Similar protocols

Pipeline publication

[…] le for counting and analysis of nuclei are often based on manual analysis. Several publications showed that manual counting of foci is time consuming, frequently inaccurate and subjected to investigator-related bias. Conversely, automated computer-based foci analysis is considered to yield better sensitivity, comparability and consistency of the data [–]. However, some current software solutions for automated analysis are unsatisfactory as they provide limited algorithms, are stand-alone tools or are simply expensive [, ]. For example, Böcker et al. developed a software based on a cost-intensive program, ImageProPlus (Media Cybernetics Inc., US) []. Another commercially available package is IMARIS (Bitplane AG) [, ]. Moreover, not all existing tools support the complete range of file formats commonly used for image acquisition []. The FociCounter, a freely available, non-customizable stand-alone tool, does not support all formats, for example files used by Zeiss (CZI and ZVI) and by Leica (LIF). Moreover, the FociCounter only allows manual selection of cells []. However, integration of automated cell selection and a batch mode performing automated analysis of various pictures would result in desirable time-saving steps for data analysis. TRI2 and CellProfiler are stand-alone tools written with the programming language Python [–]. One disadvantage of stand-alone tools can be the lack of updates by an established platform. In contrast, the platform of ImageJ offers support, frequent updates and the possibility to change the source code or to link it with additional programming tools [–, , ]. ImageJ-based solutions have already been described by several authors and institutions, but these solutions frequently provide incomplete algorithms or macros not suited for immediate use [, ]. For example, Cai and colleagues published the source code for an ImageJ macro without interface, like a menu and buttons [], and Du and colleagues developed […]

Pipeline specifications

Software tools Imaris, FociCounter, CellProfiler