Digital Image Analysis


Light microscopy offers life sciences the possibility to study a variety of organisms on widely differing spatial and temporal scales. Recent years have seen the appearance of a multitude of important light microscopy techniques. To characterise and describe biological processes, however, sheer visualisation of images is inadequate. The assembly of image‐processing algorithms, so‐called workflows, is needed to extract meaningful quantitative data. These workflows are as important as image acquisition and, therefore, are critical components for data acquisition and sample preparation. Here, we describe a variety of image‐processing workflows covering a large part of the biological landscape pointing out common themes and outlining a generic template for workflow assembly.

Key Concepts

  • Digital image analysis is an important tool to extract meaningful data out of an image.
  • Digital image analysis is the last component of a workflow comprising sample preparation and image acquisition.
  • Segmentation allows to identify objects in an image.
  • Filtering is needed to reduce noise in images from biological samples.
  • Digital image analysis is the key for reproducible workflows in life sciences.

Keywords: image processing; image analysis; segmentation; filtering; data representation; analysis workflow

Figure 1. Generic workflow for image analysis. The idea of image analysis is to extract meaningful data out of an image. The image can be seen as a filtered representation of the object. In order to identify the object in the image, a segmentation step is needed which can be typically facilitated by filtering steps. The identified object can be used to describe the object by a variety of features. All or a subset of features can be later used for a graphical representation.
Figure 2. Three different analysis workflows for biological samples. Most digital image processing with biological images follow the steps outlined here. The imaging modality is coupled to the biological question, to allow for a simple pipeline to be derived, either in 2D or 3D as needed. Object detection or ‘segmentation’ is usually done on filtered images of channels whose characteristics do not vary with the experimental conditions being tested (A: transmission image, B: average channel intensity, C: DAPI). The detection can be 1D (B,C), 2D (B) or 3D (B,C) as required. Finally, the metric being extracted can be straightforward such as an area (A) or more complex such as clustering (B) or Distance maps (C). Visualisation allows this data to be observed and understood, and the visualisation method should help to emphasize the expected behaviour of the data, while retaining something about the underlying distribution of the individual data points (dotplots vs barplots).


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Further Reading

Andrews PD, Harper IS and Swedlow JR (2002) To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era. Traffic 3 (1): 29–36.

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Burri, Olivier, Guiet, Romain, and Seitz, Arne(May 2016) Digital Image Analysis. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005781.pub2]