High Density Filter Reader - HDFR


A Java-based image recognition tool to read and analyze images of high-density filters (macroarrays). 

Background Intensity Calibration

Magnification Tool

Displaying Results File



  • Accepts all common image formats such as gif, jpeg, and tif
  • Accepts gel files
  • Provides image manipulation tools such as cropping, rotating, and adjusting the brightness and contrast
  • Simple user interaction and validation of results via magnified portions of the image
  • Automatic background subtraction

Interface and Setup

  • Simple, user-friendly
  • Easily adjustable hit threshold levels
  • Quick and easy set-up and storage of analysis templates
  • FastFlow Buttons for streamlining the analysis
  • User definable hybridization gridding patterns for maximum flexibility
  • Provisions for use of anchor clones

Analysis and Output

  • Highly efficient algorithm analyzes high density filters in seconds
  • Accurately identifies clone addresses and quantifies spot intensities
  • Multiple output formats, such as tab delimited clone/probe/hit-strength file or rearraying file for direct input for the Genetix Q-bot
  • Database-capable versions available

Windows and Unix versions

Additional Resources

HDFR White Paper

HDFR Tutorial