Average membrane thickness varies within subcompartments of the same organelle. (A) OMM distance-based classification automatically segments the IBM (purple), CJ (green), and CB (blue) in surface mesh models. (B) Area-weighted histogram of per-triangle thickness measurements shows variation between different mitochondrial subcompartments. (C) Violin plot of per-tomogram median thickness shows statistically significant variations between mitochondrial subcompartments. IBM: n = 15; CJ: n = 15; CB: n = 15. P values from the Mann–Whitney U test are indicated. **P < 0.01, ****P < 0.001. (D) Tomogram showing rough and smooth ER. Classification based on the presence or absence of bound ribosomes on the ER membrane, respectively. (E) Area-weighted histogram of per-triangle thickness measurement across ER subcompartment. (F) Violin plot of per-tomogram median thickness of each ER subcompartment. Rough ER: n = 7; smooth ER: n = 14. CB, crista bodies; CJ, crista junctions.