Fig. 8: DeepCristae reveals 3D+time cristae morphology during endo/lysosome mitochondria interactions.

a, b RPE1 cells incubated for 4 h with Cell Mask Plasma Membrane (PM) Deep Red (red) were labeled with PKMITO-Orange (green) in the last 15 min. (a-left) A Maximum Intensity Projection (MIP) (20 planes; stack time = 1.86 s/channel, time point T1 out of 60) image acquired with Live-SR microscopy is shown after DeepCristae restoration of the mitochondria (green channel), as well as after denoising (ND-SAFIR) and Richardson-Lucy (RL) deconvolution of the endo/lysosomes (red channel). Colored Insets indicate intracellular locations with dynamic events of interest. (a-right) Thumbnails show selected time points of blue and red zoomed areas, as indicated by insets. They are presented as paired images: before (left panels) and after (right panels) DeepCristae restoration. Both time points (left panels) and time frames in seconds (right panels) are indicated for comparison. Full acquisition video (T1–T60), including the four regions, is provided as Supplementary Movie 3. Scale bars are 5 µm in the full field image and 1 µm in zoomed thumbnails. b Thumbnails show selected time points of a zoomed area, from a different cell than (a), as MIP (14 planes; stack time  = 2.8 s/channel, time points T6, T8 and T9) from an image acquired with Live-SR microscopy after DeepCristae restoration (green channel), as well as after denoising (ND-SAFIR) and RL deconvolution for endo/lysosomes labeling (red channel). It represents a location where mitochondria fission is occurring. Profile lines are indicated in orange in (b) top. The bottom plots illustrate the PKMITO-Orange intensity line plot before (orange line) and after DeepCristae restoration (blue line) at the same time points. Scale bar in (b) is 1 µm. c Graphs measuring the “peak-to-peak” intervals between cristae in DeepCristae restored images, measured before, during and after fission. Measurements were first taken from 21 distinct time series, in a blinded manner (black circles; number of peak-to-peak intervals (N) are indicated in (d)), and then where endo/lysosomes contacts with mitochondria occur in the same series (13 of 21 distinct time series; red circles). Error bars indicate mean ± standard deviation (SD). d Statistics table for cristae intervals measurements, including mean, standard deviation (SD), and significance levels using Student’s and Fisher’s tests. Note that a rescaling factor of 2.6 was applied to raw Live-SR data prior to DeepCristae restoration. This is done to comply with the usage conditions of DeepCristae (see Results, “Robustness of DeepCristae with respect to noise, blur and mitochondria scale in the low-resolution images”).