Installation

• Install conda if you do not have it. We recommend miniforge.

Python packages

Create conda environment, activate the environment and install the remaining pip packages:

mamba create python=3.10 numpy scipy h5py opencv pandas pyzmq gevent future pillow msgpack-python pyyaml pyserial ipython pip git defopt flammkuchen msgpack-numpy rich fabric psutil pydaqmx pyqtgraph qtpy pyside6 zarr -c conda-forge -n etho -y
conda activate etho
pip install git+https://github.com/postpop/zerorpc-python git+https://github.com/janclemenslab/etho --no-deps

Modify versions if:

• on the rpi PC: install pandas=0.23 and python=3.7

• you want to use the old flycapture SDK (required for some older FLIR/PointGrey cameras), install python=3.6

Initialize the configuration and test

Activate the environment and initialize hte config files and folders:

conda activate etho
etho init

This will create the ~/data folder for storing all data and the ~/ethoconfig folder with:

• ethoconfig.yml with the default configuration

• playlists folder with stimulation playlists

• protocol folder with experimental protocols

• stim folder for wav files

Start the GUI in the activate etho environment with etho gui.

Optional packages (hardware, software)

• For saving videos using vidread: pip install vidgear[core]

• ximea cameras: driver and python package from ximea

• Spinnaker (FLIR cameras) cameras: driver and python package from FLIR

• flycapture (old FLIR/PointGrey cameras) cameras: driver and python package from FLIR (only works with python 3.6)

• Basler pylon:

  • drivers: pylon

  • python: pypylon pip install pypylon

• ni daqmx driver:

  • drivers: NI daqmx

  • python package pydaqmx is installed by default

• hamamatsu DCAM (e.g. Orca Flash CMOS):

  • driver: DCAM driver

  • python: conda install -c conda-forge pylablib, pylab

• lighcrafter stuff:

  • TODO

• Raspbery PI

  • gpiozero https://gpiozero.readthedocs.io/en/stable/installing.html

  • picamera should come pre-installed in raspbian https://picamera.readthedocs.io/en/latest/install.html: sudo pip install "picamera[array]"

  • soundboard

  • Temperature and humidity sensor adafruit_dht: https://docs.circuitpython.org/projects/dht/en/latest/: pip3 install adafruit-circuitpython-dht, sudo apt-get install libgpiod2