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Outputs

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Dave Barry edited this page Jan 19, 2024 · 2 revisions

Overview

Depending on the settings used, ADAPT will produce output with the following approximate tree structure:

ADAPT_OUTPUT_TREE

The first level in the directory tree, which will be referred to as the parent directory, corresponds to the name of the input file used as the cytoplasmic/reference channel (in this case, "ADAPT_Test_Data"). For each input file (or pair of input files, if a corresponding signal channel was specified), outputs are grouped into population-level and cell-level. The population-level outputs are contained in the parent directory. The levels below this (for example, "0_Output"), which will be referred to as child directories, correspond to the individual cells detected in this input file.

Population-Level Outputs

  • Params: List of parameters specified for this analysis.

  • Morphology: Morphological data for each cell analysed in every frame. The parameters are those specified using the Analyze/Set Measurements... menu command in ImageJ. A description of the different parameters can be found on the ImageJ website.

  • Fluorescence: Results of fluorescence distribution analysis in signal channel.

  • Curvature_Visualisation: Movie of cell boundaries showing estimates of curvature. Convex values are shown in green and concave in red.

  • Velocity_Visualisation: Movie of cell boundaries showing estimates of membrane velocity. Positive values (indicative of protrusion) are shown in green and negative (indicative of retraction) in red.

  • Trajectories_Visualisation: Illustration of cell migration pattern. This folder also contains a list of coordinates for each cell (trajectory.csv).

Cell-Level Outputs

  • Bleb_Data_Files: Folder containing data files pertaining to individual blebs. See below for breakdown of parameters.

  • Bleb_Signal_Maps: Folder containing individual signal maps for each bleb.

  • Detection_Visualisation: Movie of individual bleb detections overlayed onto input movie.

  • BlebsVersusTime: Lists the number of "active" blebs in each frame.

  • cell_boundary_points: CSV file containing coordinates (x,y,t) for every cell boundary point in every frame.

  • ChangeInSignalMap: derived from the signal map, this represents changes in fluorescence intensity over time.

  • ColorVelocityMap: A color representation of the velocity map - a scale bar is also output.

  • CurvatureMap: Image of curvature map. The x-dimension corresponds to time, the y-dimension to boundary positions and pixel values correspond to curvature estimates.

  • MeanFluorescenceIntensity: Mean signal intensity distribution from the cell periphery (0) to the cell centre (1).

  • SignalMap: Image of signal map. The x-dimension corresponds to time, the y-dimension to boundary positions and pixel values correspond to signal values at the cell periphery.

  • STDFluorescenceIntensity: Standard deviation of signal intensity from the cell periphery (0) to the cell centre (1).

  • VelMap_AutoCorrelation: Result of applying an auto-correlation function to the velocity map.

  • VelMap_ChangeInSigMap_CrossCorrelation: Result of correlating the velocity map with the change in signal map.

  • VelMap_SigMap_CrossCorrelation: Result of correlating the velocity map with the signal map.

  • Velocity_Map_with_Detected_Regions: Image of velocity map showing initial bleb detections.

  • VelocityAnalysis: The percentage of cell boundary the is extending/retracting in each frame and the mean velocity of each.

  • VelocityMap: Image of velocity map. The x-dimension corresponds to time, the y-dimension to boundary positions and pixel values correspond to velocity estimates at the cell periphery.

  • VelocityScaleBar: Calibration bar associate with colour velocity map.

Can't find what you're looking for? Post a question on the image.sc forum using the #adapt hashtag.

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