outofculture / acq4

Data acquisition for patch clamp ephys / optogenetics / imaging experiments

ACQ4

Neurophysiology acquisition and analysis for Python

http://www.acq4.org

ACQ4 is a platform for data acquisition, management, and analysis in neurophysiology experiments, especially focusing on patch clamp electrophysiology, optogenetics, and related techniques. It is used both as a platform for developing customized data acquisition tools and as an application that handles the most common requirements in whole-cell recording, calcium imaging, and photostimulation.

Requirements

• python 2.7
• PyQt 4.9+
• numpy, scipy
• six
• h5py
• optional:
  • pyopengl
  • pyserial
  • pyparsing 2.0.3 (later versions do not work)
  • pillow

Documentation

http://www.acq4.org/documentation

Support

Post at the mailing list / forum

Installation

The easiest way to get all of the requirements is by installing the Anaconda python distribution plus a few extra packages.

1. Download and install Anaconda or Miniconda for python 2.7 (64-bit recommended)

2. Create a conda environment for acq4 (windows users must do this from the anaconda prompt):

       $ conda config --set restore_free_channel true
       $ conda create --name=acq4 python=2.7 pyqt=4 numpy scipy pyserial pyparsing=2.0.3 pillow h5py
       $ conda activate acq4

3. Clone the ACQ4 source repository (this requires git to be installed):

       $ git clone https://github.com/acq4/acq4.git

4. Install acq4 into your new conda environment:

       $ cd acq4
       $ python setup.py develop

Starting ACQ4

Activate your acq4 conda environment, then start acq4:

       $ conda activate acq4
       $ python -m acq4

This should load the main manager window, from which you can interact with some devices and load modules.