neuron_morphology.transforms.tilt_correction.compute_tilt_correction
¶
Module Contents¶
Functions¶
get_tilt_correction (morphology: Morphology, soma_voxel: List[int], slice_angle_matrix: float, closest_path) |
Find the tilt angle between the slice plane and the nearest streamline |
find_closest_path (soma_voxel: List[int], ccf_path: Union[str, IO], n_sublists: int = 2) |
Finds closest path to soma_voxel |
determine_slice_flip (morphology: Morphology, soma_marker: Dict, slice_image_flip: bool) |
Determines whether the tilt correction should be positive or negative |
read_soma_marker (marker_path: str) |
|
run_tilt_correction (morphology: Morphology, soma_marker: Dict, ccf_soma_location: Dict, slice_transform: aff.AffineTransform, slice_image_flip: bool, ccf_path: Union[str, IO]) |
|
main () |
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
CCF_SHAPE
= [1320, 800, 1140]¶
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
CCF_RESOLUTION
= 10¶
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
get_tilt_correction
(morphology: Morphology, soma_voxel: List[int], slice_angle_matrix: float, closest_path)¶ Find the tilt angle between the slice plane and the nearest streamline
Parameters: - morphology: Morphology object
- soma_voxel: soma voxel in ccf {‘x’: , ‘y’: , ‘z’: }
- slice_angle_matrix: 4 x 4 affine matrix of the slice plane
relative to ccf
- closest_path: 3 x N array of voxel coordinates in closest streamline,
only first (wm end) and last (pia end) coordinates are used. In future the tilt correction may be refined to use the entire path.
Returns: - tilt angle correction (radians)
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
find_closest_path
(soma_voxel: List[int], ccf_path: Union[str, IO], n_sublists: int = 2)¶ Finds closest path to soma_voxel
Parameters: - soma_voxel: List containing soma voxel ccf coordinates
- ccf_path: str, FilePath, or File-like object openable by H5PY
- n_sublists: will seperate path_ids into n sublists to load in
at a time. Higher values decrease memory usage but increase processing time. n = 1 uses about 16GB
Returns: - closest_path: array of voxel coordinates of the closest streamline
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
determine_slice_flip
(morphology: Morphology, soma_marker: Dict, slice_image_flip: bool)¶ Determines whether the tilt correction should be positive or negative
Parameters: - morphology: Morphology object
- soma_marker: soma marker dictionary from reconstruction marker file
- slice_image_flip: indicates whether the image was flipped relative
to the slice (e.g the z axis of the image is opposite to the z axis in the slice)
Returns: - flip_toggle -1 or 1 to be multiplied against tilt correction
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
read_soma_marker
(marker_path: str)¶
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
run_tilt_correction
(morphology: Morphology, soma_marker: Dict, ccf_soma_location: Dict, slice_transform: aff.AffineTransform, slice_image_flip: bool, ccf_path: Union[str, IO])¶
-
neuron_morphology.transforms.tilt_correction.compute_tilt_correction.
main
()¶