Installation

Prerequisites

improv depends on certain OS-specific libraries and these can be installed as followed.

Ubuntu

apt-get update
apt-get install -y gcc g++ libgl1 libgl1-mesa-glx libqt5x11extras5

macOS

xcode-select --install

Windows

Please consult installation for Windows.

Installation

1. Install Miniconda (a package manager for Python).

2. Install mamba:

conda install -n base -c conda-forge mamba

1. Install CaImAn.

   git clone https://github.com/pearsonlab/CaImAn/
   cd CaImAn
   git checkout lite
   mamba env create -n improv -f environment.yml
   conda activate improv
   pip install .
   cd ..

2. Install improv (see also Building and Packaging)

   mamba install pyqtgraph
   pip install build 
   git clone https://github.com/pearsonlab/improv
   cd improv
   python -m build 
   pip install -e .

3. Set the environmental variables for proper CaImAn functionality.

   export MKL_NUM_THREADS=1
   export OPENBLAS_NUM_THREADS=1

Note that the environmental variables has to be redefined every time a new shell is started. A more permanent solution would be to include these commands into the .bashrc or .zshrc file so that the variables are automatically redefined.

echo "export MKL_NUM_THREADS=1" >> ~/.bashrc
echo "export OPENBLAS_NUM_THREADS=1" >> ~/.bashrc