tasks.circuit¶

Luigi tasks for circuit and atlas processings.

Classes¶

`CreateAtlasLayerAnnotations`	Create the annotation file for layers from an atlas.
`CreateAtlasPlanes`	Create plane cuts of an atlas.
`CreateBoundaryMask`	Create mask at the boundary of the region to prevent placing somata too close to boundary.
`BuildCircuit`	Generate cell positions and me-types from atlas, compositions and taxonomy.
`SliceCircuit`	Create a smaller circuit file for subsampling.

Module Contents¶

class CreateAtlasLayerAnnotations(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create the annotation file for layers from an atlas.

layer_annotations_path¶

Path to save layer annotations constructed from atlas.

Type:: str
Default value:: layer_annotation.nrrd

class CreateAtlasPlanes(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create plane cuts of an atlas.

plane_type¶

Type of planes creation algorithm. It can take the value ‘centerline’, so the center line is computed between first_bound and last_bound with internal algorithm (from atlas-analysis package), or the value ‘aligned’ (warning: experimental) so center line is a straight line, along the centerline_axis.

Type:: str
Choices:: {centerline_curved, centerline_straight, aligned}
Default value:: aligned

plane_count¶

Number of planes to create slices of atlas.

Type:: int
Permitted values:: int in [1, 1000000000.0)
Default value:: 10

slice_thickness¶

Thickness of slices (in micrometer).

Type:: float
Default value:: 100

centerline_first_bound¶

(only for plane_type == centerline) Location of first bound for centerline (in voxcell index).

Type:: list(int)

centerline_last_bound¶

(only for plane_type == centerline) Location of last bound for centerline (in voxcell index).

Type:: list(int)

centerline_axis¶

(only for plane_type = aligned) Axis along which to create planes.

Type:: str
Default value:: 0

atlas_planes_path¶

Path to save atlas planes.

Type:: str
Default value:: atlas_planes

class CreateBoundaryMask(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create mask at the boundary of the region to prevent placing somata too close to boundary.

boundary_thickness¶

Thickness to create a mask to prevent placing cells near boundary, in units of voxel size.

Type:: int
Default value:: 0

mask_path¶

class BuildCircuit(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Generate cell positions and me-types from atlas, compositions and taxonomy.

density_factor¶

The density of positions generated from the atlas.

Type:: float
Permitted values:: float in (0, 1]
Default value:: 0.5

seed¶

Pseudo-random generator seed.

Type:: int
Default value:: 42

mtype_taxonomy_file¶

Filename of taxonomy file to provide to BrainBuilder

Type:: str
Default value:: mtype_taxonomy.tsv

class SliceCircuit(*args, **kwargs)¶

Bases: luigi_tools.task.WorkflowTask

Create a smaller circuit file for subsampling.

mtypes¶

List of mtypes to consider.

Type:: list

sliced_circuit_path¶

Path to save sliced circuit.

Type:: str
Default value:: sliced_circuit_somata.h5

n_cells¶

Number of cells per mtype to consider.

Type:: int
Default value:: 10