In one mouse visual cortex volume, mitochondria of layer 2/3 pyramidal cells followed dendrite caliber, synapse density, depth and a stable cell trait; in vivo activity explained little

Question: do layer 2/3 pyramidal cells that are more active in vivo have more mitochondria? Data: one public mouse V1 EM volume (MICrONS Layer 2/3, pinky100 v185; Turner et al. 2022) with 2.41 million mitochondria, skeletons of 363 pyramidal cells and two-photon calcium traces of 127 of them. Method: we cut dendrites into 10 µm segments and modelled log mitochondria volume per µm from diameter, input synapse density and path distance. A cell's 'excess' is the mean residual of its segments. We related excess to the inferred calcium event rate with Spearman partial correlations, permutations and bootstraps over cells. Two tests were preregistered. Results: in 37,463 basal segments, mitochondria per µm rose with diameter (log-log slope 0.95) and by 24% per added synapse per µm (R² 0.37). The excess was a stable whole-cell trait: split-half r 0.83; the same cells had more mitochondria in apical dendrites (ρ 0.61), soma (0.41) and axon (0.43); deeper cells had more (0.48). Within imaging scans, activity followed the excess only weakly: ρ +0.19 (95% CI 0.00 to 0.35), positive in all 5 scans, pooled +0.20 (0.01 to 0.37); 1 SD of activity matched 1.8% more mitochondria while cells differed by 11.6% (SD). With segment position in the model, ρ was +0.14 (-0.03 to 0.32). The preregistered basal test gave partial ρ +0.24 (Holm p 0.014) but needed caliber and scan covariates (raw ρ -0.04); somatic mitochondria per nucleus volume did not follow activity (ρ +0.01). By contrast, fast-spiking basket and chandelier cells had 2.3-5.1 times the perisomatic mitochondria per nucleus volume of pyramidal cells. Limitations: one animal and 127 imaged cells; calcium rates are in noise units, are comparable only within a scan, and are not firing rates; activity was recorded before fixation; skeleton diameters are noisy; the segment excess and within-scan tests were not preregistered. The package has code, derived tables, figures and a preregistration file.

mitochondria · connectomics · MICrONS · electron microscopy · calcium imaging · structure and function · pyramidal cell · layer 2/3 · mouse visual cortex · dendrite caliber · synapse density · energy budget · basket cell · chandelier cell · cortical depth · preregistration