DOI: 10.5061/dryad.cjsxksnkb
title: Data from: Diffusive spreading across dynamic mitochondrial network architectures

description: Networks of physical units can vary from a stationary set of
 spatially-embedded links to a collection of mobile agents that undergo
 transient social interactions. In living cells, mitochondria form
 architectures that span across these regimes, transitioning between
 fragmented, partly connected, and highly fused structures depending on
 cell type and state. Diffusive transport of biomolecular components
 through these networks limits the heterogeneity of the mitochondrial
 population. Here we address the connection between dynamic network
 architecture and the rate of diffusive mixing through simulations and
 analytic models that incorporate fusion, fission, and rearrangement. We
 find that the material delivered from a source to the rest of the network
 depends on the network dimensionality and a balance of competing
 timescales for encounter, fusion, and diffusive dispersion. We extract
 morphological and dynamic parameters for mitochondrial networks in three
 human cell lines, demonstrating that different cells span across both the
 physical and social network regimes. Mixing in mitochondrial networks is
 shown to be limited by material transport through connected tubules for
 slowly-diffusing particles and by inter-mitochondrial encounter rates for
 rapidly diffusing ones. These results provide a quantitative basis for
 predicting the homogenization of proteins, lipids, ions, or genetic
 material through the mitochondrial population. The general principles
 identified in this work capture diffusive spreading through both social
 and physical networks, unifying a continuum of spatial network
 architectures. These data comprise Airyscan fluorescence micrographs of
 mitochondrial network dynamics in human fibroblast, osteosarcoma, and
 neuroblastoma cells labeled with Mitotracker dye and SYBR Gold, and
 accompanying capture metadata.
description: # Data from: Diffusive spreading across dynamic mitochondrial network
 architectures Dataset DOI:
 [10.5061/dryad.cjsxksnkb](10.5061/dryad.cjsxksnkb) ## Description of the
 dataset #### Dataset Overview For a comprehensive overview and the
 methodology used to generate and process all the data in this repository,
 please see the corresponding preprint
 at [https://arxiv.org/abs/2506.05643](https://arxiv.org/abs/2506.05643).
 ## Notes for Files ### Microscopy and Image Acquisition All images were
 acquired using a Zeiss LSM 980 with Airyscan 2 laser scanning confocal
 microscope, equipped with 405-, 488-, 561-, and 639-nm laser lines and
 Fast Airyscan detector array. Images were acquired using an inverted
 63×/1.4 numerical aperture oil objective. All live imaging was done in a
 humidified chamber at 37°C and in the presence of 5% CO2. Airyscan
 processing was performed using Zeiss ZEN Blue software version 3.7 (Carl
 Zeiss). ### *Holt_et_al_live_imaging.zip* The compressed master directory
 contains 3 sub-directories corresponding to the three cell types imaged
 for the study, including all time-lapse microscopy analyzed and
 representative image shown in the main figures. ### File Names File names
 follow the pattern: `(celltype)_(fluorescent protein or dye(s))_(passage
 number).ome.tiff` Movie file abbreviations: pN: where N equals passage
 number of cell culture at time of image acquisition mtdr: MitoTracker Deep
 Red (Thermo Fisher Scientific Catalog No. M22426) sybr: SYBRGold (Thermo
 Fisher Scientific catalog no. S11494) imr90: Fibroblast (IMR90) sy5y:
 Neuroblastoma (SH-SY5Y) u2os: Osteosarcoma Cas9-expressing (U2OS Cas9) NT:
 no treatment ### File Types * .ome.tiff: Zeiss Airyscan processed
 microscopy time-lapse video. * .txt: plain text file containing image
 metadata. ### Description of Directories and File Structure ```
 FILENAME_Data |- IMR90/ |---MitoTracker_SYBRGold |- Neuroblastoma/
 |---MitoTracker_SYBRGold |---Mito-eGFP |- U2OS/ |---Mito-BFP
 |---MitoTracker ``` ### Sub-directories ``` #### *IMR90*
 |---MitoTracker_SYBRGold ``` This folder contains all 3D live-cell
 fluorescence microscopy timelapse videos of mitochondrial networks in
 fibroblasts (IMR90). Each movie is provided as a .ome.tiff file along with
 a corresponding text file containing acquisition metadata. Images are
 matched to corresponding metadata by a shared capture number in the file
 name. ``` #### *Neuroblastoma* |---MitoTracker_SYBRGold |---Mito-eGFP ```
 This folder contains all 3D live-cell fluorescence microscopy timelapse
 videos of mitochondrial networks in neuroblastoma cells (SH-SY5Y). Each
 movie is provided as a .ome.tiff file along with a corresponding text file
 containing acquisition metadata. Images are matched to corresponding
 metadata by a shared capture number in the file name. ``` #### *U2OS*
 |---Mito-BFP |---MitoTracker ``` This folder contains all 3D live-cell
 fluorescence microscopy timelapse videos of mitochondrial networks in
 osteosarcoma cells (U2OS). Each movie is provided as a .ome.tiff file
 along with a corresponding text file containing acquisition metadata.
 Images are matched to corresponding metadata by a shared capture number in
 the file name. ### Code/Software Airyscan processing was performed using
 Zeiss ZEN Blue software version 3.7 (Carl Zeiss), RRID:SCR_013672.