README.md 2.1 KB
The mechanism for directional hearing in fish
This repository contains data related to the manuscript "The mechanism for directional hearing in fish". Github: https://github.com/danionella/veith_et_al_2024
Behavior data
The behavior folder contains pickled dataframe objects with fish trajectories around playback events. (5s before playback, 7s after playback, 120fps).
65fish_nolla.zipData on 65 female and male adult Danionella cerebrum without lateral line ablation.74fish_lla.zipData 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
coming soon