Imaging: Installation

Step by step installation (some optional and windows only):

  • Download github desktop and

  • Clone this repository

  • Clone Suite2P python into helpers/suite2p-python (it is also possible to pip install, but chose this way to get most recent updates/bugfixes more directly)

  • Optional: Clone rastermap into helpers/rastermap

  • Mount file servers and make sure entries for shares are correct in network_drives.cfg. Important Make sure no trailing slashes are in the drive configuration. Meaning: Do not write F:/, but F:

  • In network_drives.cfg also edit the section [suite2yops] if you want to run suite2p python locally (it specifies a local “fast” disk for processing suite2p python jobs - see network_drives.sample)

  • copy the auth.sample file and rename to auth.cfg. Edit section [dj_auth] and if you want slack interaction to work also [slack_auth]. If you do not have a any slack API token do not delete that section but fill it with something.

Windows specific

  • Install git (windows)

  • Install miniconda3

  • conda create -n analysis python=3.6 - will create a python3.6 environment called analysis

  • activate environment with activate analysis

Ubuntu specific

  • pip: sudo apt-get install python3-pip

  • python3.6: sudo apt-get install python3.6-dev

    • find out where python3.6 was installed: which python3.6. This path will be inserted in the virtualenv command below.

  • virtualenv: sudo pip3 install virtualenv

  • virtualenv -p /usr/bin/python3.6 dj36 - will create a python3.6 environment called dj36 (can be called analysis as well of course). /usr/bin/python3.6 refers to the path that was found above when running which python3.6.

  • activate environment with source dj36/bin/activate (or whatever you called your environment)

Common

  • Change into the dj-moser-imaging folder and pip install -r requirements.txt

    • > February 2020: The following requirements text files work well on MAC and WINDOWS:

      • MacOS: requirements_horst_11022020.txt

      • Windows10: requirements_torstl_11022020.txt

  • pip install datajoint==0.12.4 (newer versions should be safe to install but not are not tested)

  • Install scanreader package pip install git+https://github.com/atlab/scanreader.git

  • Install opexebo pip install git+https://github.com/kavli-ntnu/opexebo.git@v0.4.2. If this runs into an error on Windows, follow these instructions to download/install Microsoft Build Tools 2019 from Microsoft

  • Create the folder log inside dj-moser-imaging if it does not exist

For using helper notebooks

  • pip install tabulate

For using session viewer GUI

  • pip install --pre "pyqtgraph>0.10" Careful: Pyqtgraph requires PyQt5==5.14 or older. If newer versions are installed you are running the risk of not being able to click buttons.

Additional packages:

  • To use the notebooks, install jupyter lab

    • pip install jupyter_contrib_nbextensions

    • Install jupyterlab ipywidgets as described on https://ipywidgets.readthedocs.io/en/latest/user_install.html

  • Install Graphviz to visualize the tree (ERD). Be sure it is accessible from your path. For example, you can call gvpr and be sure you get some kind of output and not a ‘program not found’ notice.