Journal
COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION
Volume 5, Issue 5, Pages 359-367Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/21681163.2015.1016243
Keywords
segmentation; phase contrast microscopy; trainable segmentation; Basic Image Features; local feature histograms; random forest
Categories
Funding
- British Heart Foundation [SP/08/004]
- EPSRC [EP/I005471/1] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [EP/I005471/1] Funding Source: researchfish
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Phase contrast microscopy (PCM) is routinely used for the inspection of adherent cell cultures in all fields of biology and biomedicine. Key decisions for experimental protocols are often taken by an operator based on typically qualitative observations. However, automated processing and analysis of PCM images remain challenging due to the low contrast between foreground objects (cells) and background as well as various imaging artefacts. We propose a trainable pixel-wise segmentation approach whereby image structures and symmetries are encoded in the form of multi-scale Basic Image Features local histograms, and classification of them is learned by random decision trees. This approach was validated for segmentation of cell versus background, and discrimination between two different cell types. Performance close to that of state-of-the-art specialised algorithms was achieved despite the general nature of the method. The low processing time (< 4s per 1280 x 960 pixel images) is suitable for batch processing of experimental data as well as for interactive segmentation applications.
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