PDAC cells vs Immune cells perfusion tracking dataset

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 µg/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

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