Stytra
A modular package to control stimulation and track behavior in zebrafish experiments.
If you are using Stytra for your own research, please cite us!
Stytra is divided into independent modules which can be assembled depending on the experimental requirements. For a complete description, look at the full documentation.
Instructions to create your first experiment in Stytra and usage examples can be found in the example gallery.
Quick installation guide
Stytra relies on opencv for some of its fish tracking functions. If you don't have it installed, open the Anaconda prompt and type:
pip install opencv-python
If you are using Windows, git (used for tracking software versions) might not be installed. Git can also be easily installed with conda:
conda install git
This should be everything you need to make ready before installing stytra.
> PyQt5 is not listed as an explicit requirement because it should come with the Anaconda package. If you are not using Anaconda, make sure you have it installed and updated before installing Stytra!
The simplest way to install Stytra is with pip:
pip install stytra
You can verify the installation by running one of the examples in stytra examples folder. To run a simple looming stimulus experiment, you can type:
python -m stytra.examples.looming_exp
If the GUI opens correctly and pressing the play button starts the stimulus: congratulations, installation was successful! If it crashes, check if you have all dependencies correctly installed. If it still does not work, open an issue on the Stytra github page.
Editable installation
On the other hand, if you want to modify the internals of stytra or use the unreleased features, clone or download stytra from github and install it with:
pip install path_to_stytra/stytra
If you want to be able to change the stytra code and use the changed version, install using the -e argument:
pip install -e path_to_stytra/stytra
Now you can have a look at the stytra example gallery, or you can start configuring a computer for Stytra experiments. In the second case, you might want to have a look at the camera APIs section below first.
Note
Stytra might raise an error after quitting because of a bug in the current version of pyqtgraph (a package we are using for online plotting). If you are annoyed by the error messages when closing the program you can install the develop version of pyqtgraph from their github repository. The problem will be resolved once the next pyqtgraph version is released.
For further details on the installation please consult the relative documentation page.
