MorphoHELM is a new benchmark for Cell Painting morphology representations that tests methods across increasing batch effect levels and finds classic computer vision strategies remain the strongest general-purpose performers.
Cell painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.Nature Protocols, 11(9):1757–1774, August 2016
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DINO-based ViT models pretrained on HPA FOV achieve macro F1 of 0.822 zero-shot and 0.860 after fine-tuning for protein localization on OpenCell, demonstrating effective transfer from SSL pretraining.
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MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays
MorphoHELM is a new benchmark for Cell Painting morphology representations that tests methods across increasing batch effect levels and finds classic computer vision strategies remain the strongest general-purpose performers.
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Using Deep Learning Models Pretrained by Self-Supervised Learning for Protein Localization
DINO-based ViT models pretrained on HPA FOV achieve macro F1 of 0.822 zero-shot and 0.860 after fine-tuning for protein localization on OpenCell, demonstrating effective transfer from SSL pretraining.