post:post-processing_toolbox [FAST]

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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:

  * [[post:matlab_to_df.R]]: Converts [[usage:tracking#outputs|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.

  * [[post:splitFluoPopulationsTracks.m]]: Splits tracks into populations based on fluorescence levels in two channels.
  * [[post: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.

  * [[post:labelThresholdEvents.m]]: Marks events when a specific track-associated variable drops above or below a specified threshold.
  * [[post:labelUnusualEvents.m]]: Marks events when a specific track-associated variable moves far awy from its average, taking into account the typical fluctuations in its value.

==== Data manipulation ====

These functions allow you to extract or adjust data associated with your tracks.

  * [[post:meanIntInEllipse.m]]: Creates an elliptical mask based on the specified object's geometry and measures the intensity of an image within that mask.
  * [[post:filterTracks.m]]: Allows you to filter tracks with features (e.g. length, fluorescence intensity) that exceed or fall below a user-specified value.
  * [[post:extractTimePoints.m]]: Allows you to switch from track to slice-based representation of a specified data field.
  * [[post:coarsegrainTrackData.m]]: Converts motility data from track-based view to coarsegrained flowfield view.
==== Lineage tree navigation and manipulation ====

The [[usage:division_detection|division detection]] module updates tracks to encode a lineage tree. These functions help manipulate and navigate this tree.

  * [[post: getLineageIndices]]: Allows you to get the indices and generation numbers of all descendants of a target cell.