NeuroInfo enables whole brain investigation of circuits, neuronal populations, and biochemical marker expression using widely accepted brain atlases for anatomic reference. Visual and quantitative measurements from 2D and 3D brain images are characterized and visualized within brain region delineations from a standardized reference space. NeuroInfo supports a variety of brain imaging techniques including; whole and semi brain volumes from cleared tissue specimens, serial section series, MRI and micro-CT imagery, and even single serial section whole slide images. Advanced AI segmentation and registration methods provide accurate results that are standardized and repeatable. NeuroInfo streamlines sophisticated computational pipelines into a single, powerful application that can be used in laboratories of every size.
Go from Raw Images to Quantitative Results, Instantly
NeuroInfo automates whole-brain analysis of cell populations and biochemical markers, generating quantitative reports across hundreds of brain regions. Powered by advanced deep learning, it eliminates the need for manual cell counting and hand-drawn anatomical boundaries.
Seamlessly align your experimental data with standardized digital brain atlases for fast, accurate, and reproducible analysis. Developed in collaboration with the Allen Institute for Brain Science, NeuroInfo ensures anatomical precision and consistency across studies.
Anchor Your Data in a Standardized Anatomical Context
NeuroInfo registers brain images to expertly validated atlases developed by leading neuroanatomists. Anchoring your data to these coordinate frameworks enables reliable comparisons across samples, time points, and research groups.
NeuroInfo supports a growing library of atlases:
The gold standard in mouse neuroanatomy. Register mouse brain volumes to this open-access, expertly curated atlas from the Allen Institute. Conduct region-specific studies of structure, function, and cell populations across the entire mouse brain.
A high-resolution reference for rat brain research. Standardize your rat brain analysis with automated registration to the Waxholm Space atlas (Sprague Dawley). Ensure consistent anatomical comparisons across samples and studies.
The first comprehensive 3D atlas of the adult zebrafish brain. It is ideal for labs studying neural circuits, behavioral genetics, or pharmacological effects. Automate zebrafish brain segmentation and analysis using AZBA:
A powerful set of developmental mouse brain atlases that contain multiple embryonic and postnatal timepoints and reference brain modalities.
Work with almost any species that has a 3D digital atlas. NeuroInfo’s open, documented atlas architecture makes it easy to integrate your own digital atlases and use preferred coordinate systems for custom workflows.
Recommended Hardware Requirements
NeuroInfo is powerful software that works with image data of any size and complexity. Because of its flexibility, our computing resource recommendations vary to balance affordability and performance required for large, multi-channel data.
Please contact us to help you specify a computing configuration that best suits your imaging and research needs.
| 64-bit Windows 11 operating system |
| CPU with at least 18-24 cores (36-48 threads). More cores improve performance when using large data sets. |
| Solid state hard drive(s). Preferably non-volatile memory express (NVMe) drives. |
| 128 GB of system memory. More memory is better for large data sets and 3D brain registration. |
| Graphics card with 8 GB memory or more. Graphics cards from NVIDIA and AMD have been tested with MBF Bioscience software. |
| Minimum Hardware Requirements (not recommended) |
|---|
| 64-bit Windows 11 operating system |
| 12 core processor (24 threads) |
| 32 GB memory |
| Graphics card with 2 GB memory or more |
| Computer-Hardware Upgrade Priorities |
|---|
| To upgrade your system for better performance with MBF Bioscience software, we suggest that you prioritize computer hardware upgrades as follows: |
|
|
|
Ventral Tegmental Dopamine Initiates Fear Extinction by Activating Reward-Processing Circuits in the Amygdala
>> Learn More
Neuron-Specific Thalamic Connectivity Patterns Encode Spontaneous Movement in Sensory Cortex
>> Learn More
How Certain Movement Control Cells Go Into Overdrive and Cause Unwanted Movements in Parkinson’s
>> Learn More
Quantitative Brain-Wide Neuronal Mapping Through Three-Dimensional Reconstruction and Atlas Alignment of Serial Tissue Sections
>> Learn More
Molecular Taxonomy Links Transcriptional Identity to Functional Specialization in Brain-Wide Spinal Projecting Neurons
>> Learn More
Automated Brain Mapping Tool Helps Scientists Accurately Identify Where They’re Looking in the Brain
>> Learn More
Different Brain Cells Use Different Strategies to Communicate with Movement Control Centers
>> Learn More
Download NeuroInfo brochure here.
