mcmodels.core.Experiment¶

class mcmodels.core.Experiment(injection_density=None, projection_density=None)[source]¶

Class containing the data from an anterograde injection

Experiment conveniently compiles the relevant information from a given anterograde viral tracing experiment data.

Parameters:	voxel_model_cache : VoxelModelCache object This supplies the interface for pulling experimental data. experiment_id : int AllenSDK id assigned to given experiment

Examples

>>> from mcmodels.core import Experiment, VoxelModelCache
>>> cache = VoxelModelCache()
>>> eid = 100141273
>>> exp = Experiment(voxel_model_cache, eid)
>>> exp.injection_density.shape
(132,80,114)

Attributes:

bilateral_injection: Returns injection hemisphere
centroid: Returns centroid of the injection density.
injection_hemisphere_id: Returns injection hemisphere
injection_volume: Returns total injection volume = sum(injection_density)
normalized_injection_density: Returns injection density normalized to have unit sum.
normalized_projection_density: Returns projection_density normalized by the total injection_density
projection_volume: Returns total projection volume = sum(projection_density)

Methods

`flip`(self)	Reflects experiment along midline.
`from_cache`(cache, experiment_id[, …])	Alternative constructor allowing for pulling grid data.

get_injection
get_projection

__init__(self, injection_density=None, projection_density=None)[source]¶

Methods

`__init__`(self[, injection_density, …])
`flip`(self)	Reflects experiment along midline.
`from_cache`(cache, experiment_id[, …])	Alternative constructor allowing for pulling grid data.
`get_injection`(self[, normalized])
`get_projection`(self[, normalized])

bilateral_injection¶: Returns injection hemisphere

centroid¶: Returns centroid of the injection density.

flip(self)[source]¶

Reflects experiment along midline.

Returns:	self - flipped experiment

classmethod from_cache(cache, experiment_id, data_mask_tolerance=None)[source]¶

Alternative constructor allowing for pulling grid data.

Parameters:

cache : VoxelModelCache or MouseConnectivityCache instance.: Object used to pull grid data.
experiment_id : int: Experiment id of the experiment from which to pull grid data.
data_mask_tolerance : float, optional (default = None): Tolerance with which to mask ‘bad’ data. data_mask array has values on the interval [0,1], where a nonzero element indicates a ‘bad’ voxel. If None is passed, the parameter defaults to DEFAULT_DATA_MASK_TOLERANCE (0.5).

injection_hemisphere_id¶: Returns injection hemisphere

injection_volume¶

normalized_injection_density¶: Returns injection density normalized to have unit sum.

normalized_projection_density¶: Returns projection_density normalized by the total injection_density

projection_volume¶