title: Spectral mapping tools from the earth sciences applied to spectral microscopy data.
abstract: BACKGROUND
  Spectral imaging, originating from the field of earth remote sensing, is a powerful tool that is being increasingly used in a wide variety of applications for material identification. Several workers have used techniques like linear spectral unmixing (LSU) to discriminate materials in images derived from spectral microscopy. However, many spectral analysis algorithms rely on assumptions that are often violated in microscopy applications. This study explores algorithms originally developed as improvements on early earth imaging techniques that can be easily translated for use with spectral microscopy.
  
  
  METHODS
  To best demonstrate the application of earth remote sensing spectral analysis tools to spectral microscopy data, earth imaging software was used to analyze data acquired with a Leica confocal microscope with mechanical spectral scanning. For this study, spectral training signatures (often referred to as endmembers) were selected with the ENVI (ITT Visual Information Solutions, Boulder, CO) "spectral hourglass" processing flow, a series of tools that use the spectrally over-determined nature of hyperspectral data to find the most spectrally pure (or spectrally unique) pixels within the data set. This set of endmember signatures was then used in the full range of mapping algorithms available in ENVI to determine locations, and in some cases subpixel abundances of endmembers.
  
  
  RESULTS
  Mapping and abundance images showed a broad agreement between the spectral analysis algorithms, supported through visual assessment of output classification images and through statistical analysis of the distribution of pixels within each endmember class.
  
  
  CONCLUSIONS
  The powerful spectral analysis algorithms available in COTS software, the result of decades of research in earth imaging, are easily translated to new sources of spectral data. Although the scale between earth imagery and spectral microscopy is radically different, the problem is the same: mapping material locations and abundances based on unique spectral signatures.
authors.affiliation: Global Services Consultant, ITT Visual Information Solutions, Boulder, CO 80301, USA. tharris@ittvis.com
authors.forename: A Thomas
authors.initials: AT
authors.lastname: Harris
mesh_terms: D000465:Algorithms; D003952:Diagnostic Imaging; D007091:Image Processing, Computer-Assisted; D018613:Microscopy, Confocal; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods*; D010811:Natural Science Disciplines / Q000295:instrumentation / Q000379:methods*; D013050:Spectrometry, Fluorescence / Q000295:instrumentation / Q000379:methods*