Microscopy and Biomedical Imaging

Researchers are presented with ever larger volumes of data as a result of the increasing resolution and sensitivity of cameras and the automation of microscopy workflows. This data often contains insights linking structure and function at the molecular, cellular, or tissue level, and it can be used to decipher mechanisms and energetics of biological processes. Scientists need to deal with large datasets spanning a variety of microscopy modalities including bright field, fluorescence, laser confocal, AFM, TEM, and SEM.

MATLAB® provides a platform not just for microscopy, but for all types of biomedical imaging including cytology, histology, in vivo-imaging, and behavior tracking. This platform is flexible and customizable, enabling you to include your own unique workflows and analytics, and allowing you to integrate with other tools. It scales to deal with large data or to combine different modalities and types of data. As a result, MATLAB has become a platform of choice for researchers seeking to:

Community Apps and Toolboxes

  • Bio-Formats: Standalone library for life sciences image formats
  • CCD Camera Characterization: Characterization of CCD cameras for TEM
  • CellAnimation: MATLAB framework for microscopy assays
  • CellSegm: High-throughput 3D cell segmentation
  • CellTracker: Cell tracking tool
  • Easy-DHPSF: Hyper-resolution 3D localization of single molecules
  • Fluctuation Microscopy: Electron nanodiffraction pattern analysis for EM
  • FocusStack: Two-photon calcium neuronal imaging
  • IceImarisConnector: Simple commodity class that eases communication between BITPLANE and MATLAB
  • iSMS: Single molecule FRET microscopy
  • KiT: Kinetochore motion tracking
  • MATLABStarter: A series of startup functions for MATLAB to set up a multi-user environment
  • MATrack: Time lapse fluorescent microscopy
  • Micro-Manager: Open-source microscopy software
  • NeuroPG: Optical pattern generation pipeline
  • Phase Stretch Transform: Image feature detection using phase stretch transform
  • plusTipTracker: Microtubule dynamics tracking
  • QuHAnT: High-throughput quantitative histology
  • rFRET: Ratiometric FRET microscopy
  • ScanBox: Simultaneous imaging and electrophysiology
  • SFMetrics: SFM for biomolecules
  • SimToolbox: Structured illumination fluorescence microscopy
  • SPM: Platform for functional imaging data
  • StimServer: Two-photon calcium neuronal imaging
  • TACTICS: High content bioimaging platform
  • TLM-Tracker: Time-lapse cell segmentation, tracking, lineage analysis
  • u-track: Multiple particle tracking and other capabilities

Videos and Webinars


Technical Articles

User Stories

Examples and How To

Medical Image Processing with MATLAB

You might already have access to MATLAB through your university.

Ask the Expert

Email Jeffrey Gruneich, Ph.D., Biological Sciences Industry Manager