allensdk.api.queries.cell_types_api module¶
- class allensdk.api.queries.cell_types_api.CellTypesApi(base_uri=None)[source]¶
Bases:
RmaApi
- HUMAN = 'Homo Sapiens'¶
- MARKER_FILE_TYPE = '3DNeuronMarker'¶
- MOUSE = 'Mus musculus'¶
- NWB_FILE_TYPE = 'NWBDownload'¶
- SWC_FILE_TYPE = '3DNeuronReconstruction'¶
- filter_cells(cells, require_morphology, require_reconstruction, reporter_status, species)[source]¶
Filter a list of cell specimens to those that optionally have morphologies or have morphological reconstructions.
- Parameters:
- cells: list
List of cell metadata dictionaries to be filtered
- 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 a particular cell reporter status
- species: list
Filter for cells that belong to one or more species. If None, return all. Must be one of [ CellTypesApi.MOUSE, CellTypesApi.HUMAN ].
- filter_cells_api(cells, require_morphology=False, require_reconstruction=False, reporter_status=None, species=None, simple=True)[source]¶
- get_cell(id)[source]¶
Query the API for a one cells in the Cell Types Database.
- Returns:
- list
Meta data for one cell.
- get_ephys_sweeps(specimen_id)[source]¶
Query the API for a list of sweeps for a particular cell in the Cell Types Database.
- Parameters:
- specimen_id: int
Specimen ID of a cell.
- Returns:
- list: List of sweep dictionaries belonging to a cell
- get_morphology_features()[source]¶
Query the API for the full table of morphology features for all cells
Notes
by default the tags column is removed because it isn’t useful
- list_cells(id=None, require_morphology=False, require_reconstruction=False, reporter_status=None, species=None)[source]¶
Query the API for a list of all cells in the Cell Types Database.
- Parameters:
- id: int
ID of a cell. If not provided returns all matching cells.
- require_morphology: boolean
Only return cells that have morphology images.
- require_reconstruction: boolean
Only return cells that have morphological reconstructions.
- reporter_status: list
Return cells that have a particular cell reporter status.
- species: list
Filter for cells that belong to one or more species. If None, return all. Must be one of [ CellTypesApi.MOUSE, CellTypesApi.HUMAN ].
- Returns:
- list
Meta data for all cells.
- list_cells_api(id=None, require_morphology=False, require_reconstruction=False, reporter_status=None, species=None)[source]¶
- save_ephys_data(specimen_id, file_name)[source]¶
Save the electrophysology recordings for a cell as an NWB file.
- Parameters:
- specimen_id: int
ID of the specimen, from the Specimens database model in the Allen Institute API.
- file_name: str
Path to save the NWB file.
- save_reconstruction(specimen_id, file_name)[source]¶
Save the morphological reconstruction of a cell as an SWC file.
- Parameters:
- specimen_id: int
ID of the specimen, from the Specimens database model in the Allen Institute API.
- file_name: str
Path to save the SWC file.
- save_reconstruction_markers(specimen_id, file_name)[source]¶
Save the marker file for the morphological reconstruction of a cell. These are comma-delimited files indicating points of interest in a reconstruction (truncation points, early tracing termination, etc).
- Parameters:
- specimen_id: int
ID of the specimen, from the Specimens database model in the Allen Institute API.
- file_name: str
Path to save the marker file.