ibl_alignment_gui.handlers.alignment_handler

Classes

AlignmentHandler	Handles the alignment of electrophysiology data to histology data.
CircularIndexTracker	A class to manage circular buffer indexing.

class ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler(xyz_picks, chn_depths, brain_atlas)

Bases: object

Handles the alignment of electrophysiology data to histology data.

The location of the electrodes along the probe trajectory are adjusted according user defined reference lines that are placed on the electrophysiology (feature) and histology (track) data. Uses a circular buffer to keep a history of the alignment steps the user performs to adjust the locations of the electrodes in the brain to match the observed features in th ephys data.

Parameters:

• xyz_picks (np.ndarray) – An array of xyz coordinates in 3D space that define the trajectory of the probe through the brain. The most ventral point defines the initial estimate of the probe tip.

• chn_depths (np.ndarray) – An array containing the depths of the recording channels along the probe.

• brain_atlas (AllenAtlas) – An AllenAtlas object containing a volume to do a lookup between xyz coordinates and brain region.

buffer

Circular buffer to store and manage multiple alignments steps.

Type:

CircularIndexTracker

brain_atlas

An AllenAtlas object

Type:

AllenAtlas

ephysalign

An EphysAlignment object used to perform alignment logic

Type:

EphysAlignment

hist_mapping

Defines histology mapping mode, e.g. ‘Allen’

Type:

str

tracks

A list of arrays, each containing the position of the track reference lines along the probe at a specific alignment step

Type:

list

features

A list of arrays, each containing the position of the feature reference lines along the probe at a specific alignment step

Type:

list

property current_idx

See CircularIndexTracker.current_idx() for details.

property feature: ndarray

Feature array at the current index of the circular buffer.

Returns:

An array of positions of the feature reference lines for the current index

Return type:

np.ndarray

get_scaled_histology()

Compute the brain regions along the probe track using the current alignment.

Return type:

tuple[Bunch, Bunch, Bunch]

Returns:

• hist_data (Bunch) – Scaled histology regions and axis labels for the current track.

• hist_data_ref (Bunch) – Reference histology data for comparison.

• scale_data (Bunch) – Scaling factors applied to the histology regions.

property idx: int

The current index in the circular buffer.

Returns:

The current index

Return type:

int

property idx_prev: int

The previous index in the circular buffer.

Returns:

The previous index

Return type:

int

next_idx()

See CircularIndexTracker.next_idx() for details.

Return type:

bool

offset_hist_data(offset)

Apply an offset to the brain regions along the probe track.

Adds the new alignment state into next buffer index of the feature and track arrays.

Parameters:

offset (float) – Offset value to apply to the track alignment.

Return type:

None

prev_idx()

See CircularIndexTracker.prev_idx() for details.

Return type:

bool

reset_features_and_tracks()

Reset features and tracks to their initial alignment state.

Return type:

None

scale_hist_data(line_track, line_feature, extend_feature=1, lin_fit=True)

Scale brain regions along the probe track.

Scales based on location of the user chosen track and feature reference lines. Adds the new alignment state into next buffer index of the feature and track arrays.

Parameters:

• line_track (np.ndarray) – An array of positions of the track reference lines

• line_feature (np.ndarray) – An array of positions of the feature reference lines

• extend_feature (int, optional) – Factor for extending the feature alignment beyond original extremes.

• lin_fit (bool, optional) – Whether to apply linear fitting to adjust extremes. Only applied when number of fit lines >= 5

Return type:

None

set_init_feature_track(feature=None, track=None)

Set the initial feature and track values for the current buffer index.

Parameters:

• feature (np.ndarray, optional) – Initial feature alignment.

• track (np.ndarray, optional) – Initial track alignment.

Return type:

None

property total_idx: int

See CircularIndexTracker.total_idx() for details.

property track

Track array at the current index of the circular buffer.

Returns:

An array of positions of the track reference lines for the current index

Return type:

np.ndarray

property track_lines: list[ndarray]

Return the perpendicular vectors (lines) at the position of each track reference line.

Estimates using the values stored at the current index of the circular buffer.

Returns:

List of arrays containing points defining perpendicular vector at each track reference line

Return type:

list of np.ndarray

property xyz_channels: ndarray

Return xyz channel locations estimated using the fit from the track and feature arrays.

Estimates using the values stored at the current index of the circular buffer.

Returns:

xyz positions of channels in 3D space

Return type:

np.ndarray

property xyz_samples: ndarray

Return the xyz coordinates along the probe trajectory.

The coordinates are extended to the full extent of the Atlas volume sampled at 10 um intervals.

Returns:

xyz positions of samples in 3D space

Return type:

np.ndarray

property xyz_track: ndarray

Return the xyz coordinates along the probe trajectory.

The coordinates are extended to the top and bottom of the brain surface.

Returns:

xyz positions of trajctory in 3D space

Return type:

np.ndarray

class ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker(max_idx)

Bases: object

A class to manage circular buffer indexing.

Parameters:

max_idx (int) – Size of the circular buffer.

max_idx

Size of the circular buffer.

Type:

int

current_idx

The current index in logical (non-wrapped) space.

Type:

int

total_idx

The highest index filled so far in logical space.

Type:

int

last_idx

The last recorded total index.

Type:

int

diff_idx

Offset between current index and last index used in reset logic.

Type:

int

idx

The wrapped index used in the circular buffer.

Type:

int

idx_prev

The previous wrapped index.

Type:

int

next_idx()

Move to the next index in the buffer.

If no further index is available, remain at current index.

Return type:

bool

Returns: bool

Whether the tracker moved to the next index.

next_idx_to_fill()

Advance to the next index.

If the next index doesn’t exist create it.

Return type:

None

prev_idx()

Move to the previous index in the buffer.

If no previous index is available, remain at current index.

Return type:

bool

Returns: bool

Whether the tracker moved to the previous index.

reset_idx()

Reset the index.

Return type:

None