StarDist_BF_cancer_cell_dataset_10x

<p>This repository includes a StarDist deep learning model and its training dataset designed for segmenting cancer cells perfused over an endothelial cell monolayer captured at 10x magnification. The model was trained on 77 manually annotated images, with the dataset being computationally augmented during training by a factor of 8. The model was trained for 500 epochs and achieved an average F1 Score of 0.968, indicating high accuracy in segmenting cancer cells on endothelial cells.</p> <h3>Specifications</h3> <ul> <li> <p>Model: StarDist for cancer cell segmentation on endothelial cells (10x magnification)</p> </li> <li> <p>Training Dataset:</p> </li> <ul> <li> <p>Number of Images: 77 paired brightfield microscopy images and label masks</p> </li> <li> <p>Augmented Dataset: Computational augmentation by a factor of 8 during training</p> </li> <li> <p>Microscope: Nikon Eclipse Ti2-E, 10x objective</p> </li> <li> <p>Data Type: Brightfield microscopy images with manually segmented masks</p> </li> <li> <p>File Format: TIFF (.tif)</p> </li> <ul> <li> <p>Brightfield Images: 16-bit</p> </li> <li> <p>Masks: 8-bit or 16-bit</p> </li> </ul> <li> <p>Image Size: 1024 x 1022 pixels (pixel size: 1.3148 &mu;m)</p> </li> </ul> <li> <p>Training Parameters:</p> </li> <ul> <li> <p>Epochs: 500</p> </li> <li> <p>Patch Size: 992 x 992 pixels</p> </li> <li> <p>Batch Size: 2</p> </li> </ul> <li> <p>Performance:</p> </li> <ul> <li> <p>Average F1 Score: 0.968</p> </li> <li> <p>Average IoU: 0.882</p> </li> </ul> <li> <p>Model Training: Conducted using ZeroCostDL4Mic (<a href="https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki/Stardist">https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki</a>)</p> </li> </ul> <div> <h3>Reference</h3> <div><strong>Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers</strong></div> </div> <div>Gautier&nbsp;Follain,&nbsp;Sujan&nbsp;Ghimire,&nbsp;Joanna W.&nbsp;Pylv&auml;n&auml;inen,&nbsp;Monika&nbsp;Vaitkevičiūtė,&nbsp;Diana&nbsp;Wurzinger,&nbsp;Camilo&nbsp;Guzm&aacute;n,&nbsp;James RW&nbsp;Conway,&nbsp;Michal&nbsp;Dibus,&nbsp;Sanna&nbsp;Oikari,&nbsp;Kirsi&nbsp;Rilla,&nbsp;Marko&nbsp;Salmi,&nbsp;Johanna&nbsp;Ivaska,&nbsp;Guillaume&nbsp;Jacquemet</div> <div>bioRxiv&nbsp;2024.09.30.615654;&nbsp;doi:&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2024.09.30.615654v1">https://doi.org/10.1101/2024.09.30.615654</a></div>