期刊
MICROSCOPY AND MICROANALYSIS
卷 19, 期 5, 页码 1281-1289出版社
CAMBRIDGE UNIV PRESS
DOI: 10.1017/S1431927613012737
关键词
X-ray fluorescence microscopy; cluster analysis; soft clustering; hard clustering; Gaussian mixture models; k-means clustering; expectation maximization; image segmentation; bioinorganic chemistry; Plasmodium falciparum
资金
- U.S. Department of Energy, Office of Science, Basic Energy Sciences program [DE-AC02-06CH11357]
- National Institutes of Health [GM038784-22S1]
X-ray fluorescence (XRF) microscopy is an important tool for studying trace metals in biology, enabling simultaneous detection of multiple elements of interest and allowing quantification of metals in organelles without the need for subcellular fractionation. Currently, analysis of XRF images is often done using manually defined regions of interest (ROIs). However, since advances in synchrotron instrumentation have enabled the collection of very large data sets encompassing hundreds of cells, manual approaches are becoming increasingly impractical. We describe here the use of soft clustering to identify cell ROIs based on elemental contents, using data collected over a sample of the malaria parasite Plasmodium falciparum as a test case. Soft clustering was able to successfully classify regions in infected erythrocytes as parasite, food vacuole, host, or background. In contrast, hard clustering using the k-means algorithm was found to have difficulty in distinguishing cells from background. While initial tests showed convergence on two or three distinct solutions in 60% of the cells studied, subsequent modifications to the clustering routine improved results to yield 100% consistency in image segmentation. Data extracted using soft cluster ROIs were found to be as accurate as data extracted using manually defined ROIs, and analysis time was considerably improved.
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