Decomposing scanner batch effects and their impact on pathology foundation models
Jonghyun Lee, Lina Takemaru, Yutong Zhu, William Sullivan, Matthew Lee, Angela Ge, Portia A. Kreiger, Amy E. Baxter, Zhi Huang, Dokyoon Kim, Derek A. Oldridge
This study decomposes scanner batch effects in pathology foundation models and shows that image corrections based on measured properties improve alignment but do not fully match model representations.
bioRxiv · Oct 14, 2026 · PreprintBioinformatics