65,000 shades of grey: Use of digital image files in light microscopy

Sidney L. Shaw, Edward H. Hinchcliffe

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Abstract

Computers dominate image capture and analysis in modern light microscopy. The output of an imaging experiment is a binary coded file, called an image file, which contains the spatial, temporal and intensity information present in the sample. Understanding what comprises an image file, and how these files are generated is necessary in order to optimize the use of the digital light microscope. In this chapter, we discuss image file formats, and the various components of these files, such as bit-depth, sampling rate, color theory, and compression, from the perspective of the non-computer scientist. We also discuss the problem of proprietary file formats, and how these often are incompatible with certain types of imaging software. We present several solutions to this issue. Finally, we present the use of digital movie formats, compression routines, and provide some real world examples for optimizing the generation of digital movies.

Original languageEnglish (US)
Title of host publicationMethods in Cell Biology
PublisherAcademic Press Inc.
Pages317-336
Number of pages20
DOIs
StatePublished - 2013

Publication series

NameMethods in Cell Biology
Volume114
ISSN (Print)0091-679X

Keywords

  • Codec
  • Color
  • Compression
  • File format
  • Image file

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