NeuroInfo® Version 2024.1.1
Released August 2024
View Full Version History Here.
Sagittal maximum intensity projection through a BINAREE cleared mouse brain imaged by the ClearScope theta lightsheet microscope. Blue is autofluorescence; orange displays a trace from an rAAV -CAG -TdT virus injection.
Sagittal maximum intensity projection through a BINAREE cleared mouse brain imaged by the ClearScope theta lightsheet microscope. Blue is autofluorescence; orange displays a trace from an rAAV -CAG -TdT virus injection.
BINAREE cleared mouse brain imaged by the ClearScope theta lightsheet microscope.
BINAREE cleared mouse brain imaged by the ClearScope theta lightsheet microscope.
Demonstrates registering a hemisphere into the Allen Brain Atlas. The 3D registration of the right hemisphere of a cleared mouse brain imaged with light sheet microscopy.
NeuroInfo 3D registration of a light sheet image of cleared mouse brain tissue, shown alongside the Allen average mouse brain CCF.
NeuroInfo performs automatic registration of intact whole brains, partial brain samples, and serial sections to a common 3D reference atlas, facilitating standardized anatomical mapping and quantitative cross-experiment analysis.
NeuroInfo supports 3D registration of large light sheet imaging volumes to a common reference atlas, providing precise anatomical localization and consistent alignment across experiments.
Tone mapping in NeuroInfo applies local contrast adjustments for improved visualization of anatomical details across large cleared tissue volumes or whole brain sections.
Brain-wide analysis of rodent brains using standardized mouse and rat reference atlases
NeuroInfo uses BrainMaker technology to automatically create full-resolution 3D brain (or any organ!) volumes from serial sections on whole slide images. Simply load high resolution images of serial sections acquired from a slide scanner or research microscope and then let the software do the work of automatically aligning and reconstructing them. Reconstructed brain volume offer full anatomical context at just a glance, you can identify neurons that are expressing a particular gene or visualize axonal projections of specific neurons through a brain.
Once mouse or rat brain sections are registered to a standardized atlas, it immediately becomes possible to automatically delineate brain regions in the experimental sections under study. With NeuroInfo you can choose to use a subset of brain regions you customize for your specific research, or all of the hundreds of distinct anatomically delineated regions in a given brain atlas.
Identify labeled cells in brain volumes using an intuitive AI 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.
Once mouse or rat brain sections are registered to a standardized atlas, it immediately becomes possible to automatically accumulate and compare measurements made on those sections (e.g., cell counts per brain region) across animals, cohorts, and laboratories.
NeuroInfo supports 3D registration of large light sheet imaging volumes to a common reference atlas, providing precise anatomical localization and consistent alignment across experiments.
MBF Bioscience is always working to ensure that scientific image data in a wide variety of file formats are supported. Our development team works closely with all major microscope and slide scanner vendors to make sure that our support for the latest big-data file formats is supported in NeuroInfo.
Tone mapping applies local contrast adjustments that make it easier to visualize details in both bright and dark regions of an image simultaneously. You can now explore large images with a high dynamic range between the brightest and darkest parts of the image to truly see what you’re looking for.
