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Microsoft Launches Open-Source GigaTIME to Convert Routine H&E Slides Into Virtual mIF Maps

A Cell paper details training on 40 million cells with validation across Providence plus TCGA cohorts to enable population-scale tumor–immune studies.

Overview

  • GigaTIME is available now as an open-source research tool on Microsoft Foundry Labs and Hugging Face.
  • The model generates single-cell, spatial protein maps from standard H&E slides in seconds, replacing lab mIF workflows that take days and cost thousands per sample.
  • Applied across 14,256 Providence patients, the system produced about 300,000 virtual mIF images spanning 24 cancer types and 306 subtypes.
  • Independent external validation on roughly 10,200 TCGA patients supported the model’s generalizability.
  • Large-scale analyses reported 1,234 significant links between protein activations and clinical attributes, with a 21-channel signature outperforming individual markers like CD3 and CD8 for stratification.