Automatically align serial sections and visualize an entire 3D organ
MBF Bioscience > TissueMaker®

Product Overview

TissueMaker automatically creates full-resolution 3D reconstructions of entire organs or other structures from serial sections or whole slide images. 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 sections and reconstructing the specimen in 3D.


With just a glance and full anatomical context, you can identify cells or structures that express a particular gene or visualize morphologies that span multiple individual fields of view. Use TissueMaker to assist you with cell mapping, cytoarchitectonics and other characteristics of organs or structures to create a comprehensive anatomical reference.

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Key Benefits

TissueMaker generates high-resolution 3D volume reconstructions from serial sections imaged using whole slide scanners and research microscopes. Load the images into TissueMaker and then direct your attention to other projects while TissueMaker 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, TissueMaker 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.

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. 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.

Who Is Using TissueMaker?

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

Cited in Peer Reviewed Scientific Publications

MBF’s software 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 TissueMaker?

TissueMaker works with images acquired from most slide scanners and research microscope imaging systems.

What imaging modality is supported by TissueMaker?

Any single-plane group of images will work, whether they come from a slide scanner, brightfield or fluorescence wide-field microscope or confocal. TissueMaker 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 TissueMaker.

Can I use TissueMaker software with any type of organ?

Absolutely. TissueMaker uses the shape and image information to do the alignment irrespectively of the tissue, species, sectioning orientation, markers or labels you are using.

Can TissueMaker resolve inverted sections?

Yes. TissueMaker 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 TissueMaker. 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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