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
BrainMaker®
Automatically align sections to visualize brains in 3DProduct Overview
BrainMaker 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.
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Key Benefits
- Create easy-to-visualize 3D volumes from series of sections
- Control the reconstruction process as much or as little as desired using an intuitive workflow
- Start with almost any whole slide image format; most are supported
- Dynamically visualize reconstructions as a 3D volume, sliced image, or multiple projections
- Save to an open and FAIR file format for easy collaboration
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.
BrainMaker® Version 2019.1.11
Released May 2019
New Features and Enhancements:
- Support for Huron, HDF5, and BigTiff formats
- 3D automated cell detection: Improved speed; text number box included with the filter strength sliders
- 3D contour tracing added
- 3D marker placement added
View Full Version History Here.
BrainMaker: Key Features
Quantify your data
Use the 3D anatomical reference created with BrainMaker to make measurements within the entire organ, something that was not possible using the serial sections directly. Analyze the size and shape of neuronal structures within the 3D reconstruction using Neurolucida 360. Or assess cell distribution within a lesion using stereology with Stereo Investigator.
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: Key Features
View, store and share your whole-slide images and 3D reconstructions
Reconstructions created with BrainMaker can be stored, viewed, and shared with Biolucida – our platform for organizing and sharing big image data. Never run out of storage space, or spend hours searching for an image again. And instead of publishing a 2D image of your 3D reconstruction, you can share the actual 3D reconstruction and allow others to dynamically visualize it using our free Biolucida 3D image viewer.
BrainMaker: Key Features
Real-time interactive 3D visualization
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.
- Visualize large, complex 3D images (including multichannel images) and reconstructions
- 2D and 3D image data from two-photon, confocal, brightfield or light sheet microscopy
- 3D volume, image slicing, and simultaneous views
- Multiple projections: XY, YZ, XZ, alpha, minimum, and maximum
- Transparency, rendering (wireframe, centerline, surface, texture) and other display options for images and traced structures that can be adjusted on the fly
- Loads complex surfaces in seconds
- Export options include 3D graphics suitable for third-party applications
BrainMaker: Key Features
Generate DATA that's standardized, reliable and FAIR
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.
Who Is Using BrainMaker?
BrainMaker is used across the globe by the most prestigious laboratories.
News About BrainMaker
Huron Digital Pathology and MBF Bioscience Partner to Enable Large-scale, Repeatable Whole Slide Imaging Workflows for Life Science Research
MBF Bioscience now offers customized models of Huron Digital Pathology’s TissueScope™, a line of whole slide scanners, and supports TissueScope images
MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with 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
Cited in Peer Reviewed Scientific Publications
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
Frequently Asked Questions (FAQ)
What image files can I use with BrainMaker?
BrainMaker works with images acquired from most slide scanners and research microscope imaging systems.
What imaging modality is supported by BrainMaker?
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.
Can I use BrainMaker software with any type of species?
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.
Can BrainMaker resolve inverted sections?
Yes, BrainMaker uses the shape and image information across multiple sections to detect laterality and flip the sections to the right orientation.
Testimonials
"I rarely have encountered a company so committed to support and troubleshooting as MBF."
"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 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."
Robust Professional Support
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:
- Forums
We have over 25 active forums where open discussions take place.
>> Learn More - On-Site/Training
We’ve conducted over 750 remote software installations.
>> Learn More - Webinars
We’ve created over 55 webinars that demonstrate our products & their uses.
>> Learn More
Request an Expert Demonstration
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.
