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 current directory when launching python can hold all the specifics needed to connect to a database. This can include different directories for different pipelines. If only the Spyglass base is specified, other subfolder names are assumed from defaults. See dj_local_conf_example.json for the full set of options. This example 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.

Note that raw and analysis folder locations should be specified under both stores and custom sections of the config file. The stores section is used by DataJoint to store the location of files referenced in database, while the custom section is used by Spyglass. Spyglass will check that these sections match on startup.

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 unix settings file (e.g., .bashrc or .bash_profile) in your home directory.

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).

Subfolders¶

If subfolders do not exist, they will be created automatically. If unspecified by either method above, they will be assumed as recording, sorting, video, etc. subfolders relative to the base path.

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, see dj_local_conf_example.json or set the following variables in your unix settings file (e.g., .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.

from spyglass.common import Nwbfile

Nwbfile()