Educational Resources

Learn spatial biology & digital pathology

Free video tutorials on AI-assisted image analysis, QuPath and open-source tools

Featured tutorial

Integrating AI and pathology: a novel approach to multiplex data segmentation and classification

Overview: How artificial intelligence enhances segmentation and classification of multiplexed imaging data.
Tutorial: A step-by-step guide to applying AI algorithms to multiplexed pathology datasets and classifying complex tissue structures.
Benefits: More accurate, efficient analysis, supporting more precise diagnostics and personalized treatment strategies.

QuPath

Overview: Integrating the Segment Anything Model (SAM) into QuPath for advanced image segmentation.
Tutorial: Installing SAM and using it to segment tissue, nuclei and other structures.
Benefits: Faster workflows, less manual annotation and more accurate segmentation.

Visualization

Overview: Viewing digital pathology in VR with QuPath and an Oculus Rift S headset.
Tutorial: Navigating and interacting with whole-slide images in an immersive environment.
Benefits: A new way for pathologists and researchers to explore complex tissue structures.

Open-source formats

Overview: Converting proprietary microscopy formats into open formats with ChatGPT-generated pyvips scripts.
Tutorial: Prompting for conversion scripts and comparing them with code written by the libvips developers.
Cautions: AI-generated code isn't always correct; human-developed scripts often perform better and expertise still matters.

Image analysis

Overview: Automatically measuring the area covered by mycelium on a Petri dish.
Tutorial: Processing dish images with open-source tools and scripts to measure growth.
Benefits: Fewer manual measurement errors and time saved in fungal growth studies.

Personalized sessions in QuPath, Python and spatial biology workflows, built around your own data.