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