Once this file is loaded, the main CellProfiler Analyst user interface is displayed and Tracer is selected from the row of icons presented. The data set used in this example consists of dividing cells in a Drosophila embryo download , in which the genes were modified to make the DNA fluorescent. CellProfiler was used to analyze this movie using the TrackObjects module to track the individual cells across time, and collect measurements such as intensity, morphology and texture; the pipeline is available here download. When starting Tracer, this tracking data is read in order to construct a network graph that is displayed in two complementary formats:.
The panel on the left is an XYT plot which shows the evolution of the individual cells across time; the spatial axes are the horizontal plane with the vertical axes representing time. Below both is a control panel with various operations that can be used to re-display or interrogate the data. Display measurement heatmap…: Displays a heatmap of measurements averaged across all trajectroies for each timepoint.
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You can select which measurements to display. The display is shown using the current colormap.
Additional context menu options are also shown:. The trajectories in both panels can be color-coded according to network graph topological metrics; it is these metrics which allow for assessment of tracking quality. At this point, the user has several buttons for how to treat these nodes:.
We have two sample datasets available to use with Tracer. The image data is in the form of individual image frames; the movies shown below are for illustrative purposes. Note that CellProfiler 2. Contributed by Albert Yeh Ramaswamy lab. Contributed by Victoria Foe Foe lab. Note that when using the properties files associated with these datasets, the images and output subfolders must stay in the same location relative to the properties files and the SQLite database. The source code is available as a branch from the main CellProfiler Analyst public repository on GitHub.
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