Overview of tracking projects¶
In this overview we explain the basic principles.
Understanding tracking¶
To build a tracking project there are several steps
Crop and mask the image to remove any unwanted bits of images that might produce spurious results.
Preprocess the images for tracking. Different methods require different things. Some need binary black and white images, others need grayscale. You can also perform a lot of operations to improve how easy it is to track the objects you’re interested in.
Track - which means to locate the position of objects within a frame. There are 3 main methods that are currently implemented in this software:
Trackpy an existing particle tracking library for tracking “blobs”
Link the tracks together so that you know which particle is which in consecutive frames
Postprocess. Calculate results based on the tracking. For example you might want to know which particles are neighbours or how fast particles are moving.
Annotate. This is useful for checking your tracking is working as expected but also to visualise values. eg you could colour code the value of an order parameter on each particle to see if they are clustered.
In general we use the track_gui to optimise all these different stages. However, once we have found the optimum set of conditions for tracking the settings can be saved to a .param file and used to setup all future tracking. Then if necessary you can automatically process batches of movies with the same settings.
Basic orientation for using the track_gui¶
Watch the video
The track_gui is divided into a few key areas: Toolbar / Menus, the Viewer, the Settings Panel
The Viewer¶
The viewer displays a single frame from your movie with the annotations if you have added these. Since most tracking projects require you to preprocess the image you can also view the preprocessed image by toggling the button “Preprocessed Image”. This is particularly useful in optimising the parameters before tracking. It is also useful to toggle between the preprocessed image and the tracked image with some form of annotation to assess whether the tracking could be improved by improving the preprocessing. There is also a slider with spinbox to allow you to scroll through the frames in the movie. The slider auto updates when released, the spinbox updates after you hit the enter key. You can also limit the range of frames being processed by selecting the settings wheel.
You can interact with the image:
scroll wheel zooms on image
right mouse button hold and drag zooms on selected region
left mouse button hold and drag pans zoomed image
double-click right mouse button resets zoom
double-click left mouse button displays coordinates and image intensities at clicked point.
The Settings Panel¶
The settings panel consists of a series of tabs. Each tab connects to a different stage of the tracking process outlined above. Each tab has a checkbox which indicates whether the actions on this tab are active or not. Within each tab there are two sections: “Method Selectors” and “Parameter Adjustors”
The Method Selectors¶
Within each tab, the top half of the Settings Panel displays the methods. A method can be added by selecting from the drop down menu and clicking “Add Method”. Initially this will appear at the bottom of the list below “—-inactive—-” place holder. The methods can be activated by dragging and dropping them (left mouse button) into the list above the “—-inactive—-” place holder. The methods are run in the order, from top to bottom, that they are listed in this dialogue. To remove a method temporarily move it below “—-inactive—-”. To remove it more permanently you can right click on the method and it will disappear. In some cases you may want to apply the same method more than once with different parameters. This is not allowed for tracking methods but can be done for other processes. This will create a “methodname*1”, “methodname*2” etc which can then be setup.
Parameter Adjustors¶
Each method has a set of parameters that need to be adjusted in order for it to work. These differ from method to method. These appear dynamically for all active methods in the bottom of the settings panel. There are several types of adjustor:
Sliders with a spinbox. The limits of the sliders can be adjusted using the settings icon. This requires some care as we don’t check that the new limits you put in are acceptable and hence there is a risk of crashing.
Drop down menus with a fixed list of choices.
Text boxes. Here the input may be quite varied. If you are unsure you can consult the reference for each method.
The crop section has a slightly different interface. One can manually enter the coordinates for a crop or mask functon but this is not recommended. Click the check box and then on the image click and hold the left mouse button and drag the shape and release to select the appropriate area. Afterwards the areas can be adjusted using the handles. Once finished uncheck the check box to apply the crop or mask. This can be readjusted at any future point by simply rechecking the check box. Finally one can remove the crop / masks by clicking the reset button.