Annotation of time-lapse data provides an important tool to highlight dynamic processes. Particularly, arrows, circles and arrowheads are useful to pinpoint a specific process, stationary or evolving over time. Here, we describe a user-friendly Fiji plugin to facilitate annotation of movies with arrows, arrowheads and circles. The plugin also enables saving and loading of annotated tracks.
Effective scientific communication relies on highlighting and annotating relevant processes in images and movies. For this, circles, arrows and arrowheads are among the most used graphical symbols for scientific illustrations (Wong, 2011). They effectively guide us through complex data and images. 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. 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. Consequently, most scientists have been adding graphical symbols in a tedious frame by frame manner. Here, we present a novel, user-friendly Fiji plugin for annotating stationary and non-stationary processes with circles, arrows and arrowheads. 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. Moreover, the trajectory of the process of interest can be saved for further analysis and transferred to annotate another movie. This is particularly useful for applying the same annotation to several color channels.
We designed a user-friendly plugin for Fiji (Schindelin et al., 2012) to add custom graphical symbols such as arrows to movies (Fig. 1). We chose Fiji as platform as it is a widely used, freely available and open-source platform that runs on Windows, Mac and Linux. The plugin was implemented as ImageJ 1.x plugin in Java. An overview about the Java classes at play is given in the Materials and Methods section and the commented source code of the plugin is available at: _arrow_in_movies. Here, we describe how a user can use the plugin to easily annotate a movie. A tutorial video about how to use the plugin is also available ( ).
The workflow to annotate the movie consists of first establishing or loading a trajectory, then selecting and modifying the desired graphical symbol such as an arrow, arrowhead, or circle, and then lastly save the annotated movie and/or trajectory (Fig. 3). In detail, the subsequent steps should be followed:
If you are satisfied with the trajectory, customize your desired graphical symbol in the array option panel. There are five different available arrow head styles, an option to fill the shape, different available colors, and parameters to adjust the length of the arrow head, the overall length of the arrow, and its thickness. To preview the arrow as it will be displayed in the movie, an arrow preview window is updated with every change of parameters.
Workflow of annotation process. The workflow is comprised of (A) labeling of your process of interest in selected frames, (B) interpolation to establish the trajectory also in frames that were not labeled, (C) iterative refinement of the trajectory until the process of interest is correctly labeled, (D) instead of generating a new trajectory, an already established trajectory can be loaded, (E) design your desired graphical symbol, such as an arrow, arrowhead or circle, (F) adding the arrow to the movie in the proper orientation and distance to the process of interest, and (G) saving the annotated movie and trajectory.
We have presented a user-friendly Fiji plugin that simplifies annotation of stationary and non-stationary processes of interest in movies with custom symbols such as arrows, circles or arrowheads. It facilitates this process by providing an intuitive graphical user interface that enables clicking on the process of interest in selected frames to establish a trajectory. Moreover, the layout and buttons of the option panel intuitively guide the user through the annotation process.
The Fiji plugin was written in Java as an ImageJ 1.x plugin and is available on github _arrow_in_movies or in the Supplementary Material of this paper. It consists of four classes, which are described below.
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