Necessity of microscopy-specific foundation models versus general-purpose SAM3

Determine whether microscopy-specific segmentation foundation models (such as μSAM, PathoSAM, CellPoseSAM, and CellSAM) remain necessary for microscopy instance segmentation or whether the general-purpose model SAM3 can supplant them without domain-specific adaptation.

Background

SAM3 extends SAM with concept-based segmentation (including text and example prompts) and includes some microscopy data in its training, raising the question of whether dedicated microscopy foundation models are still needed.

The authors evaluate SAM3 alongside microscopy-specific models across many datasets, motivating a formal determination of whether general-purpose models can replace domain-specific ones in microscopy.

References

These developments open up the following questions: (ii) Are specific (foundation) models for microscopy segmentation still needed or do general-purpose segmentation models, in particular SAM3, make them obsolete?

— Revisiting foundation models for cell instance segmentation  (2603.17845 - Archit et al., 18 Mar 2026) in Section 1, Introduction