DOI: 10.5281/zenodo.13643589
title: PDAC cells vs Immune cells perfusion tracking dataset

description: This dataset contains tracking results of PDAC (AsPC1, MiaPaca, and Panc10) and immune cells (Mononucleated cells and neutrophils) perfused on endothelial monolayer under physiological flow speeds and with or without IL-1β treatment. Imaged using brightfield microscopy using a Nikon Eclipse Ti2-E microscope and 20x objective.

Perfused cells from the generated videos were segmented using custom 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). It also contains the segmented images of the endothelial cell-cell junctions and nuclei (Landmark.zip).

Specifications





Sample information






PDAC (AsPC1, MiaPaca, and Panc10) and immune cells (Mononucleated cells and neutrophils) 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). 




Control and IL-1β treated (10 ng/ml for 2 h) 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 






Cancer cells: Linking max distance: 15 px; Gap-closing max distance: 15 px; Gap-closing max frame gap: 2. Track filtering: min number of spots in the tracks 7.74 




Immune cells: Linking max distance: 15 px; Gap-closing max distance: 15 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




Landmark.zip




As_Ctrl.zip




As_IL1b.zip




Mia_IL1b.zip




Mia_Ctrl.zip




P10_ctrl.zip




P10_IL1b.zip




Mon_ctrl.zip




mon_IL1b.zip




Neu_ctrl.zip




neu_IL1b.zip


Cluster_arrest.zip: contains the result of the co-arrest analysis, as shown in the updated paper


 



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