Installation¶

Note: Developers, or those who wish to add features or otherwise work on the codebase should follow the same steps below, but install Spyglass as editable with the -e flag: pip install -e /path/to/spyglass

Basic Installation¶

For basic installation steps, see the Setup notebook 'local installation' section, including python, mamba (for managing a virtual environment), VSCode, Jupyter, and git. This notebook also covers database access.

Additional Packages¶

Some pipelines require installation of additional packages.

The spike sorting pipeline relies on spikeinterface and optionally mountainsort4.

pip install spikeinterface[full,widgets]
pip install mountainsort4

WARNING: If you are on an M1 Mac, you need to install pyfftw via conda BEFORE installing ghostipy:

conda install -c conda-forge pyfftw

The LFP pipeline uses ghostipy:

pip install ghostipy

Database access¶

For basic installation steps, see the Setup notebook 'database connection' section. For additional details, see the DataJoint documentation.

Config¶

Via File (Recommended)¶

A dj_local_conf.json file in your Spyglass directory (or wherever python is launched) can hold all the specifics needed to connect to a database. This can include different directories for different pipelines. If only the base is specified, the subfolder names below are included as defaults.

{
  "custom": {
    "database.prefix": "username_",
    "spyglass_dirs": {
      "base": "/your/base/path",
      "raw": "/your/base/path/raw",
      "analysis": "/your/base/path/analysis",
      "recording": "/your/base/path/recording",
      "spike_sorting_storage": "/your/base/path/spikesorting",
      "waveforms": "/your/base/path/waveforms",
      "temp": "/your/base/path/tmp"
    }
  }
}

dj_local_conf_example.json can be copied and saved as dj_local_conf.json to set the configuration for a given folder. Alternatively, it can be saved as .datajoint_config.json in a user's home directory to be accessed globally. See DataJoint docs for more details.

Via Environment Variables¶

Older versions of Spyglass relied exclusively on environment for config. If spyglass_dirs is not found in the config file, Spyglass will look for environment variables. These can be set either once in a terminal session, or permanently in a .bashrc file.

export SPYGLASS_BASE_DIR="/stelmo/nwb"
export SPYGLASS_RECORDING_DIR="$SPYGLASS_BASE_DIR/recording"
export SPYGLASS_SORTING_DIR="$SPYGLASS_BASE_DIR/sorting"
export SPYGLASS_VIDEO_DIR="$SPYGLASS_BASE_DIR/video"
export SPYGLASS_WAVEFORMS_DIR="$SPYGLASS_BASE_DIR/waveforms"
export SPYGLASS_TEMP_DIR="$SPYGLASS_BASE_DIR/tmp"
export DJ_SUPPORT_FILEPATH_MANAGEMENT="TRUE"

To load variables from a .bashrc file, run source ~/.bashrc in a terminal.

Temporary directory¶

A temporary directory will speed up spike sorting. If unspecified by either method above, it will be assumed as a tmp subfolder relative to the base path. Be sure it has enough free space (ideally at least 500GB).

File manager¶

kachery-cloud is a file manager for Frank Lab collaborators who do not have access to the lab's production database.

To customize kachery file paths, the following can similarly be pasted into your .bashrc. If unspecified, the defaults below are assumed.

export KACHERY_CLOUD_DIR="$SPYGLASS_BASE_DIR/.kachery-cloud"
export KACHERY_TEMP_DIR="$SPYGLASS_BASE_DIR/tmp"

Be sure to load these with source ~/.bashrc to persist changes.

Test connection¶

Finally, open up a python console (e.g., run ipython from terminal) and import spyglass to check that the installation has worked.