3/7/2024 0 Comments Download imagej fiji![]() It defines at what distance (in pixels) two spots in different channels are considered to be localized. There is an additional parameter in case of colocalization: maximum distance between spots’ centers. If you uncheck it, then only detection will be performed. To get colocalization analysis you need to check “ Calculate colocalization?” box. ![]() If your image contains multiple channels then after pressing Detect Particles the dialog will look differently:įirst, the plugin will show the window above with general setup and later it will proceed with a series of parameter windows, specifying detection parameters for each channel. In this case only particles in that ROI will be detected (also supported in “ Preview.” mode):ĭetection and colocalization in multi-channel image (two or more channels) If you want detection to be performed in some specific region instead of whole image, select some ROI using any ImageJ ROI selection tools before launching plugin: I recommend to play with parameters to get a nice detection result. ROIs will have names in the format of ind(detection# in Results table)_ch(#channel)_sl(#slice)_fr(#frame).Īfter pressing OK plugin runs and add ovals/rectangles in overlay on top of detected particles.Īlso it will provide you Results table containing particles’ coordinates (see below) and Summary table. If you choose Add to ROI Manager option (“All particles”), plugin will add detected rectangular ROIs around particles to ROI Manager. As its name suggests, this procedure requires computational power and can be slow, especially on big images. If “ Segment larger particles (slow)?” box is checked, plugin will try to further split large particles into a smaller dots, if it is possible. If you check “ Include larger particles?” box, it will also try to quantify bigger spots. The “ROI shape” option allows you to choose, if you want your detection to be displayed as “Ovals” or “Rectangles”.īy default, plugin looks only for particles of specified size. Checkbox “ Preview…” allows to see detection on the current picture and simplifies this task. To have good detection usually you need to play with parameters and see how it goes. Specify estimated particles size and intensity threshold (particle brightness) and press OK. If the image is not multi-channel image, the following dialog window will appear: Launch the detection by choosing Plugins › ComDet › Detect Particles. Plugin auto-detects the number of channels and if it is more than one then the plugin will automatically switch to the second mode (see below). particles detection and colocalization analysis (whole image or ROI).įor colocalization you need a color composite image containing multiple color channels (two or more).particles detection (whole image or ROI).In general, the plugin works in two modes: Plugin for finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc).įor help with plugin installation, see instructions.
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