Source data and analysis code for multi-electrode recordings of auditory midbrain activity in response to µLED-based optogenetic activation of the auditory nerve

Custom-written Matlab code (R2019b) for the analysis and visualization of multi-unit activity recorded via linear 32-electrode-probes in the inferior colliculus of Mongolian gerbils in response to optogenetic stimulation of spiral ganglion neurons via 16-channel, µLED-based optical cochlear implants, as used in Dieter and Klein et al, 2020, EMBO Molecular Medicine. “data_EMM_uLED.zip” contains source data, while “analysis_final.zip” contains the analysis code. Both are accompanied by a read-me file.
Zipped archive with source data (4 GB download).
Zipped archive with Matlab analysis code (3 MB download).

Routines for the analysis of inner hair cell calcium imaging

• Custom-written Igor pro routines for the analysis of depolarization-evoked calcium hotspots in IHCs; as used in Jean et al., 2020.
  Zipped archive with Igor pro scripts.
  For questions, please contact Philippe Jean.
  

Supplementary information for "Mapping developmental maturation of inner hair cell ribbon synapses in the apical mouse cochlea" by Michanski et al., PNAS

• SI Appendix Movie S1: FIB-SEM visualization of the basolateral compartment of a P15 inner hair cell (MP4 video).
  Movie scanning through a representative FIB-SEM z-stack of a P15 IHC, showing 3D reconstruction of the basolateral IHC contour, part of the nucleus, mitochondria, innervating nerve fibers, synaptic ribbons and their corresponding SVs. The movie starts at the nuclear region and extends towards the base of the cochlear IHC.
  
• SI Appendix Movie S2: FIB-SEM z-stack of the supranuclear part of two P9 inner hair cells (MP4 video).
  Movie scanning through a FIB-SEM z-stack of the supranuclear part of two neighboring P9 IHCs, shown in Fig. S7K. No ribbon precursors or ribbons could be observed in this dataset. Scale bar: 5 μm.
  

CalC script for the simulation of AZ Ca²⁺ spread in IHCs

• CalC script for the simulation of AZ Ca²⁺ spread in IHCs, as used in Neef, Urban, Ohn et al., 2018.
  Zipped archive with script and Ca²⁺ influx tables
  For questions, please contact Jakob Neef.

Routines for the analysis of whole-cell capacitance measurements

• Custom-written Igor pro routines for the analysis of depolarization-evoked capacitance changes from Patch Clamp data (Pulse or Patchmaster format).
  Igor procedure file v. 2.2.4.2, last updated 23.08.2017
  For questions, please contact Jakob Neef.

Modes and Regulation of Endocytic Membrane Retrieval in Mouse Auditory Hair Cells

• Supplementary information for "Modes and Regulation of Endocytic Membrane Retrieval in Mouse Auditory Hair Cells" by Neef et al., J Neurosci 2014

A Probing the functional equivalence of otoferlin and synaptotagmin 1 in exocytosis

• A Probing the functional equivalence of otoferlin and synaptotagmin 1 in exocytosis", by Reisinger et al.,  J. Neuroscience 2011. (AVI format)

Materials for on-cell capacitance measurements (if interested contact Andreas Neef)

• Guide to low noise on-cell capacitance measurements using the EPC-10
• Patchmaster files (for recent files and program version visit the download section at www.heka.com) On Cell CM
• Igor Pro Template for analysis of on-cell lock-in experiments, inlcuding example data Software LockIn Analysis IGOR, PXT format

Materials for ASSR measurements

• Matlab-routine for recording the modulation transfer function and the ASSR threshold detection ASSR-Matlab-routine

Materials for non-stationary fluctuation analysis of whole cell capacitance measurements (if interested contact Andreas Neef)

• Poster presented at the 31^th Goettingen Neurobiology Conference, 2007
  Matlab-routines for importing ASCII-data to extract multiple DC_m-steps per sweep ImportASCII_GetSteps-Matlab-routines
• Matlab-routines for automatic jackknife and bootstrap Jack_and_Boot-Matlab-routines

Material for estimation of synapse distribution in 3D image stacks

• Custom-written matlab routines for the estimation of the cellular synapse distribution in 3D image stacks. Matlab-routines
  For questions, please contact Gerhard Hoch.