biostudies-literaturePan ZDeutsche ForschungsgemeinschaftBundesministerium für Forschung, Technologie und Raumfahrt57https://www.ebi.ac.uk/biostudies/studies/S-EPMC12594752biostudies-literatureUnknown3(1)Reliable biomedical imaging demands rigorous quality control, yet high-throughput microscopy remains prone to diverse artifacts. We present AutoQC-Bench, a software based on a reconstruction-driven diffusion model flagging abnormal images without prior knowledge, and along with a benchmark of 8000 images capturing common quality issues. The software outperforms existing methods, generalizes across modalities, and supports large-scale bioimaging studies. The software and benchmark are openly shared to advance robust microscopy quality control.Npj imagingAutoQC-Bench: a diffusion model and benchmark for automatic quality control in high-throughput microscopy.PMC12594752CRC TRR332161L0272528777169GU 769/10-1Pan ZChen JNagel DSonneck JHasenberg AGunzer MShi YfalseAutoQC-Bench: a diffusion model and benchmark for automatic quality control in high-throughput microscopy.Reliable biomedical imaging demands rigorous quality control, yet high-throughput microscopy remains prone to diverse artifacts. We present AutoQC-Bench, a software based on a reconstruction-driven diffusion model flagging abnormal images without prior knowledge, and along with a benchmark of 8000 images capturing common quality issues. The software outperforms existing methods, generalizes across modalities, and supports large-scale bioimaging studies. The software and benchmark are openly shared to advance robust microscopy quality control.2025-01-01T00:00:00Z2025 Nov2026-06-05T13:48:09.428Z2026-06-05T03:07:16.967ZS-EPMC125947524120393110.1038/s44303-025-00117-8