Fluorescence microscopy became a common tool in cell and molecular biology. Image analysis of fluorescent molecules provides key information about the location, interactions, and dynamic behavior of target molecules. Usually user needs to recognize, characterize and classify particles, and in many cases to do statistical inferences from data collected. FluoJ is a software tool to automate many of these steps. It can be used to measure sperm quality, cells movement, virus infection in plants, apoptosis in cancer cells...In general it can be used to detect motifs, measure features on them, differentiate them into classes and even automate the classification. These results are achieved providing a customizable environment for particles detection, measurement and classification. A wide number of predefined features can be used to characterize fluorescent specimens (e.g. area, circularity, brightness, etc), and new descriptors can be easily added. Once configured, software can be trained to automatically classify particles or used directly for automatic image processing.

To run this plugin we need to create an empty database named fluoj on postgres, owned by the user specified in the persistence.xml file. Then we generate a project jar containing the classes under the target folder, that should be named FluoJ_.jar (The uderscore is needed to indicate to ImageJ that the jar contains plugins). This jar should be then installed in ImageJ under plugins/Fluoj. The project dependencies also need to be added to ImageJ, into the plugins/jars folder. They can be obtained running the command: mvn dependency:copy-dependencies -DoutputDirectory=my-extracted-jars