Tissue Mapper®

Comprehensive annotation and delineation tool used for mapping tissue structures
MBF Bioscience > Tissue Mapper®

Product Overview

Tissue Mapper enables you to easily delineate structures and create 3D models from image data using easily imported and customizable ontology lists. The program works with images acquired with brightfield, confocal, two-photon, widefield fluorescence, and light sheet microscopes, as well as with MRI and Micro CT images.  The annotated imaged can then be visualized in the interactive 3D environment, where you can export screenshots and movies. MBF Bioscience’s file format is open and FAIR (Findable, Accessible, Interoperable, and Reusable) allowing for easy collaboration between the scientific community.

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Key Benefits

A comprehensive annotation tool for mapping of anatomical structures

With Tissue Mapper, you can quickly delineate and annotate histological sections in 2D to create a 3D model or to build an atlas. With a click of a button, you can populate a customized contour list with anatomies specific to your organ with a simple file import. Easily access your compiled anatomy term list to automatically or manually delineate regions of interest at any resolution on your computer screen or Wacom tablet. By annotating 2D sections, you can create a data file that models the structures within your tissue that can be visualized in the interactive 3D environment, where you can take high resolution screenshots or export 3D movies for publications and presentations.

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), which was recently endorsed by the INCF. 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.

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: iScience
Mapping the Neurons of the Rat Heart in 3D
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Case Study: iScience
Researchers Map and Explore the Heart’s “Little Brain”
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Achanta, S., J. Gorky, et al. (2020). "A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System." iScience 23(6): 101140. https://doi.org/10.1016/j.isci.2020.101140 

Kim, S.-H., S. H. Hadley, et al. (2020). "Mapping of Sensory Nerve Subsets within the Vagal Ganglia and the Brainstem Using Reporter Mice for Pirt, TRPV1, 5-HT3, and Tac1 Expression." eNeuro 7(2): ENEURO.0494-0419.2020. https://doi.org/10.1523/ENEURO.0494-19.2020  

Leung, C., S. Robbins, et al. (2020). "SPARC: Distribution of Intrinsic Cardiac Neurons in 3D Reconstructed Hearts of F344 Rat." The FASEB Journal 34(S1): 1-1. https://doi.org/10.1096/fasebj.2020.34.s1.06522 

Leung, C., S. Robbins, et al. (2021). "3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system." iScience 24(7): 102795. https://doi.org/10.1016/j.isci.2021.102795 

Osanlouy, M., A. Bandrowski, et al. (2021). "The SPARC DRC: Building a Resource for the Autonomic Nervous System Community." Frontiers in physiology 12: 693735-693735. https://doi.org/10.3389/fphys.2021.693735 

Sullivan, A. E., S. J. Tappan, et al. (2021). "A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling." Neuroinformatics. https://doi.org/10.1007/s12021-021-09530-x  

Surles-Zeigler, M. C., T. Sincomb, et al. (2021). "Extending and using anatomical vocabularies in the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program." bioRxiv: 2021.2011.2015.467961. https://doi.org/10.1101/2021.11.15.467961  

Download Tissue Mapper product sheet here.

Who Is Using Tissue Mapper?

Tissue Mapper is used across the globe by the most prestigious laboratories. 

Cited in Peer Reviewed Scientific Publications

Tissue Mapper’s 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 Tissue Mapper?

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

Can I use established vocabularies from online ontologies?

Yes! Ask us today about Tissue Mapper with "SPARC Mode". With SPARC Mode, you can access organ-specific vocabulary term lists from ontologies such as UBERON and FMA through Tissue Mapper's API connection to SciCrunch. These terms are curated by a team of anatomy experts and have ontologically-persistent, unique identifiers that will help to ensure that your data is FAIR.

Is data generated with Tissue Mapper FAIR?

Yes. Tissue Mapper supports the collaborative goals of Open Science through the practice of data openness, integrity, and reproducibility, by using the published MBF Bioscience digital reconstruction data file format, the Neuromorphological File Specification (NFS), which was recently endorsed by the INCF. Data elements in NFS format were specifically implemented to ensure the files are Findable, Accessible, Interoperable, and Reusable (FAIR).


Are there any automatic tools for delineating?

 Yes, tools such as Outline Objects, Auto Contour, Outline Sections, you can automatically delineate your regions of interest.  You can also use the Mark Objects tool to automatically detect objects within the entire image or within specific anatomical regions.

Does this only work with whole organ?

No, you can use it on any smaller anatomical region within an organ that you are studying. It is flexible and can be used with all types of tissue and tissue preparations, from cleared tissue to serial sections.

Do you have a complete solution for imaging and mapping?

Yes, you can pair Tissue Mapper with our TissueScope slide scanner for an efficient imaging to mapping pipeline. 


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 Tissue Mapper. 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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