Veith_et_al_2024/README.md

The mechanism for directional hearing in fish

• Here you can find the paper.
  
• Github is your entry point for code.
  
• Click here for an interactive online viewer of hearing apparatus anatomy (also on MorphoSource)

This repository contains data related to the manuscript:

Behavior data

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.

Micro CT data

PMA (phosphomolybdic acid)-stained, adult, male Danionella cerebrum.

Raw data

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.

Segmentation (DragonFly)

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.

Meshgrids (Blender)

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.

Vibrometry data

The vibrometry folder contains the reflectance confocal microscope data of auditory structures of two adult male Danionella cerebrum during sound playback. The Matlab code on https://github.com/danionella/veith_et_al_2024/tree/main/figure_3 produces the motion phase maps presented in Fig. 3 and Extended Data Fig. 11 from these data.