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

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Download TissueMaker product sheet here.

Who Is Using TissueMaker?

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

News About TissueMaker

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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