select window threshold imagej macro language

#SELECT WINDOW THRESHOLD IMAGEJ MACRO LANGUAGE MANUAL#
#SELECT WINDOW THRESHOLD IMAGEJ MACRO LANGUAGE SOFTWARE#
#SELECT WINDOW THRESHOLD IMAGEJ MACRO LANGUAGE CODE#

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. One disadvantage of stand-alone tools can be the lack of updates by an established platform. TRI2 and CellProfiler are stand-alone tools written with the programming language Python.

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.

#SELECT WINDOW THRESHOLD IMAGEJ MACRO LANGUAGE MANUAL#

Moreover, the FociCounter only allows manual selection of cells. 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, not all existing tools support the complete range of file formats commonly used for image acquisition. Another commercially available package is IMARIS (Bitplane AG).

#SELECT WINDOW THRESHOLD IMAGEJ MACRO LANGUAGE SOFTWARE#

developed a software based on a cost-intensive program, ImageProPlus (Media Cybernetics Inc., US). However, some current software solutions for automated analysis are unsatisfactory as they provide limited algorithms, are stand-alone tools or are simply expensive. Conversely, automated computer-based foci analysis is considered to yield better sensitivity, comparability and consistency of the data.

Several publications showed that manual counting of foci is time consuming, frequently inaccurate and subjected to investigator-related bias. However, the programs currently available for counting and analysis of nuclei are often based on manual analysis. To evaluate formation and processing of these DNA damage foci, a reliable and accurate image analysis is required.ĭue to the wide use of methods retrieving images of foci and cells, multiple evaluation procedures have been developed. This method takes advantage of the fact that many repair proteins and repair associated proteins, such as γ-H2.AX, 53BP1 and RAD51, accumulate and co-localize at the site of DNA damage. Another possibility is to fuse the proteins of interest with fluorescent proteins, such as green fluorescence protein GFP.

phospho-histone 2.AX (γ-H2.AX)) antibodies directly linked to a fluorophore or detected by using a secondary fluorophore-labeled antibody. p53 binding protein 1 (53BP1)) or phospho-protein-specific (e.g. For this purpose the proteins of interest or their specific phosphorylated isoform are visualized by immunofluorescence using protein-specific (e.g. To evaluate the efficacy of IR alone or in combination with chemotherapy or drugs inducing DNA damage and targeting DNA repair, radiation biologists usually count fluorescence-labeled protein-foci in the nucleus using fluorescence microscopy. Radiotherapy (RT) is a mainstay in modern cancer treatment. As innovative option, the macro offers a combination of multichannel evaluation including colocalization analysis and the possibility to run all analyses in a batch mode. The macro allows improved foci evaluation regarding accuracy, reproducibility and analysis speed compared to manual analysis. The Focinator is a costless, user-friendly tool for fast high-throughput evaluation of DNA repair foci. Importantly, there was no difference in nuclei detection between the Focinator and ImageJ alone. Furthermore, different user groups were able to achieve a similar counting velocity. It significantly reduced the analysis time of radiation-induced DNA-damage foci. The Focinator turned out to be an easily adjustable tool for automation of foci counting. Additionally, measurements were performed by users with different backgrounds and experience. The use of the Focinator was tested by analyzing γ-H2.AX foci in murine prostate adenocarcinoma cells (TRAMP-C1) at different time points after IR with 0.5 to 3 Gray (Gy). We added different export options and a batch analysis. Methodsįor this purpose we integrated a user-friendly interface into ImageJ and selected parameters to allow automated selection of regions of interest (ROIs) depending on their size and circularity. Therefore, we aimed to develop a tool for costless, automated, quantitative and qualitative analysis of foci. Many current software solutions describe instructions for time-consuming and error-prone manual analysis, provide incomplete algorithms for analysis or are expensive. Consistency in counting and interpretation of foci remains challenging. In radiation biology and molecular radiation oncology, DNA damage and DNA repair kinetics upon ionizing radiation (IR) are evaluated by counting protein clusters or accumulations of phosphorylated proteins recruited to DNA damage sites. The quantitative analysis of foci plays an important role in many cell biological methods such as counting of colonies or cells, organelles or vesicles, or the number of protein complexes.

Select window threshold imagej macro language