Supervised machine learning versus expert assessment of ultrastructural changes in wild-type and OGT knockout macrophages

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Automated transmission electron microscopy (TEM) generates large datasets that challenge traditional qualitative analysis of cellular ultrastructure. Quantitative assessment of structural differences between different samples remains difficult due to structural variability in thin sections of organelles. Here we applied supervised machine learning (sML) to segment, quantify and compare cellular structures -including nuclei, chromatin, mitochondria, rough endoplasmic reticulum, and endocytic vesicles- in large TEM images of wild-type macrophages versus those with altered cellular physiology due to deficiency in O-GlcNAc Transferase (OGT). sML revealed that OGT knockout macrophages are larger and more oval, with increased euchromatin, nucleoli size, and relative mitochondrial and rER surface areas. Comparison with six TEM experts showed sML provides more objective and sensitive quantification of subtle differences, while expert consensus is only achieved for larger structural variations. These findings demonstrate that sML enhances quantitative TEM analysis and complements human expertise in ultrastructural studies.

Authors 5

1. Thijs van der Meer Aachen Electron Microscopy Facility Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Electron Microscopy Facility, Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands

2. Graham A. Heieis Aachen Department of Parasitology, Leiden University Medical Centre

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Department of Parasitology, Leiden University Medical Centre, Leiden, The Netherlands

3. Bart Everts Aachen Department of Parasitology, Leiden University Medical Centre

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Department of Parasitology, Leiden University Medical Centre, Leiden, The Netherlands

4. Frank G. A. Faas Aachen Electron Microscopy Facility Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Electron Microscopy Facility, Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands

5. Roman I. Koning corresponding Aachen Electron Microscopy Facility Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Electron Microscopy Facility, Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands