Open Laboratory Notebook

Scientific blogging as open laboratory notebook

This is a way for me to post regularly about the process of my research without having to rely on positive results to tell a story. I will try to share concise how-to guides (some more conceptual and others more technical) about what I do, directly and indirectly, during my research. In short, I will try to compile short and readable stories about actual notes in my laboratory notebook. These posts may include seminar notes, open source code and statistical analysis, as well as just anything I might have deemed interesting at any point.

Sure, you can just wait a while and then check my publications, but here you may find some interesting methods that never made it to a final publication, some insights into the behind the scenes process towards that specific publication, as well as (let’s not jinx it) some negative results. Please get in touch if you are looking for details, I would love to discuss any of this.

A small step towards open science:

Software - PigeonSuperModel

The Pigeon Super Model is an open source implementation of multiple pre-trained deep-learning models for markerless pose tracking in pigeons.

Software - syncFLIR

SyncFLIR is a repository with code and instructions to build a synchronized multi-view video recording setup using computer vision cameras from FLIR on Windows.

S112726 Computational Ethology - Project Seminar in Biopsychology

What is behavior, and how can we measure it?

S118924 Tracking Animal Behavior – Block Seminar

How new advances in computer vision allow us to measure animal behavior.

Refining your DeepLabCut Model – Learning from Mistakes

How to re-train your old model with new data using jupyter notebooks.

Training your first DeepLabCut Model – A step by step example

How to start your first DLC project using jupyter notebooks and google colab.

How to keep your Python code tidy with these 4 easy tips

Define functions, classes, modules and config files to upgrade your workflow in python.

Installing DeepLabCut - A three step guide

Getting started with DeepLabCut for markerless tracking.

A quick machine learning guide to analyze facial expressions

Upgrade your next zoom meeting with some facial expression analysis using unsupervised machine learning.