Automatically align sections to visualize brains in 3D
MBF Bioscience > BrainMaker®

Product 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

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

Case Study
A GPS for the brain and so much more
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Gergues, M. M., K. J. Han, et al. (2020). "Circuit and molecular architecture of a ventral hippocampal network." Nature Neuroscience 23(11): 1444-1452. 10.1038/s41593-020-0705-8

Hooks, B. M., A. E. Papale, et al. (2018). "Cell type-specific variation of somatotopic precision across corticostriatal projections." bioRxiv: 261446. 10.1101/261446

Lindberg, P. T., J. W. Mitchell, et al. (2019). "Pituitary Adenylate Cyclase-Activating Peptide (PACAP)-Glutamate Co-transmission Drives Circadian Phase-Advancing Responses to Intrinsically Photosensitive Retinal Ganglion Cell Projections by Suprachiasmatic Nucleus." Frontiers in Neuroscience 13.

Paletzki, R. and C. R. Gerfen (2015). "Whole Mouse Brain Image Reconstruction from Serial Coronal Sections Using FIJI (ImageJ)." Current Protocols in Neuroscience 73(1): 1.25.21-21.25.21.

Zepecki, J. P., K. M. Snyder, et al. (2019). "Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor." Oncogene 38(10): 1734-1750. 10.1038/s41388-018-0546-z

Zhang, L., V. S. Hernandez, et al. (2021). "Behavioral role of PACAP signaling reflects its selective distribution in glutamatergic and GABAergic neuronal subpopulations." eLife 10: e61718.

Lerchner, W., A. A. Adil, et al. (2021). "RNAi and chemogenetic reporter co-regulation in primate striatal interneurons." Gene Therapy.

Naskar, S., J. Qi, et al. (2021). "Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs." Cell Reports 34(8): 108774.

Weber-Adrian, D., R. H. Kofoed, et al. (2021). "Systemic AAV6-synapsin-GFP administration results in lower liver biodistribution, compared to AAV1&2 and AAV9, with neuronal expression following ultrasound-mediated brain delivery." Scientific Reports 11(1): 1934.

Fedakar, H. I. (2021). "Developing New Empirical Formulae for the Resilient Modulus of Fine-Grained Subgrade Soils Using a Large Long-Term Pavement Performance Dataset and Artificial Neural Network Approach." Transportation Research Record: 03611981211057054.

Inácio, S. V., J. F. Gomes, et al. (2021). "Automated Diagnostics: Advances in the Diagnosis of Intestinal Parasitic Infections in Humans and Animals." Frontiers in veterinary science 8: 715406-715406. doi: 10.3389/fvets.2021.715406

Eastwood, B. S., Hooks, B. M., Paletzki, R. F., O'Connor, N. J., Glaser, J. R., & Gerfen, C. R. (2019). Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections. Journal of Comparative Neurology, 0(0). doi: 10.1002/cne.24602.

Hooks, B. M., Papale, A. E., Paletzki, R., Feroze, M., Eastwood, B. S., Couey, J. J., . . . Gerfen, C. R. (2018). Cell type-specific variation of somatotopic precision across corticostriatal projections. bioRxiv, 261446. doi: 10.1101/261446.

Hooks, B. M., Papale, A. E., Paletzki, R. F., Feroze, M. W., Eastwood, B. S., Couey, J. J., . . . Gerfen, C. R. (2018). Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area. Nature Communications, 9(1), 3549. doi: 10.1038/s41467-018-05780-7.

Paletzki, R., & Gerfen, C. R. (2015). Whole Mouse Brain Image Reconstruction from Serial Coronal Sections Using FIJI (ImageJ). Current Protocols in Neuroscience, 73(1), 1.25.21-21.25.21. doi: 10.1002/0471142301.ns0125s73.

Download our product sheet here.

Who Is Using BrainMaker?

BrainMaker is used across the globe by the most prestigious laboratories. 

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.

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.


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.
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  • On-Site/Training
    We’ve conducted over 750 remote software installations.
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  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
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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.

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