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


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


Request a free trial


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


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

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.

Associated Products

Still Have Questions? Just Ask!