txt file should be provided as one line per frame in the format: ‘x-position, y-position, frame number,’. This will open a dialog window to specify the file path to an established trajectory. for another channel of the movie, load the trajectory by pressing ‘Load points (l)’ in the array option panel or by pressing ‘l’ on the keyboard. If you have already established a trajectory, e.g. If you are annotating a new movie, skip this step. click on selected frames and interpolate until you are satisfied with the established trajectory. If this is not the case as the movement is not linear, refine it by repeating step A and B, i.e.
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The newly calculated trajectory is displayed in the movie as brown circles between the first and last selected frames.Īfter the brown interpolated trajectory is displayed, check whether the process of interest is labeled correctly throughout all frames. Overall, taking the median for interpolation ensures that you can ‘override’ easily a label at a wrong position in step A by clicking once again.Īfter calculating the median in every frame with labels, the plugin calculates the trajectory between the first and last selected frame of the process of interest by linear interpolation. This is also much faster than, for example, manually editing a text file to remove miss-clicks. For example, one miss-click is corrected by two clicks at the right location, two miss-clicks by three clicks. While this sounds like a cumbersome way to operate the plugin at first, it is easy to click several times at the right location. Note: the points are not averaged but the median of the points is taken for the following reason: a median ignores outliers, and therefore clicking several times at the right location easily overrides a miss-click. The interpolation first calculates for every frame with labels the median position of all clicked points in the frame. Repeat this for the last frame of occurrence of your process of interest and on selected frames in-between.Īfter labeling the process of interest in few selected frames, press ‘Interpolate (i)’ in the arrow options panel or ‘i’ on your keyboard. If you miss-click, correct it by clicking few times at the right position (see note in step B). A yellow circle now labels the position where you clicked. To annotate a movie for the first time, select the rectangle tool in the Fiji toolbar and click with the mouse on the selected process of interest at its first frame of occurrence in the movie. If you want to load an already established trajectory, skip to step D.
This is particularly useful for applying the same annotation to several color channels. Moreover, the trajectory of the process of interest can be saved for further analysis and transferred to annotate another movie. Specifically, the plugin enables easy labeling of processes by clicking, and interpolation between frames to reduce the number of frames that have to be annotated. Here, we present a novel, user-friendly Fiji plugin for annotating stationary and non-stationary processes with circles, arrows and arrowheads. Consequently, most scientists have been adding graphical symbols in a tedious frame by frame manner. While efforts have been put into making these tools applicable for annotating processes in movies ( Carpentier, 2007 Straatman, 2018), the applicability and user-friendliness of these tools to highlight non-stationary processes is limited.
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Therefore, many software and visualization tools such as the Arrow Tool ( Tinevez et al., 2017) in ImageJ/Fiji ( Schindelin et al., 2012) have been designed to facilitate drawing these graphical symbols. They effectively guide us through complex data and images. For this, circles, arrows and arrowheads are among the most used graphical symbols for scientific illustrations ( Wong, 2011). Effective scientific communication relies on highlighting and annotating relevant processes in images and movies.
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