Data/Software for "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse"

Published: 29 Oct 2019 | Version 4 | DOI: 10.17632/v88r5t5myz.4

Description of this data

Contains data and software from the publication: "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse" published in the The Journal of Neuroscience (
The preprint to this data set has been published on bioRxiv (

In this study, we created a helper-dependent adenoviral vector (HdAd) to co-express cytoplasmic EGFP and a genetically encoded peroxidase marker (mito-APEX2) at the calyx of Held, an excellent model for deciphering regulatory mechanisms of presynaptic function.

The calyx of Held, a large glutamatergic presynaptic terminal in the auditory brainstem undergoes developmental changes to support the high action-potential firing rates required for auditory information encoding. In addition, calyx terminals are morphologically diverse which impacts vesicle release properties and synaptic plasticity. Mitochondria influence synaptic plasticity through calcium buffering and are crucial for providing the energy required for synaptic transmission. Therefore, it has been postulated that mitochondrial levels increase during development and contribute to the morphological-functional diversity in the mature calyx. However, the developmental profile of mitochondrial volumes and subsynaptic distribution at the calyx of Held remains unclear. To provide insight on this, we developed a helper-dependent adenoviral vector (HdAd) that expresses the genetically encoded peroxidase marker for mitochondria, mito-APEX2, at the mouse calyx of Held. We developed protocols to detect labeled mitochondria for use with serial block face scanning electron microscopy to carry out semi-automated segmentation of mitochondria, high-throughput whole terminal reconstruction and presynaptic ultrastructure in mice of either sex. Subsequently, we measured mitochondrial volumes and subsynaptic distributions at the immature postnatal day 7 (P7) and the mature (P21) calyx. We found an increase of mitochondria volumes in terminals and axons from P7 to P21 but did not observe differences between stalk and swelling subcompartments in the mature calyx. Based on these findings, we propose that mitochondrial volumes and synaptic localization developmentally increase to support high firing rates required in the initial stages of auditory information processing.

Data are sorted by the figures they appear in. Media (movies and 3D models) and custom-written software are located in separate folders.

Experiment data files

  • Code/software

    custom-written software used for analysis for Matlab (RRID:SCR_001622) and Python (RRID:SCR_008394)

    • Matlab

      Functions used in Matlab 2018a and newer, but should work in older versions as well (>2013b).

      • @HEKA_Importer

        Class to import HEKA Patchmaster files into Matlab. Please see the file description and Readme_HEKA_Importer.txt for further details. This is the version used at the time point of publication, please see for updates.

    • Python

      Functions used in Python 3, not tested for use in Python 2

  • Data sets for Figures

    Data sorted by Figure in which they are displayed. Data are stored as CSV format. Original images are stored as TIFF.

    • Figure 01

      Data for Figure 1: Expression of EGFP-mito-APEX2 at the calyx of Held terminal.

    • Figure 02

      Data for Figure 2: Double labeling of EGFP and mito-APEX2 using a combination of pre-embedding DAB-reaction labeling and post-embedding immunogold labeling.

    • Figure 03

      Data for Figure 3: Expression of mito-APEX2 does not affect synaptic transmission at the calyx of Held-MNTB synapse.

      • raw data

        Raw data files recorded with HEKA Patchmaster. Can be loaded into Patchmaster or imported to Matlab using functions from Data > Code/software > Matlab > @HEKA_Importer.

    • Figure 04

      Data for Figure 4: Mito-APEX2 labeling visualized by SBF-SEM at P7 (A, B) and P21 (C, D, E1) allows for identification of transduced calyx of Held terminals

    • Figure 05

      Data for Figure 5: Large volume reconstructions of mito-APEX2-positive calyx of Held terminals using SBF-SEM at P7 and at P21.

    • Figure 06

      Data for Figure 6: Volumetric reconstructions of mitochondria from the same whole terminals and axons shown in Figure 5 using SBF-SEM at P7 and P21.

    • Figure 07

      Data for Figure 7: Full resolution reconstructions of sub-compartments and mitochondria of calyx of Held terminals at P7 and P21 using SBF-SEM.

    • Figure 08

      Data for Figure 8: Mitochondria and membrane surface details of a segment of mito-APEX2-positive calyx of Held terminal reconstructed at full resolution from a SBF-SEM dataset at P7.

    • Figure 09

      Data for Figure 9: Mito-APEX2 labeling visualized by ssSEM at P7 (A, B) and P21 (C, D, E1) allows for identification of transduced calyx of Held terminals.

    • Figure 10

      Data for Figure 10: Mito-APEX2 labeling visualized by ssSEM at P7 and P21 allows for identification of transduced calyx of Held terminals as well as subsequent 3D synaptic analysis.

  • Movies and 3D models

    Movies and 3D models of reconstructions.

    • 3D models

      3D reconstructions. Stored as *.obj, *.blender (RRID:SCR_008606), or Amira (RRID:SCR_014305) files.

    • Movies

      Movies of 3D reconstructions stored as MP4 format.

Steps to reproduce

All data are stored in CSV-files with periods as decimal point and columns separated by commas. The first line in the CSV file corresponds to the header which identifies the groups.

Related links

This data is associated with the following publication:

Presynaptic Mitochondria Volume and Abundance Increase during Development of a High-Fidelity Synapse

Published in: Journal of Neuroscience

Latest version

  • Version 4


    Published: 2019-10-29

    DOI: 10.17632/v88r5t5myz.4

    Cite this dataset

    Thomas, Connon I.; Keine, Christian; Okayama, Satoko; Satterfield, Rachel; Musgrove, Morgan; Guerrero-Given, Debbie; Kamasawa, Naomi; Young, Jr., Samuel M. (2019), “Data/Software for "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse"”, Mendeley Data, v4


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University of Iowa, Max Planck Florida Institute


Microscopy, Synaptic Physiology, Electron Microscopy, Fluorescence Microscopy, Mitochondrion, Mitochondrial Metabolism, Synapse, Genetic Marker, Fluorescence Labeling, Ultrastructure, Presynaptic Mechanism, Contrast Enhancement, Mitochondrial Function, Light Microscopy, Synaptic Vesicle


CC BY 4.0 Learn more

The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

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You can share, copy and modify this dataset so long as you give appropriate credit, provide a link to the CC BY license, and indicate if changes were made, but you may not do so in a way that suggests the rights holder has endorsed you or your use of the dataset. Note that further permission may be required for any content within the dataset that is identified as belonging to a third party.