Automatically Align Serial Sections and Visualize an Entire 3D Organ

Use TissueMaker to assist with cell mapping, cytoarchitectonics, and other measures that require visualizing neuronal circuitry to create a comprehensive anatomical reference. TissueMaker can generate a true 3D reconstruction of the entire organ so that you can easily view cells, structures and lesions. With just a glance, you can locate cells expressing a particular gene or visualize axonal projections of specific neurons with full anatomical context.

Go From This

 To This

On the left are a series of serial sections of lung. On the right is the 3D reconstruction from those whole slide images created by TissueMaker. After the 3D reconstruction, the full organ can be viewed in 3D.  Images courtesy of the Thomas Taylor-Clark Lab at the University of Southern Florida.

Introduction to: TissueMaker


With TissueMaker, generating 3D reconstructions of entire organs has never been easier. Scientists around the world trust TissueMaker because it is fast, accurate, and automatic. Watch the video to check it out for yourself!


TissueMaker Automatically Aligns and Reconstructs Serial Sections  

TissueMaker automatically generates full resolution 3D reconstructions from serial sections imaged with 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 thanks to 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, researchers can easily edit the 3D reconstruction.


Digital reconstruction of lower urinary tract (LUT) afferents of the lumbosacral spinal cord

In this video, spinal cord sections were aligned using TissueMaker to visualize the rostro-caudal distribution of sensory inputs from the LUT. CTB-labelled LUT afferents in the sacral dorsal commissural nucleus and sacral preganglionic nucleus were detected and further analyzed in Neurolucida 360 and Neurolucida Explorer.

Read the paper: https://doi.org/10.1523/ENEURO.0364-21.2021

Video Courtesy: Drs. Fuller-Jackson, Osborne, and Keast at the University of Melbourne

Customer Reviews

"MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
Wilma Van De Berg, Ph.D.
VU University Medical Center - Neuroscience Campus Amsterdam
"MBF Bioscience is extremely responsive to the needs of scientists and is genuinely interested in helping all of us in science do the best job we can."
Sigrid Veasey, M.D.
University of Pennsylvania
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
Bogdan A. Stoica, M.D.
University of Maryland

Quantify Your Data


Use the 3D anatomical reference created with TissueMaker 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 TissueMaker 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!

During your demonstration, you'll 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 an Expert Demonstration


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 that 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
  • Supports almost all file formats

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.

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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