Tissue Mapper®
Comprehensive annotation and delineation tool used for mapping tissue structuresProduct 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.
Key Benefits
- Populate custom anatomy lists for comprehensive annotation
- Quickly delineate and annotate histological sections
- Automatically outline periphery of histological sections
- Map anatomical features
- Visualize completed annotations in 3D
- File format is open and FAIR allowing for easy collaboration
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.
Tissue Mapper: Key Features
Quickly populate a custom anatomy list
With the click of a button, you can import a custom list with anatomies specific to your organ. You can easily customize names and colors of anatomies, dock the toolbar for easy access to anatomical terms as you map tissue structures, and conveniently share list files with others.
Tissue Mapper: Key Features
Mapping anatomical features
Automatically or manually delineate and edit anatomical regions on your computer screen or Wacom tablet.
Tissue Mapper: Key Features
Visualize completed annotations in 3D
By annotating 2D sections, create a data file that models the structures within your tissue that can be visualized in the interactive 3D environment.
Tissue Mapper: Key Features
Create screenshots and movies in 3D
Using the interactive 3D environment, you can take high resolution screenshots or export movies for publications and presentations.
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.
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.View Publication
Sullivan, A. E., S. J. Tappan, et al. (2021).
"A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling." Neuroinformatics.View Publication
Osanlouy, M., A. Bandrowski, et al. (2021).
"The SPARC DRC: Building a Resource for the Autonomic Nervous System Community." Frontiers in physiology 12: 693735-693735View Publication
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.View Publication
Kim, S.-H., S. H. Hadley, et al.
"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.View Publication
Achanta, S., J. Gorky, et al. (2020)
"A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System." iScience 23(6): 101140.View Publication
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.
Testimonials
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.
"I rarely have encountered a company so committed to support and troubleshooting as MBF."
"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."
"I am so happy to be a customer of your company. I always get great help related with your product or not. With the experienced members, you are the best team I've ever met. All of your staff are very kind and helpful. Thank you for your great help and support all the time."
"We’ve been very happy for many years with MBF products and the course of upgrades and improvements. Your service department is outstanding. I have gotten great help from the staff with the software and hardware."
"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."
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.
>> Learn More - On-Site/Training
We’ve conducted over 750 remote software installations.
>> Learn More - Webinars
We’ve created over 55 webinars that demonstrate our products & their uses.
>> Learn More
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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