Visualization

Along with Plots.jl and StatsPlots.jl for normal plotting of collapsed_data in scatter plot form, MicroTracker comes with handy tools to view the full multi-dimensional nature of microbot trajectories.

For full interactivity, use the included Pluto notebook (see the Pluto docs page). This allows input arguments to the trajectory_analyzer to be rapidly changed with sliders and drop-down menus.

MicroTracker.trajectory_analyzer — Function

trajectory_analyzer(linked_data, collapsed_data, particle_unique::AbstractString, [framenumber; [size_variable="Major_um"], [annotationkwargs...])

Display a comphrehensive dashboard of a single microbot, including instantaneous velocity, a chosen size_variable, and the FFT of the size_variable.

Arguments

linked_data : AbstractDataFrame, time-series linked data, as returned by load_linked_data or batch_particle_data_to_linked_data.
collapsed_data : AbstractDataFrame, collapsed data with a row per microbot, as returned by collapse_data.
particle_unique : AbstractString. The unique identifier of the microbot to be analyzed.
framenumber : (Optional) Int The frame number to be displayed. If not provided, the last frame is used.
size_variable : (Optional) AbstractString, The column name of the size variable to be displayed. Defaults to "Major_um".
annotationkwargs : (Optional) Keyword arguments passed to plotannotatedframe_single().

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MicroTracker.animate_trajectory_analyzer — Function

animate_trajectory_analyzer(linked_data, collapsed_data, particle_unique, savepath, [framerange]; animation_speed_multiplier=1, size_variable="Major_um", annotationkwargs...)

Export an animation of the trajectory analyzer and save it to savepath.

Arguments

linked_data : AbstractDataFrame, time-series linked data, as returned by load_linked_data or batch_particle_data_to_linked_data.
collapsed_data : AbstractDataFrame, collapsed data with a row per microbot, as returned by collapse_data.
particle_unique : AbstractString. The unique identifier of the microbot to be analyzed.
savepath : AbstractString. The path to save the animation to.
framerange : (Optional) UnitRange{Int64}. The range of frames to be displayed. If not provided, the entire trajectory is animated.
animation_speed_multiplier : (Optional) Int. The speed of the animation. Defaults to 1.
size_variable : (Optional) AbstractString, The column name of the size variable to be displayed. Defaults to "Major_um".
annotationkwargs : (Optional) Keyword arguments passed to plotannotatedframe_single().

Example

julia> trajectory_analyzer(linked_data, collapsed_data, "5_13p5_61p35-2", "my_animation.mp4")
[ Info: Creating animation: Frame = 5
...
[ Info: Saved animation to ~/my_animation.mp4

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