PhD

🧠 Interactive Cell Segmentation with CellSAM

This repository provides an interactive pipeline for threshold-based preprocessing and segmentation of biological images using the CellSAM deep learning framework. The workflow includes image cropping, brightness adjustment, interactive thresholding, segmentation, and exporting results as TIFF masks and Excel summaries.

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📂 Features

• Crop and preprocess PNG images
• Stretch image contrast dynamically
• Interactive threshold slider using ipywidgets
• Deep learning segmentation with CellSAM
• Object counting using connected component labeling
• Export results as .tif masks and Excel .xlsx summary

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CellSAM:

@article{israel2023foundation, title={A Foundation Model for Cell Segmentation}, author={Israel, Uriah and Marks, Markus and Dilip, Rohit and Li, Qilin and Schwartz, Morgan and Pradhan, Elora and Pao, Edward and Li, Shenyi and Pearson-Goulart, Alexander and Perona, Pietro and others}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory Preprints}, doi = {10.1101/2023.11.17.567630}, }

📦 Requirements

Install the required packages:

pip install -r requirements.txt