Stardist_MiaPaCa2_from_CD44

This repository contains a StarDist deep learning model designed for segmenting MiaPaCa2 cells from the CD44 channel in fluorescence microscopy images. The model is capable of accurately segmenting individual MiaPaCa2 cells while excluding HUVECs. Trained on a small dataset, the model achieved an Intersection over Union (IoU) score of 0.884 and an F1 Score of 0.950, indicating high precision in cell segmentation.

Specifications





Model: StarDist for segmenting MiaPaCa2 cells from the CD44 fluorescence channel




Training Dataset:






Number of Images: 8 paired fluorescence microscopy images and label masks




Microscope: Spinning disk confocal microscope (3i CSU-W1) with a 20x objective, NA 0.8




Data Type: Fluorescence microscopy images of the CD44 channel, obtained after immunofluorescence staining with primary and secondary antibodies and manually segmented masks




File Format: TIFF (.tif)






Fluorescence Images: 16-bit




Masks: 8-bit





Image Size: 920 x 920 pixels (Pixel size: 0.6337 x 0.6337 µm²)





Model Capabilities:






Segment MiaPaCa2 Cells: Accurately detects individual MiaPaCa2 cells while ignoring HUVECs




Measure CD44 Intensity: Allows for the measurement of CD44 intensity around MiaPaCa2 cells, specifically from the CD44 channel





Performance:






Average IoU: 0.884




Average F1 Score: 0.950





Model Training: Conducted using ZeroCostDL4Mic (https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki)





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