Automatically Align Sections to Visualize Brains in 3D

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 automatically creates full-resolution, 3D reconstructions of the entire brain (or any organ) from serial sections of whole slide images. It allows you to easily view cells, structures, and lesions. With just a glance, you can locate neurons expressing a particular gene or visualize axonal projections of specific neurons with full anatomical context.

Go From This

To This


BrainMaker generates high-resolution 3D volume reconstructions from serial sections imaged with 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 thanks to 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, researchers can easily edit the 3D reconstruction.

Read this paper to see how BrainMaker was used in a recently published study


Customer Reviews

"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."
Sigrid Veasey, M.D.
University of Pennsylvania
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Bogdan A. Stoica, M.D.
University of Maryland
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Mazhar ÖZKAN, PhD
Marmara Üniversitesi Tıp Fakültesi, Turkey

Introduction to: BrainMaker



BrainMaker assists researchers by enhancing their studies. With BrainMaker you can generate high-resolution, 3D reconstructions. Watch the video to see how fast, easy, and accurate our software is!



A rendering of a whole brain volume registered and compiled at full resolution by BrainMaker from coronal mouse brains sections imaged at 10x. Images courtesy of Dr. Nuo Li and Dr. Alyse Thomas (Baylor College of Medicine) and Dr. Charles Gerfen (NIMH).

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.

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. 

Real-Time Interactive 3D Visualization

As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable to effective data interpretation.

Our software 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 image and traces that can be adjusted on the fly
  • Create dynamic movies
  • Export options including exporting 3D graphics to third-party applications
  • Loads complex surfaces in seconds
  • Works with the most advanced “gaming class” graphics cards to deliver high performance at an affordable price
  • Support almost all file formats


Try it Out!

During your demonstration, you'll 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.

Request an Expert Demonstration

BrainMaker has been developed with support from the National Institute of Mental Health (NIMH)


Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

MBF Bioscience Forum

Get answers to your most pressing research and technical questions from MBF scientists and fellow researchers.


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We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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