title: Comparison of two automatic cell-counting solutions for fluorescent microscopic images.
abstract: Cell counting in microscopic images is one of the fundamental analysis tools in life sciences, but is usually tedious, time consuming and prone to human error. Several programs for automatic cell counting have been developed so far, but most of them demand additional training or data input from the user. Most of them do not allow the users to online monitor the counting results, either. Therefore, we designed two straightforward, simple-to-use cell-counting programs that also allow users to correct the detection results. In this paper, we present the Cellcounter and Learn123 programs for automatic and semiautomatic counting of objects in fluorescent microscopic images (cells or cell nuclei) with a user-friendly interface. Although Cellcounter is based on predefined and fine-tuned set of filters optimized on sets of chosen experiments, Learn123 uses an evolutionary algorithm to determine the adapt filter parameters based on a learning set of images. Cellcounter also includes an extension for analysis of overlaying images. The efficiency of both programs was assessed on images of cells stained with different fluorescent dyes by comparing automatically obtained results with results that were manually annotated by an expert. With both programs, the correlation between automatic and manual counting was very high (R(2) < 0.9), although Cellcounter had some difficulties processing images with no cells or weakly stained cells, where sometimes the background noise was recognized as an object of interest. Nevertheless, the differences between manual and automatic counting were small compared to variations between experimental repeats. Both programs significantly reduced the time required to process the acquired images from hours to minutes. The programs enable consistent, robust, fast and accurate detection of fluorescent objects and can therefore be applied to a range of different applications in different fields of life sciences where fluorescent labelling is used for quantification of various phenomena. Moreover, Cellcounter overlay extension also enables fast analysis of related images that would otherwise require image merging for accurate analysis, whereas Learn123's evolutionary algorithm can adapt counting parameters to specific sets of images of different experimental settings.
authors.affiliation: Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: J
authors.initials: J
authors.lastname: Lojk
authors.affiliation: Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: U
authors.initials: U
authors.lastname: Čibej
authors.affiliation: Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: D
authors.initials: D
authors.lastname: Karlaš
authors.affiliation: Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: L
authors.initials: L
authors.lastname: Šajn
authors.affiliation: Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: M
authors.initials: M
authors.lastname: Pavlin
mesh_terms: D000465:Algorithms; D001331:Automation; D002452:Cell Count / Q000379:methods*; D002467:Cell Nucleus / Q000648:ultrastructure; D002470:Cell Survival; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008856:Microscopy, Fluorescence; D053758:Nanoparticles; D012984:Software
keywords: Automatic cell counting; Cellcounter; Learn123; cell viability; evolutionary algorithm; fluorescence microscopy; transfection