Global gray-level thresholding based on object size.

Ranefall P, Wählby C

Cytometry A 89 (4) 385-390 [2016-04-00; online 2016-01-23]

In this article, we propose a fast and robust global gray-level thresholding method based on object size, where the selection of threshold level is based on recall and maximum precision with regard to objects within a given size interval. The method relies on the component tree representation, which can be computed in quasi-linear time. Feature-based segmentation is especially suitable for biomedical microscopy applications where objects often vary in number, but have limited variation in size. We show that for real images of cell nuclei and synthetic data sets mimicking fluorescent spots the proposed method is more robust than all standard global thresholding methods available for microscopy applications in ImageJ and CellProfiler. The proposed method, provided as ImageJ and CellProfiler plugins, is simple to use and the only required input is an interval of the expected object sizes. © 2016 International Society for Advancement of Cytometry.

BioImage Informatics [Technology development]

QC bibliography QC xrefs

PubMed 26800009

DOI 10.1002/cyto.a.22806

Crossref 10.1002/cyto.a.22806

http://www.cb.uu.se/~petter/downloads/SIP/ [ImageJ and CellProfiler plugins]

http://www.cb.uu.se/~petter/downloads/CellClusters/ [Images]

http://murphylab.web.cmu.edu/data/2009_ISBI_Nuclei.html [Images]

http://smal.ws/wp/software/synthetic-data-generator/ [Synthetic image data generator]