bio-image-analysis

A repository showcasing a Python workflow for image processing, cell segmentation and downstream image analysis. Image stitching and alignment across rounds also implemented.

Software

General Image Analysis

• Napari
• Python Imaging Library
• OpenCV
• Scikit-image

Image Processing and Segmentation

• Cellpose

Analysis

• Scikit-Learn
• Scipy

Visualization

• Matplotlib
• Seaborn

General use

• Numpy
• Pandas

Data

• JUMP Cell Painting Consortium Data
• Tumor Sample 20X Tissue Data

Check out the workflows!