awakenting/master-thesis

everything related to my master thesis: A neuronal model for visually evoked escape responses in schooling fish

A neuronal model for visually evoked escape responses in schooling fish

This repository contains everything related to my master thesis.

Research questions

1. How does the mauthner circuit produce experimentally observed escape responses when presented with a looming stimulus ?
   • How should the input that arrives at the Mauthner cell look like to create experimentally observed escape responses ?
   • How is this input related to the visual scene that the fish observes ?
2. What happens if we present two simultaneous looming stimuli to a model that can reproduce results for one stimulus ?
3. What happens if we use a model that can reproduce results for one stimulus for fish that move in a school ?
   • Would this induce spontaneous startles in fish ? How many startles would we see in a certain time window ?

Repository structure

• code: all code that is used in this project
• defense_presentation: slides for the master defense
• figures: figures for the manuscript and the slides
• manuscript: the thesis manuscript
• poster: the posters I presented at the DPG Tagung 2018 (link) and the Bernstein Conference (link) in Berlin

Reproducibility

Requirements:

See requirements.txt file.

If you use Anaconda, you can just use the enviroment file to create an environment with all necessary packages. To do so ... (coming soon)

Materials

Cite the code:

Do you want to do the same for your code? See this guide.

Cite the generated data: (from model fitting and collective behavior simulations)

Literature

I collect relevant literature in this spreadsheet. There is also a bibtex file in the "manuscript" folder. The bibtex file is more likely to be up to date. Feel free to add other papers if you think they're relevant, even if you don't have the time to fill all columns. It would be nice if you could put the paper in the correct row according to the last name of the first Author. Also, if you want, you can add your name in the "Contributor" column and I will acknowledge your contribution in the thesis.

Related models

• (coming soon)

TODO

• create conda environment and explain how to install it
• explain how to reproduce results
• add related models
• Optional
  • create graphical abstract
  • create gif abstract

Miscellaneous

Here is an emoji abstract of the thesis:

⚫ 🔜 💥 🐟 ➡️ 🐟 ↪️

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1️⃣ 👀 ➡️ ❓ ➡️ 🐟 ↪️

2️⃣ 🐟 🐟 🐟 🐟 ❓