Automatically Align Serial Sections and Visualize an Entire 3D Brain

Use BrainMaker to assist you with cell mapping, cytoarchitectonics and other areas requiring the visualization of neuronal circuitry to create a comprehensive anatomical reference.  BrainMaker can generate a true 3D reconstruction of the entire brain (or any organ)  so that you can easily view cells, structures and lesions. With just a glance, you can see the location of all neurons expressing a particular gene or visualize the axonal projections of specific neurons with full anatomical context. 

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BrainMaker Automatically Aligns and Reconstructs Serial Sections  

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.


Quantity 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. 


Try it Out!

We offer both a free evaluation and a free trial copy of BrainMaker. During your trial, 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.

Request a free trial

  • Free evaluation: Submit some of your image data and let us evaluate how BrainMaker can match your research experiment.
  • Free 14-day trial copy: Download of a copy of BrainMaker 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.

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


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 than 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

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.

Still Have Questions? Just Ask!