CellTracksColab - Filopodia dataset

Dataset used in the manuscript "CellTracksColab—A platform for compiling, analyzing, and exploring tracking data"

This Zenodo archive contains:

• The raw video (Raw_ zip files)
• The tracking files as XML and CSV files (Tracks.zip)
• The CellTracksColab dataframes storing the dataset (CellTracksColab_results.zip)
• The CellTracksColab outputs used to make the figures in the paper (CellTracksColab_results.zip)

In brief:

U2-OS cells expressing MYO10-GFP, a MYO10 MyTH/FERM deletion construct (EGFP-MYO10ΔFERM), or a MYO10/TLN1 chimera construct (EGFP-MYO10TH) were plated for at least 2 h on fibronectin before the start of live imaging. Images were taken every 5 s at 37 C on an Airyscan microscope, using a 40x objective. 

MYO10 puncta were tracked using TrackMate using the custom Stardist detector and the simple LAP tracker (Linking max distance=1 micron, Gap-closing max distance=2 microns, Gap-closing max frame gap=2 micron). Briefly, this model was trained for 200 epochs on 11 paired image patches [image dimensions: (512, 512), patch size: (512,512)] with a batch size of 2 and a mean absolute error (MAE) loss function, using the StarDist 2D ZeroCostDL4Mic notebook.

In CellTracksColab, we conducted a dimensionality reduction analysis employing Uniform Manifold Approximation and Projection (UMAP). The UMAP settings were as follows: number of neighbors (n_neighbors) set to 10, minimum distance (min_dist) to 0, and number of dimensions (n_dimension) to 2. This analysis utilized an array of track metrics, including:

NUMBER_SPOTS, NUMBER_GAPS, NUMBER_SPLITS, NUMBER_MERGES, NUMBER_COMPLEX, LONGEST_GAP, TRACK_DISPLACEMENT, TRACK_MEAN_QUALITY, MAX_DISTANCE_TRAVELED, CONFINEMENT_RATIO, MEAN_STRAIGHT_LINE_SPEED, LINEARITY_OF_FORWARD_PROGRESSION, MEAN_DIRECTIONAL_CHANGE_RATE, Track Duration, Mean Speed, Median Speed, Max Speed, Min Speed, Speed Standard Deviation, Total Distance Traveled, Directionality, Tortuosity, Total Turning Angle, Spatial Coverage, MEAN_MEAN_INTENSITY_CH1, MEAN_MEDIAN_INTENSITY_CH1, MEAN_MIN_INTENSITY_CH1, MEAN_MAX_INTENSITY_CH1, MEAN_TOTAL_INTENSITY_CH1, MEAN_STD_INTENSITY_CH1, MEAN_CONTRAST_CH1, MEAN_SNR_CH1, MEAN_ELLIPSE_X0, MEAN_ELLIPSE_Y0, MEAN_ELLIPSE_MAJOR, MEAN_ELLIPSE_MINOR, MEAN_ELLIPSE_THETA, MEAN_ELLIPSE_ASPECTRATIO, MEAN_AREA, MEAN_PERIMETER, MEAN_CIRCULARITY, MEAN_SOLIDITY, MEAN_SHAPE_INDEX, MEDIAN_MEAN_INTENSITY_CH1, MEDIAN_MEDIAN_INTENSITY_CH1, MEDIAN_MIN_INTENSITY_CH1, MEDIAN_MAX_INTENSITY_CH1, MEDIAN_TOTAL_INTENSITY_CH1, MEDIAN_STD_INTENSITY_CH1, MEDIAN_CONTRAST_CH1, MEDIAN_SNR_CH1, MEDIAN_ELLIPSE_X0, MEDIAN_ELLIPSE_Y0, MEDIAN_ELLIPSE_MAJOR, MEDIAN_ELLIPSE_MINOR, MEDIAN_ELLIPSE_THETA, MEDIAN_ELLIPSE_ASPECTRATIO, MEDIAN_AREA, MEDIAN_PERIMETER, MEDIAN_CIRCULARITY, MEDIAN_SOLIDITY, MEDIAN_SHAPE_INDEX, STD_MEAN_INTENSITY_CH1, STD_MEDIAN_INTENSITY_CH1, STD_MIN_INTENSITY_CH1, STD_MAX_INTENSITY_CH1, STD_TOTAL_INTENSITY_CH1, STD_STD_INTENSITY_CH1, STD_CONTRAST_CH1, STD_SNR_CH1, STD_ELLIPSE_X0, STD_ELLIPSE_Y0, STD_ELLIPSE_MAJOR, STD_ELLIPSE_MINOR, STD_ELLIPSE_THETA, STD_ELLIPSE_ASPECTRATIO, STD_AREA, STD_PERIMETER, STD_CIRCULARITY, STD_SOLIDITY, STD_SHAPE_INDEX, MIN_MEAN_INTENSITY_CH1, MIN_MEDIAN_INTENSITY_CH1, MIN_MIN_INTENSITY_CH1, MIN_MAX_INTENSITY_CH1, MIN_TOTAL_INTENSITY_CH1, MIN_STD_INTENSITY_CH1, MIN_CONTRAST_CH1, MIN_SNR_CH1, MIN_ELLIPSE_X0, MIN_ELLIPSE_Y0, MIN_ELLIPSE_MAJOR, MIN_ELLIPSE_MINOR, MIN_ELLIPSE_THETA, MIN_ELLIPSE_ASPECTRATIO, MIN_AREA, MIN_PERIMETER, MIN_CIRCULARITY, MIN_SOLIDITY, MIN_SHAPE_INDEX, MAX_MEAN_INTENSITY_CH1, MAX_MEDIAN_INTENSITY_CH1, MAX_MIN_INTENSITY_CH1, MAX_MAX_INTENSITY_CH1, MAX_TOTAL_INTENSITY_CH1, MAX_STD_INTENSITY_CH1, MAX_CONTRAST_CH1, MAX_SNR_CH1, MAX_ELLIPSE_X0, MAX_ELLIPSE_Y0, MAX_ELLIPSE_MAJOR, MAX_ELLIPSE_MINOR, MAX_ELLIPSE_THETA, MAX_ELLIPSE_ASPECTRATIO, MAX_AREA, MAX_PERIMETER, MAX_CIRCULARITY, MAX_SOLIDITY, MAX_SHAPE_INDEX

Subsequently, clustering analysis was performed using Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN). The parameters included clustering_data_source set to UMAP, min_samples at 20, min_cluster_size at 300, and the metric employed was Canberra.