10/6/2023 0 Comments Multi measure plugin imagejReceived: NovemAccepted: FebruPublished: March 19, 2014Ĭopyright: © 2014 Guzmán et al. PLoS ONE 9(3):Įditor: Rossella Rota, Ospedale Pediatrico Bambino Gesu', Italy We expect that ColonyArea will be of broad utility for cancer biologists, as well as clinical radiation scientists.Ĭitation: Guzmán C, Bagga M, Kaur A, Westermarck J, Abankwa D (2014) ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays. The bundle is freely available for download as supporting information. The ColonyArea ImageJ plugin provides a simple and efficient analysis routine to quantitate assay data of one of the most commonly used cellular assays. The relation between the potencies of the two compounds compared very well with that obtained from an absorbance based method to quantify colony growth and to published data. We demonstrate that these parameters alone or in combination allow for robust quantification of IC 50 values of the cytotoxic effect of two staurosporines, UCN-01 and staurosporine (STS) on human glioblastoma cells (T98G). Instead of counting the number of colonies, ColonyArea determines the percentage of area covered by crystal violet stained cell colonies, also taking the intensity of the staining and therefore cell density into account. ColonyArea processes image data of multi-well dishes, by separating, concentrically cropping and background correcting well images individually, before colony formation is quantitated. Here we describe the freely available ImageJ-plugin “ColonyArea”, which is optimized for rapid and quantitative analysis of focus formation assays conducted in 6- to 24-well dishes. Therefore, there is a need for a simplified and standardized analysis of colony formation assays for both routine laboratory use and for parallelized automated analysis. Alternatively, this assay is used to quantitate the transforming potential of cancer associated genes and chemical agents. Multiple plugin directoriesįor ultimate control, ImageJ also provides support for manually configuring the list of plugin paths, similar to Java’s classpath, using the system property.The clonogenic or colony formation assay is a widely used method to study the number and size of cancer cell colonies that remain after irradiation or cytotoxic agent administration and serves as a measure for the anti-proliferative effect of these treatments. See the ImageJ website’s article Changing Location of Plugins Directory. However, this can be overridden using the plugins.dir system property. The default folder is the plugins folder of the ImageJ installation. Power users may wish to configure exactly which folder(s) ImageJ scans for plugins. Configuring where ImageJ looks for plugins This is useful if you want to install some of your own plugins without affecting the system-wide ImageJ installation. plugins folder in the current user’s home folder. In addition to looking in the plugins folder of ImageJ itself, ImageJ also looks in the. After running this command once and restarting ImageJ, the plugin will become available in ImageJ’s Plugins menu. java then you typically must execute the Compile and Run command on the file to first compile it to a. class then it is usually enough to simply restart ImageJ after dropping the file into plugins. The plugin will consist of one or more files which must be downloaded and (typically) placed in ImageJ’s plugins folder: In the meantime, to install a plugin manually, follow the plugin’s installation instructions, if any. If the plugin you want is not distributed via an ImageJ update site, please encourage the plugin’s maintainer to do so! Anyone can create a hosted update site on, to easily share and maintain updated plugins. Advanced topics Installing plugins manually class files, see Installing plugins manually below. jar file, or as unpackaged directory with. If the plugin is not available via update site, but packaged as. Simply add the update site containing your plugins of interest, and they will be installed automatically for you. The ImageJ Updater is the best way to install and update plugins.
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