Database Queries (`skeleton_keys.database_queries`)#

These functions are used to interface with the private Allen Institute for Brain Science LIMS database. Users external to the Allen Institute will generally not have a use for these functions.

Queries with default engine#

`database_queries.swc_paths_from_database`(...)	Query the database for SWC paths
`database_queries.pia_wm_soma_from_database`(...)	Get path strings for pia, wm, and soma drawing
`database_queries.shrinkage_factor_from_database`(...)	Determine shrinkage factor for morphology using database information
`database_queries.layer_polygons_from_database`(...)	Obtain layer drawing polygons from database
`database_queries.determine_flip_switch`(...)	Multiplier for reversing slice angle.

Queries with specified engine#

`database_queries.query_for_swc_file`(specimen_id)	Get an SWC file path for a specimen ID using the specified query engine
`database_queries.query_for_image_series_id`(...)	Get an image series ID for a specimen ID using the specified query engine
`database_queries.query_for_cortical_surfaces`(...)	Return the pia and white matter surface drawings for an image series (and optionally specimen ID)
`database_queries.query_for_layer_polygons`(...)	Get all layer polygons for this image series
`database_queries.query_for_soma_center`(...)	Return the soma center coordinates for an image series ID and specimen ID
`database_queries.query_marker_file`(specimen_id)	Return the marker file path for a specimen ID
`database_queries.query_cell_depth`(specimen_id)	Cell depth from surface of slice for specimen
`database_queries.query_pinning_info`([...])	Get the pinned CCF coordinates for a set of projects

Query Engine#

database_queries.default_query_engine()

Get Postgres query engine with environmental variable parameters