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.
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|
|Solid state drive(s)|
|NVIDIA 1060 graphics card (1060=6GB)|
Compatible image file formats: View PDF
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. https://doi.org/10.3389/fnins.2019.01281
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. https://doi.org/10.1002/0471142301.ns0125s73
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. https://doi.org/10.7554/eLife.61718
Lerchner, W., A. A. Adil, et al. (2021). "RNAi and chemogenetic reporter co-regulation in primate striatal interneurons." Gene Therapy. https://doi.org/10.1038/s41434-021-00260-y
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. https://doi.org/10.1016/j.celrep.2021.108774
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. https://doi.org/10.1038/s41598-021-81046-5
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. https://doi.org/10.1177/03611981211057054
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. https://onlinelibrary.wiley.com/doi/abs/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. http://biorxiv.org/content/early/2018/02/07/261446.abstract
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. https://doi.org/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. https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142...
Download our product sheet here.
BrainMaker is used across the globe by the most prestigious laboratories.
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
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 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.
Intelligent brain-wide cellular screening with anatomic specificity.
A fast, and versatile whole slide scanner for quantitative analysis.
Makes it easy to view, analyze, and share big image data from many sources.
Automatically align serial sections and visualize an entire 3D organ.