allensdk.core.cell_types_cache module¶
- class allensdk.core.cell_types_cache.CellTypesCache(cache=True, manifest_file=None, base_uri=None)[source]¶
Bases:
Cache
Cache class for storing and accessing data from the Cell Types Database. By default, this class will cache any downloaded metadata or files in well known locations defined in a manifest file. This behavior can be disabled.
- Parameters:
- cache: boolean
Whether the class should save results of API queries to locations specified in the manifest file. Queries for files (as opposed to metadata) must have a file location. If caching is disabled, those locations must be specified in the function call (e.g. get_ephys_data(file_name=’file.nwb’)).
- manifest_file: string
File name of the manifest to be read. Default is “cell_types_manifest.json”.
- Attributes:
- api: CellTypesApi instance
The object used for making API queries related to the Cell Types Database
- CELLS_KEY = 'CELLS'¶
- EPHYS_DATA_KEY = 'EPHYS_DATA'¶
- EPHYS_FEATURES_KEY = 'EPHYS_FEATURES'¶
- EPHYS_SWEEPS_KEY = 'EPHYS_SWEEPS'¶
- MANIFEST_VERSION = '1.1'¶
- MARKER_KEY = 'MARKER'¶
- MORPHOLOGY_FEATURES_KEY = 'MORPHOLOGY_FEATURES'¶
- RECONSTRUCTION_KEY = 'RECONSTRUCTION'¶
- build_manifest(file_name)[source]¶
Construct a manifest for this Cache class and save it in a file.
- Parameters:
- file_name: string
File location to save the manifest.
- get_all_features(dataframe=False, require_reconstruction=True)[source]¶
Download morphology and electrophysiology features for all cells and merge them into a single table.
- Parameters:
- dataframe: boolean
Return the output as a Pandas DataFrame. If False, return a list of dictionaries.
- require_reconstruction: boolean
Only return ephys and morphology features for cells that have reconstructions. Default True.
- get_cells(file_name=None, require_morphology=False, require_reconstruction=False, reporter_status=None, species=None, simple=True)[source]¶
Download metadata for all cells in the database and optionally return a subset filtered by whether or not they have a morphology or reconstruction.
- Parameters:
- file_name: string
File name to save/read the cell metadata as JSON. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- require_morphology: boolean
Filter out cells that have no morphological images.
- require_reconstruction: boolean
Filter out cells that have no morphological reconstructions.
- reporter_status: list
Filter for cells that have one or more cell reporter statuses.
- species: list
Filter for cells that belong to one or more species. If None, return all. Must be one of [ CellTypesApi.MOUSE, CellTypesApi.HUMAN ].
- get_ephys_data(specimen_id, file_name=None)[source]¶
Download electrophysiology traces for a single cell in the database.
- Parameters:
- specimen_id: int
The ID of a cell specimen to download.
- file_name: string
File name to save/read the ephys features metadata as CSV. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- Returns:
- NwbDataSet
A class instance with helper methods for retrieving stimulus and response traces out of an NWB file.
- get_ephys_features(dataframe=False, file_name=None)[source]¶
Download electrophysiology features for all cells in the database.
- Parameters:
- file_name: string
File name to save/read the ephys features metadata as CSV. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- dataframe: boolean
Return the output as a Pandas DataFrame. If False, return a list of dictionaries.
- get_ephys_sweeps(specimen_id, file_name=None)[source]¶
Download sweep metadata for a single cell specimen.
- Parameters:
- specimen_id: int
ID of a cell.
- get_morphology_features(dataframe=False, file_name=None)[source]¶
Download morphology features for all cells with reconstructions in the database.
- Parameters:
- file_name: string
File name to save/read the ephys features metadata as CSV. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- dataframe: boolean
Return the output as a Pandas DataFrame. If False, return a list of dictionaries.
- get_reconstruction(specimen_id, file_name=None)[source]¶
Download and open a reconstruction for a single cell in the database.
- Parameters:
- specimen_id: int
The ID of a cell specimen to download.
- file_name: string
File name to save/read the reconstruction SWC. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- Returns:
- Morphology
A class instance with methods for accessing morphology compartments.
- get_reconstruction_markers(specimen_id, file_name=None)[source]¶
Download and open a reconstruction marker file for a single cell in the database.
- Parameters:
- specimen_id: int
The ID of a cell specimen to download.
- file_name: string
File name to save/read the reconstruction marker. If file_name is None, the file_name will be pulled out of the manifest. If caching is disabled, no file will be saved. Default is None.
- Returns:
- Morphology
A class instance with methods for accessing morphology compartments.