The input files for OpenComet analysis can be selected by clicking on Browse next to the "Input files" label. More details on the review process can be found here. After finishing the review process, press the Update button to overwrite the saved output images and create an updated output spreadsheet. The clicked comets will be classified as "deleted". At this point, you can click on any comet in any of the displayed output images. More details about the output generated by OpenComet can be found here.Ħ) Review and update (optional) – After clicking Run, the output images resulting from the automated analysis are displayed. The output images, as well as the calculated statistics in a spreadsheet are saved in the output folder. The final output images with marked comets and intensity profiles are shown in separate ImageJ windows. More information on the meaning and usage of analysis options can be found here.ĥ) Run – Click the Run button to perform the analysis for all the chosen input images. These settings influence the way OpenComet finds and segments comets. More information on the output generated by OpenComet can be found here.Ĥ) Set analysis options (optional) – In case you want to use the default analysis setting, you do not need to change analysis options. Make sure you have permission to write in the chose output directory (otherwise OpenComet will not be able to save the output). ![]() Optionally, you can change the name of the output file by changing it under the "Output file name" label. More information on choosing input images can be found here.ģ) Select output directory – Click the Browse button next to the "Output directory" label and choose an output directory of your choice. If OpenComet is properly installed, it will appear in the plugins list, and will run when clicked.Ģ) Select images to analyze – Click the Browse button next to the "Input files" label and choose any number of images from a single folder that you want to analyze. Use the following steps to analyze comet assay images using OpenComet.ġ) Run OpenComet plugin – Launch ImageJ, and click on the Plugins menu. Video tutorial OpenComet interface and usage Live image analysis using OpenComet in Micro-Manager Manual review and update of analysis results *You need to have write permission on the folder to be able to paste OpenComet_.jar. ![]() OpenComet will appear in ImageJ under the Plugins (note: we suggest using Fiji instead of ImageJ to compile OpenComet)Ģ) Download the latest version of "OpenComet plugin and source code" from the Downloads page and extract the zip file.ģ) Launch Fiji and choose Plugins / Compile and Run.Ĥ) Browse for the extracted OpenComet_.java and open.ĥ) The compiled OpenComet will now launch in Fiji.ġ) Download and install Micro-Manager (Micro-Manager is by default bundled with ImageJ).ĭownload the latest version of "OpenComet plugin" from the Downloads page and extract the zip file.īrowse for the extracted OpenComet_.jar and copy the file.īrowse to the installation folder of Micro-Manager and paste OpenComet_.jar into the plugins folder.*ĥ) When Micro-Manager is launched, the ImageJ interface is simultaneously shown. Click Save.*Ħ) OpenComet will now appear in ImageJ under the Pluginsġ) Download the latest version of "OpenComet plugin ImageJ bundle" from the Downloads page and extract the zip file.Ģ) Launch ImageJ from the extracted folder.ģ) OpenComet will appear in ImageJ under the Plugins menu.īrowse to the installation folder of Fiji and paste OpenComet_.jar into the plugins folder.*ĥ) When Fiji is launched, OpenComet will appear under the PluginsĬompiling OpenComet from source code in Fiji Installing OpenComet in ImageJ (Alternative method)ģ) Launch ImageJ and from the menu choose Plugins / Install.Ĥ) Browse for the extracted OpenComet_.jar and click Open.ĥ) ImageJ offers to save the OpenComet_.jar in its own plugins folder. ![]() OpenComet is released in several different packages, which can be obtained from the Downloads page. 2) Download the latest version of "OpenComet plugin" from the Downloads page and extract the zip file.ģ) Browse for the extacted OpenComet_.jar and copy the file.īrowse to the installation folder of ImageJ and paste OpenComet_.jar into the plugins folder.*ĥ) When ImageJ is launched, OpenComet will appear under the Plugins
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