Updated to match changes in jfreechart library If that is not the case, change the numbers in the dialog. To do so, go to Image › Properties…, and make sure that the number of Slices is 1, and the number of Frames is whatever the length of your stack. When the plugin does not work on your stack, or if it only works on the first image, make sure that ImageJ sees your stack as a time-lapse and not as a Z-stack. Clicking on any of the rows in the table or the red circles in the image should bring up a graph with the intensity profile. In the Spot Intensity Analysis plugin set Time Interval to 1.0, Electrons per ADU to 1.0, Check First n Frames to 10, Spot Radius (pixels) to 3, Noise tolerance to 45, and Background estimation to Median-40. Testing To test the plugin, use the data: File › Open Samples › Tracks for TrackMate. If there is significant movement during the time-lapse image, you will first need to “de-jitter” using another ImageJ plugin. The keyboard key “j” will scroll up, the key “k” will scroll down. The first two columns in the output table are the x and y position of the spot (in pixels). Data can be exported by selecting the table, followed by File › Save As in the menu. Clicking in the image itself will select the nearest by spot, select the corresponding row in the table and draw the intensity plot. When selecting a row in the resulting table, a plot is generated with the intensities plotted as a function of time. The Background image is first subtracted from each frame, and then the intensities of all pixels in a circle with given radius around the center (maximum) pixel is calculated. In the second phase the intensities of each spot at each time point is calculated. This same image is used to calculate the background (which is currently done using the ImageJ Background tool using a ball radius of 100 and “Sliding paraboloid” checked). An image constructed by averaging the first n images (“Check First n Frames”) is used for the spot finding. Local maxima are accepted when the maximum is higher than a user-defined number (“Noise tolerance”) over the average of the 4 corners of the box. It does so by scanning for local maxima in the image with a box of user-defined size (“Spot radius (pixels)”). This plugin has two phases, in the first phase it detects spots. To install this plugin check the “ValelabUtils” update site in the Fiji updater. Simple ImageJ/Fiji plugin to plot intensity of a spot over time. If you’d like to help, check out the how to help guide! The content of this page has not been vetted since shifting away from MediaWiki.
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