Tissue Mapper

Tissue MapperTM

Tissue Mapper is a comprehensive annotation and delineation tool used for mapping tissue structures. You can:

  • Easily delineate structures at any resolution to create a 3D model from image data
  • Annotate regions of interest from customizable ontology list
  • Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes and with MRI and microCT

The data is courtesy of the James Schwaber and Zixi (Jack) Cheng research teams at Thomas Jefferson University and University of Central Florida. DOI: doi.org/10.26275/wox9-gqzp

Customer Reviews

The MBF team has been highly receptive to the project needs and constantly strived to improve TissueMapper to enable smooth handling of large image stacks, in-depth annotation, and seamless mapping of external data sets onto a 3D map of the intrinsic cardiac nervous system. The all-around expertise of scientists and technologists at MBF was crucial to preprocess and assemble the large scale imaging data to jumpstart the 3D map building process. It is heartening to see MBF, a commercial entity, drive the development, standardization and dissemination of open data formats for complex anatomical annotation towards enabling friction-free exchange of these data sets in the scientific community.
Rajanikanth Vadigepalli, Ph.D.
Thomas Jefferson University
"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
"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
"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


Quickly Populate a Custom Anatomy List

  • With a click of a button, import custom list with anatomies specific to your organ
  • Easily customize name and color after import
  • Dock the toolbar for easy access to anatomical terms as you map tissue structures
  • Conveniently share list file with others

Automatically Outline Periphery of Histological Sections



Visualize Completed Annotations in Interactive 3D Environment

  • Take high resolution screenshots of annotated maps for publications
  • Easily export data files and movie files
  • Compatible with other MBF Bioscience  products
  • Supports almost all file formats


MBF Whole Slide Scanners Recommended for use with Tissue Mapper


• Brightfield slide scanner that handles up to twelve, 1”x 3” (25mm x 75mm) slides, six, 2” x 3” (50mm x 75mm) slides or any single slide up to 6” x 8” (150mm x 200mm) for larger specimens that most other scanners can’t handle. At a 60 micron section thickness/internal, an entire mouse brain can be mounted in a single tray


2D  & 3D, 5- channel laser confocal slide scanning

• Image cleared tissue up to 6mm thickness

• 2-channel, whole slide imaging in only three minutes at 10x

Our File Format is Now Open and FAIR to Allow Collaboration Between the Scientific Community

Tissue Mapper supports the collaborative goals of Open Science through the practice of data openness, integrity, and reproducibility, by using MBF Bioscience’s published digital reconstruction data file format, the Neuromorphological File Specification (NFS).

The data elements in this NFS format were specifically implemented to ensure the files are Findable, Accessible, Interoperable, and Reusable (FAIR). Abiding by these data standards and providing microscopy image and experimental data provenance enhances the ease of repurposing this data. Encoded in the well-recognized and readable format, the modeling elements specify microscopic neuroanatomies in a calibrated 3D coordinate system with appropriate units.

These Tissue Mapper files can also easily be viewed and parsed in a variety of software, e.g. MATLAB and Python. To learn more about the key elements of the file format and their relevant structural advantages, view our manuscript, A comprehensive, FAIR file format for neuroanatomical structure modeling.

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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