StarDist_BF_Monocytes_dataset

This repository includes a StarDist deep learning model and its training and validation datasets for detecting mononucleated cells perfused over an endothelial cell monolayer. The model was trained on 27 manually annotated images and achieved an average F1 Score of 0.941. The dataset and model are helpful for biomedical research, especially in studying interactions between mononucleated and endothelial cells.

Specifications

• Model: StarDist for mononucleated cell detection on endothelial cells

• Training Dataset:

• Number of Images: 27 paired brightfield microscopy images and label masks

• Microscope: Nikon Eclipse Ti2-E, 20x objective

• Data Type: Brightfield microscopy images with manually segmented masks

• File Format: TIFF (.tif)

• Brightfield Images: 16-bit

• Masks: 8-bit

• Image Size: 1024 x 1022 pixels (Pixel size: 650 nm)

• Training Parameters:

• Epochs: 400

• Patch Size: 992 x 992 pixels

• Batch Size: 2

• Performance:

• Average F1 Score: 0.941

• Average IoU: 0.831

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

Reference