HUVEC CD44 siRNA perfusion tracking dataset

This dataset contains tracking results of AsPC1 and MiaPaca cells perfused on CD44 siRNA-silenced 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). 

Specifications





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 siRNA silencing of the HUVEC monolayer





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.zip




As_HUsi1.zip dataset




As_HUsi2.zip dataset




As_HUsi3.zip dataset




As_HUsiCtrl.zip dataset




Mia_HUsi1.zip dataset




Mia_HUsi2.zip dataset




Mia_HUsi3.zip dataset




Mia_HUsiCtrl.zip dataset





Reference

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers


Gautier Follain, Sujan Ghimire, Joanna W. Pylvänäinen, Monika Vaitkevičiūtė, Diana Wurzinger, Camilo Guzmán, James RW Conway, Michal Dibus, Sanna Oikari, Kirsi Rilla, Marko Salmi, Johanna Ivaska, Guillaume Jacquemet

bioRxiv 2024.09.30.615654; doi: https://doi.org/10.1101/2024.09.30.615654