VisCy 0.2.0

VisCy 0.2.0 adds the following features:

• Application scripts for single-cell infection classification through semantic segmentation
• Tutorial notebook that demonstrates the virtual staining pipeline
• Test time augmentations in the virtual staining prediction writer
• (Alpha) Experimental support for single-cell phenotyping through contrastive learning

This release maintains compatibility with the virtual staining model weights from the v0.1.0 release (download link).

What's Changed

• Update dataset URL for demos by @ziw-liu in #103
• Bump lightning and matplotlib by @ziw-liu in #105
• Cellular infection phenotyping using annotated viral sensor data & label-free images by @Soorya19Pradeep in #70
• Pin numpy due to MONAI bug by @ziw-liu in #111
• Updating demo notebook for training by @edyoshikun in #100
• Test time augmentations by @edyoshikun in #91
• Update demo setup script by @ziw-liu in #112
• Single-cell phenotyping with contrastive learning by @ziw-liu in #113
• Migrate from wandb to tensorboard by @ziw-liu in #122
• Adding link to demos and library of VS models wiki by @edyoshikun in #119
• Tune augmentations with CLI and config for contrastive models by @ziw-liu in #126
• DLMBL 2024 notebook by @edyoshikun in #114

New Contributors

• @Soorya19Pradeep made their first contribution in #70

Full Changelog: v0.1.1...v0.2.0