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Post-processing toolbox
Once you have performed object tracking, there are many tasks that you may wish to perform with that tracking data. This page lists a number of scripts that can be downloaded that perform various post-processing tasks on FAST's track output.
Track format conversion
If you are more comfortable with programming languages other than Matlab or you are using FAST's stand-alone version, you will need to convert the tracking data structures into platform-specific structures. These scripts perform these conversions:
- matlab_to_df.R: Converts procTracks to an R dataframe.
Population labelling
Many datasets consist of mixtures of distinct populations of objects; these scripts allow you to automatically separate out and label these populations.
- splitFluoPopulationsTracks.m: Splits tracks into populations based on fluorescence levels in two channels.
- labelStartAndEndFluoCells.m: Splits tracks into populations based on fluorescence levels in a single channel from images taken at the start and end of a timelapse series. Permits population assignment with minimal phototoxicity.
Event labelling
Often, we are interested in the time at which an object performs a particular action. These scripts will help you to detect these 'events' and assign them to FAST's internal representation.
- labelThresholdEvents.m: Marks events when a specific track-associated variable drops above or below a specified threshold.
Data manipulation
These functions allow you to extract or adjust data associated with your tracks.
- meanIntInEllipse.m: Creates an elliptical mask based on the specified object's geometry and measures the intensity of an image within that mask.
- linearisePhi.m: Creates a new field, fullPhi, in the procTracks structure that keeps track of the angle of a single pole of each object.
- filterTracks.m: Allows you to filter tracks with features (e.g. length, fluorescence intensity) that exceed or fall below a user-specified value.
Lineage tree navigation and manipulation
The division detection module updates tracks to encode a lineage tree. These functions help manipulate and navigate this tree.
- getLineageIndices: Allows you to get the indices and generation numbers of all descendants of a target cell.