BrainMaker, now called NeuroInfo Lite, automatically creates full-resolution 3D reconstructions of the entire brain (or any organ) from serial sections or whole slide images. It allows you to easily view cells, structures, and lesions. Simply load high resolution images of serial sections acquired from a slide scanner or research microscope, then let the software do the work of automatically aligning and reconstructing them.
With just a glance and full anatomical context, you can identify neurons that are expressing a particular gene or visualize axonal projections of specific neurons. Use BrainMaker to assist you with cell mapping, cytoarchitectonics and other areas requiring the characterization of neuronal circuitry to create a comprehensive anatomical reference.
BrainMaker generates high-resolution 3D volume reconstructions from serial sections imaged using whole slide scanners and research microscopes. Load the images into BrainMaker and then direct your attention to other projects while BrainMaker automatically detects the individual sections on each slide, and then aligns the sections to create the full 3D organ reconstruction. Image features found in multiple serial sections are automatically aligned using innovative computational algorithms.
It's fast. And it's smart. If you mounted a section upside down, BrainMaker automatically corrects it during the alignment process. If additional adjustments need to be made to the automatic alignment, you can easily edit the 3D reconstruction.
BrainMaker has been developed with support from the National Institute of Mental Health (NIMH)
| Minimum Hardware Requirements |
|---|
| 64-bit Windows 10 operating system |
| 8-core processor |
| Solid state drive(s) |
| NVIDIA 1060 graphics card (1060=6GB) |
Compatible image file formats: View PDF
Download BrainMaker product sheet here.
New Features and Enhancements:
View Full Version History Here.
Image caption: A rendering of a whole brain volume registered and compiled at full resolution by BrainMaker from coronal mouse brains sections imaged at 10x. Courtesy of Dr. Nuo Li and Dr. Alyse Thomas (Baylor College of Medicine) and Dr. Charles Gerfen (NIMH).
BrainMaker includes a highly versatile 3D visualization environment suitable to most microscopy images, with state-of-the-art functionalities to support your analysis and publication needs.
We support open science through data sharing, accessibility, integrity, and reproducibility. The published MBF Bioscience digital reconstruction data file format, the Neuromorphological File Specification, was recently endorsed as a standard by the International Neuroinformatics Coordinating Facility (INCF).
The data elements in this file format were implemented specifically to ensure that files produced in BrainMaker are findable, accessible, interoperable, and reusable (FAIR). BrainMaker embraces open science data standards and provides microscopy image and experimental data provenance to enhance the ease of repurposing data generated with BrainMaker. Encoded in the well-recognized and readable XML format, the modeling elements specify anatomical information in a calibrated 3D coordinate system with appropriate units. To learn more about the key elements of the file format and its relevant structural advantages, read our publication.
BrainMaker is used across the globe by the most prestigious laboratories.
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BrainMaker’s utility is underscored by the number of references it receives in the worlds most important scientific publications.
Gergues, M. M., K. J. Han, et al.
“Circuit and molecular architecture of a ventral hippocampal network.”View Publication
Lindberg, P. T., J. W. Mitchell, et al.
“Pituitary Adenylate Cyclase-Activating Peptide (PACAP)-Glutamate Co-transmission Drives Circadian Phase-Advancing Responses to Intrinsically Photosensitive Retinal Ganglion Cell Projections by Suprachiasmatic Nucleus.”View Publication
Paletzki, R. and C. R. Gerfen
“Whole Mouse Brain Image Reconstruction from Serial Coronal Sections Using FIJI (ImageJ).”View Publication
Zepecki, J. P., K. M. Snyder, et al.
“Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor.”View Publication
Zhang, L., V. S. Hernandez, et al.
"Behavioral role of PACAP signaling reflects its selective distribution in glutamatergic and GABAergic neuronal subpopulations." eLife 10: e61718.View Publication
Weber-Adrian, D., R. H. Kofoed, et al.
“Systemic AAV6-synapsin-GFP administration results in lower liver biodistribution, compared to AAV1&2 and AAV9, with neuronal expression following ultrasound-mediated brain delivery.”View Publication
BrainMaker works with images acquired from most slide scanners and research microscope imaging systems.
Any single-plane group of images will work, whether they come from a slide scanner, brightfield or fluorescence wide-field microscope or confocal. BrainMaker can convert your multiplane images encompassing your entire section depth to a max projection or extended depth of focus single-plane image (i.e. using our free software MicroFile+) for ulterior analysis with BrainMaker.
Absolutely. BrainMaker uses the shape and image information to do the alignment irrespectively of the tissue, species, sectioning orientation, markers or labels you are using.
Yes, BrainMaker uses the shape and image information across multiple sections to detect laterality and flip the sections to the right orientation.
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"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 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."
"MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
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 BrainMaker. 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.
