable for researchers working with large brain specimens, especially those investigating the microscopic intricacies of the human brain.”

“By partnering with MBF Bioscience, our goal is to help accelerate life science research,” says Patrick Myles, CEO of Huron Digital Pathology. “Being able to scan any size tissue and then easily manage, visualize, and quantify the data opens up amazing new possibilities for scientific research and exploration.”

The partnership enables Stereo Investigator, NeuroInfo, Biolucida, and BrainMaker software to efficiently provide quantitative analysis workflows for large sets of slides from both individual tissue sections and series of tissue sections. Stereo Investigator – Whole Slide Edition offers analyses for counting and measuring morphological aspects relevant to disease state characterization. BrainMaker and NeuroInfo offer full-resolution section alignment and brain mapping. Biolucida offers slide management and slide access for viewing and analysis at unprecedented speeds from any web-enabled device. The customized versions of TissueScope scanners are available for purchase from MBF Bioscience.

Huron’s TissueScope whole slide scanners offer the unique ability to image any size slide, up to 6” x 8”, with superb image quality at high speed, unattended. The award-winning scanners have been deployed at many of the world’s leading research institutes. Huron’s patented TissueSnap™ workflow enhancement accessory further accelerates scanning throughput by offloading time-consuming preview and setup tasks.

Visit the MBF Bioscience website for more information about Stereo Investigator, NeuroInfo, Biolucida, and BrainMaker.

Visit the Huron Digital Pathology’s website for more information about the TissueScope line of whole slide scanners.

About MBF Bioscience
MBF Bioscience creates quantitative imaging and visualization software for stereology, neuron reconstruction, vascular analysis, c. elegans behavior analysis, and medical education—integrated with the world’s leading microscope systems—to empower research. Our development team and staff scientists are actively engaged with leading bioscience researchers, and constantly work to refine our products based on state-of-the-art scientific advances.

Founded as MicroBrightField, Inc. in 1988, we changed our name to MBF Bioscience in 2005 to reflect the expansion of our products and services to new microscopy techniques in all fields of biological research and education. While we continue to specialize in neuroscience research, our products are also used extensively in pulmonary, cardiac, kidney, cancer, stem cell, and toxicology research.

Our commitment to innovative products and unrivaled customer support has gained high praise from distinguished scientists all over the world, and resulted in MBF expanding into a global business with offices in North America, Europe, Japan, and South Korea. Our flagship products, Stereo Investigator^® and Neurolucida^®, are the most widely-used analysis systems of their kind.

About Huron Digital Pathology

Based in St. Jacobs, Ontario, Canada, Huron Digital Pathology has a 20+ year history designing sophisticated imaging instrumentation. Our end-to-end digital whole slide scanning solutions for digital pathology incorporate our award-winning TissueScope™ digital slide scanners, image management software, and our workflow-enhancing accessories, which include our innovative TissueSnap™ preview scanning station.

Press Contacts

MBF Bioscience
Pasang Sherpa
pasang@mbfbioscience.com
(802) 288-9290

Huron Digital Pathology
Patrick Myles, CEO
patrick@hurondigitalpathology.com
(519) 886-9013

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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.

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