There are flexible options for bringing NeuroInfo into your lab: choose between a perpetual license or annual subscription, with the option to add mobile licensing for flexible use across multiple workstations.
| Feature Description | NeuroInfo LITE | NeuroInfo STUDIO |
|---|---|---|
| Assemble serial sections into 3D volumes | ||
| Dynamic, full-resolution 3D visualization | ||
| Detect cells and biochemical markers automatically | ||
| Create and publish high-quality movies | ||
| Stitch whole slide and light sheet images | ||
| Align 2D sections to brain atlas | ||
| Align 3D volumes to brain atlas | ||
| Identify and delineate anatomical regions automatically |
Background: Extinguishing conditioned fear responses is vital for adaptive behavior, and its failure contributes to anxiety disorders such as PTSD. The
Background: Neuronal activity in the primary somatosensory cortex (wS1) is influenced by both sensory stimuli and spontaneous movements, yet the organization
Background: Levodopa-induced dyskinesia (LID) is a common side effect of long-term dopamine replacement therapy in Parkinson’s disease, producing involuntary movements. The
NeuroInfo is used across the globe by the most prestigious laboratories.
The utility of NeuroInfo is underscored by the number of references it receives in the world’s leading scientific publications. See examples below:
Boitet, M., H. Eun, et al.
“Non-invasive In Vivo Brain Astrogenesis and Astrogliosis Quantification Using a Far-red E2-Crimson Transgenic Reporter Mouse.” Molecular Neurobiology.View Publication
Niraula, S., J. J. Doderer, et al.
“Excitation-inhibition imbalance disrupts visual familiarity in amyloid and non-pathology conditions.” Cell ReportsView Publication
Emily, P., D. Sarah, et al.
Circuit-Specific Plasticity of Callosal Inputs Underlies Cortical TakeoverView Publication
Sandra, U. O., U. G. Roman, et al.
Organization of Cortical and Thalamic Input to Inhibitory Neurons in Mouse Motor CortexView Publication
Otomo, K., J. Perkins, et al.
In vivo patch-clamp recordings reveal distinct subthreshold signatures and threshold dynamics of midbrain dopamine neurons." Nature Communications 11(1): 6286View Publication
Gergues, M. M., K. J. Han, et al.
Circuit and molecular architecture of a ventral hippocampal network." Nature Neuroscience 23(11): 1444-1452. https://doi.org/10.1038/s41593-020-0705-8View Publication
NeuroInfo will run on most PCs running Windows 10 or later and having at least 16GB of RAM and 4GB GPU RAM. NeuroInfo will take advantage of available computer resources, so larger data sets will benefit from having more cores and memory. We’d be happy to discuss your needs with you to ensure you have the optimal computer configuration.
Yes. NeuroInfo supports multiple software seats running under one license.
NeuroInfo can register mouse and rat sections cut in coronal, sagittal, or transverse orientations.
Yes! The innovative registration algorithms in NeuroInfo account for cut angles that deviate significantly from canonical orientations.
NeuroInfo can register sections from a variety of stains and imaging methods and cytoarchitectural indicators, and has been tested with fluorescence microscopy (NeuroTrace and DAPI), brightfield microscopy (multiple structural visualizing stains), and MRI.
NeuroInfo utilizes both linear and non-linear methods that can accommodate a damaged or warped sections while registering sections to an Atlas.
Currently, NeuroInfo supports the latest versions of the Allen Mouse Brain Atlas and the Waxholm Rat Atlas.
Yes. NeuroInfo was designed to support alternate atlases, including developmental and other strains and species. Here is a description of our open atlas format.
Please contact us for guidance on including your atlas for use in NeuroInfo.
I was genuinely impressed by how effortlessly I was able to start using NeuroInfo, and the registration precision is outstanding. I have trialed many different automated counting pipelines but found that the anatomical alignment within NeuroInfo was exceptionally reliable. This tool’s intuitive interface paired with such accurate output has truly streamlined our neuroanatomical analysis.
"I rarely have encountered a company so committed to support and troubleshooting as MBF."
"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."
"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."
"I am so happy to be a customer of your company. I always get great help related with your product or not. With the experienced members, you are the best team I've ever met. All of your staff are very kind and helpful. Thank you for your great help and support all the time."
"We’ve been very happy for many years with MBF products and the course of upgrades and improvements. Your service department is outstanding. I have gotten great help from the staff with the software and hardware."
Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing. We’ve also developed a host of additional support services, including:
We offer both a free demonstration and a free trial copy of NeuroInfo. During your demonstration 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.
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.
