Open Science
EDA-Analysis App
The EDA-Analysis App is a MATLAB App that computes EDA results from raw data acquired with Biopac and Brainvision systems using graphical tools. The app has a graphical user interface that allows the user to view and verify the raw data and the results. Furthermore, there are several export options to save the results in different file formats. To facilitate data exchange with other workgroups, the app offers the possibility to export the EDA data in BIDS format.
Here is the link: https://gitlab.ruhr-uni-bochum.de/ikn/eda-analysis
MATLAB Toolbox
The OTBR toolbox helps scientists to take care of their experiments without worrying too much about the technical implementation of the tools. In addition to the help provided by our tools, our toolbox also offers the possibility of graphical representation, which we have realized with the well-known Psychophysics Toolbox. This has the advantage that experienced users are able to use their code for the psychophysics toolbox whereas novices could use our user-friendly functions for graphical requirements. In general, the OTBR Toolbox distinguishes between human experiment mode and animal experiment mode. Of course, the boundaries of these two modes are blurred, but since our toolbox evolved from two different experimental requirements, we decided to stick with it.
Here is the link: https://gitlab.ruhr-uni-bochum.de/ikn/OTBR
Pigeon Brain Atlas
Pigeons are classic animal models for learning, memory, and cognition. The majority of the current understanding about avian neurobiology outside of the domain of the song system has been established using pigeons. Since MRI represents an increasingly relevant tool for comparative neuroscience, a 3-dimensional MRI-based atlas of the pigeon brain becomes essential. Using multiple imaging protocols, we delineated diverse ascending sensory and descending motor systems as well as the hippocampal formation. This pigeon brain atlas can easily be used to determine the stereotactic location of identified neural structures at any angle of the head. In addition, the atlas is useful to find the optimal angle of sectioning for slice experiments, stereotactic injections and electrophysiological recordings. This pigeon brain atlas is freely available for the scientific community.
The atlas and its manual can be freely downloaded and can be interactively explored with MRIcro.
Pigeon Super Model
The PigeonSuperModel is an open source repository of multiple pre-trained deep-learning models for markerless pose tracking in pigeons. We provide pre-trained weights for different ResNet and UNet models to be used in DeepLabCut and SLEAP, as well as a manually labeled dataset with 1151 frames to train and evaluate further models.With this PigeonSuperModel we provide multiple pre-trained neural networks for out-of-the-box video analysis of pigeon behavior. Using a shared PigeonSuperModel across labs, we advocate for a standardized set of markers for pigeon tracking and generalizable models across experiments, animals, and camera views.
Here is the link: https://pigeonsupermodel.com
syncFLIR Video Recording Software
SyncFLIR is a repository with code and instructions to build a synchronized multiview video recording setup using computer vision cameras from FLIR on Windows. Instead of using independent action cameras to record behavioral experiments and painfully trying to synchronize the different video tracks by e.g. hand-clapping cues or blinking LEDs, make your life easier using triggered cameras. Such an array of wired cameras is scalable without considerable extra effort, allowing for synchronized multiview video recording and 3D triangulation. This project will help you solve half the problem, you only need to set it up.
Here is the link: IKN / syncFLIR · GitLab (ruhr-uni-bochum.de)