CD44 Blocking Antibody perfusion tracking dataset

This dataset contains tracking results of different combinations of CD44 antibody-blocked AsPC1 and MiaPaca cells perfused on CD44 antibody-blocked endothelial monolayers under physiological flow speeds. Videos were recorded using a Nikon Eclipse Ti2-E microscope and 20x objective. Perfused cells from the generated videos were segmented using custom-trained Stardist models. Tracking was performed using TrackMate, and tracking results were analyzed using a custom CellTracksColab notebook. The dataset here contains the CSV files generated by TrackMate (Track and Spots information), the tracking data stored in the CellTracksColab format (Analysis.zip), and the analysis output used in the paper (Analysis.zip). Sample information AsPC1 and MiaPaca cells perfused on HUVEC cells under physiological flow speeds: 400 µm/s (p1), 200 µm/s (p2), 100 µm/s (p3) and 400 µm/s (p4). CD44 antibody blocking of PDACs, HUVECs, or both prior to perfusion Imaging specs Microscope: Nikon Eclipse Ti2-E, 20x objective Data Type: Brightfield microscopy images (16-bit) Image Size: 1024 x 1022 pixels (Pixel size: 650 nm) Recording speed 25 frames/s DL models: Cancer cells: https://doi.org/10.5281/zenodo.10572122 Neutrophils: https://doi.org/10.5281/zenodo.10572231 Mononucleated cells: https://doi.org/10.5281/zenodo.10572200 Model Training and predictions: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) Tracking parameters (TrackMate): Detection: label detector Tracking: Simple LAP detector: Linking max distance: 20 px; Gap-closing max distance: 20 px; Gap-closing max frame gap: 4. Track filtering: min number of spots in the tracks 11.79 Tracking analysis Tracks were analyzed using a customized CellTracksColab notebook (https://github.com/CellMigrationLab/PDAC_DL/tree/main/CellTracksColab) Contents of the repository Analysis_AsPC1.zip dataset Analysis_Miapaca.zip dataset As_blockboth.zip dataset As_ctrlblock.zip dataset As_HUblock.zip dataset As_TCblock.zip dataset Mia_blockboth.zip Mia_ctrlblock.zip Mia_HUblock.zip Mia_TCblock.zip Reference Biorxiv paper