| Both sides previous revision Previous revision Next revision | Previous revision |
| post:post-processing_toolbox [2019/11/11 18:40] – [Lineage tree navigation and manipulation] pseudomoaner | post:post-processing_toolbox [2023/03/07 22:18] (current) – [Event labelling] pseudomoaner |
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| ==== Track format conversion ==== | ==== Track format conversion ==== |
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| If you are more comfortable with programming languages other than Matlab, these scripts will convert the tracking data structures into something more to your liking. | 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: |
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| * [[post:matlab_to_df.R]]: Converts [[usage:tracking#outputs|procTracks]] to an R dataframe. | * [[post:matlab_to_df.R]]: Converts [[usage:tracking#outputs|procTracks]] to an R dataframe. |
| ==== Population labelling ==== | ==== Population labelling ==== |
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| Many experiments consist of mixtures of distinct populations of cells; these scripts allow you to automatically separate out and label these populations. | Many datasets consist of mixtures of distinct populations of objects; these scripts allow you to automatically separate out and label these populations. |
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| * [[post:splitFluoPopulationsTracks.m]]: Splits tracks into populations based on fluorescence levels in two channels. | * [[post:splitFluoPopulationsTracks.m]]: Splits tracks into populations based on fluorescence levels in two channels. |
| ==== Event labelling ==== | ==== Event labelling ==== |
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| Often, we are interested in the time at which a cell performs a particular action. These scripts will help you to detect these 'events' | 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. |
| 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. |
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| ==== Data manipulation ==== | ==== Data manipulation ==== |
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| * [[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: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 ==== | ==== Lineage tree navigation and manipulation ==== |
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| The [[usage:division_detection|division detection]] module updates cell tracks to encode a lineage tree within them. These functions help manipulate and navigate this tree. | The [[usage:division_detection|division detection]] module updates tracks to encode a lineage tree. These functions help manipulate and navigate this tree. |
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| * [[post: getLineageIndices]]: Allows you to get the indices and generations of all descendants of a target cell. | * [[post: getLineageIndices]]: Allows you to get the indices and generation numbers of all descendants of a target cell. |