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
Quickly Populate a Custom Anatomy List
Automatically Outline Periphery of Histological Sections
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
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.
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.