This repository contains data related to Veith, Chaigne et al. 2024
JohAn
6c51efa518
Add vibrometry data
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7 months ago | |
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| behavior | 7 months ago | |
| microCT | 7 months ago | |
| vibrometry | 7 months ago | |
| LICENSE | 9 months ago | |
| README.md | 7 months ago | |
| datacite.yml | 7 months ago |
This repository contains data related to the manuscript "The mechanism for directional hearing in fish". Github: https://github.com/danionella/veith_et_al_2024
The behavior folder contains pickled dataframe objects with fish trajectories around playback events. (5s before playback, 7s after playback, 120fps).
65fish_nolla.zip Data on 65 female and male adult Danionella cerebrum without lateral line ablation.74fish_lla.zip Data on 74 female and male adult Danionella cerebrum after lateral line ablation.Load like this (in python):
import pandas as pd
df = pd.read_pickle('65fish_nolla.zip')
To generate paper figures based on this data, see: https://github.com/danionella/veith_et_al_2024/tree/main/figures
The subfolder sleap_model contains the fish skeleton, parameters, and the trained model that was used to track a single Danionella cerebrum in a 336 x 336 pixel recording, spanning a ~ 11 x 11cm field of view.
PMA (phosphomolybdic acid)-stained, adult, male Danionella cerebrum.
Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328.raw
When opening file in ImageJ Fiji, choose 16-bit Unsigned and Little-endian byte order. Opening as virtual stack is recommended. The voxel size is 1.29702 µm.
Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_segmentation.ORSSession
Dragonfly (https://www.theobjects.com/dragonfly) project file, which contains raw data cropped around the inner ear (1224x1224x1645, anchor at 369,246,412), handlabelled planes, interpolated binary ROIs (interpolated by biomedisa, https://biomedisa.info/), and meshgrids derived from these binary ROIs.
Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_meshgrid.blend
This Blender project file contains downsampled meshgrids of segmented inner ear structures and an animation.
coming soon
| datacite.yml | |
|---|---|
| Title | The mechanism for directional hearing in fish |
| Authors |
Veith,Johannes;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany - Institute for Biology, Humboldt University, Berlin, Germany
Chaigne,Thomas;Aix Marseille University, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France - Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany Svanidze,Ana;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany Dressler,Lena;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany Hoffmann,Maximilian;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany Gerhardt,Ben;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany Judkewitz,Benjamin;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany |
| Description | We provide trajectory data of directional acoustically evoked startles in adult Danionella cerebrum, Micro CT raw data and segmentation of the Danionella cerebrum hearing apparatus, and laser scanning confocal reflectance vibrometry data of inner ear structures. |
| License | Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) |
| References |
The mechanism for directional hearing in fish [doi:10.xxx/zzzz] (IsSupplementTo)
The mechanism for directional hearing in fish [url:https://github.com/danionella/veith_et_al_2024] (IsReferencedBy) |
| Funding | |
| Keywords |
Neuroscience
Danionella cerebrum Directional Hearing Startle Behavior Inner Ear Anatomy Schuijf Model Neuroethology Particle Motion Vibrometry Fish Hearing |
| Resource Type |
Dataset |