morphology_workflows.annotation

Annotation functions.

Module Contents

Functions

assign_mtypes(row, data_dir[, mtype_regex])

Assign mtype to morphologies.

calculate_y_extent(morph, neurite_type)

Find min/max y value of morphology based on neurite_type.

compute_hard_limits(row, data_dir[, skip_axon, ...])

Compute hard limits.

plot_hard_limits(row, data_dir[, with_plotly])

Plotting placement annotations on morphologies.

find_apical_point(row, data_dir[, tuft_percent])

Find apical point.

plot_apical_point(row, data_dir[, with_plotly])

Plotting apical points on morphologies.

detect_cut_leaves(row, data_dir[, bin_width, ...])

Detect cut leaves and save status in df.

plot_cut_leaves(row, data_dir[, with_plotly])

Plotting cut leaves on morphologies.

Attributes

logger

SEGMENT_TO_NEURITE

morphology_workflows.annotation.logger
morphology_workflows.annotation.assign_mtypes(row, data_dir, mtype_regex=None)

Assign mtype to morphologies.

morphology_workflows.annotation.calculate_y_extent(morph, neurite_type)

Find min/max y value of morphology based on neurite_type.

Taken from morphology_repair_workflow.placement_annotations.py

morphology_workflows.annotation.SEGMENT_TO_NEURITE
morphology_workflows.annotation.compute_hard_limits(row, data_dir, skip_axon=False, dendrite_hard_limit='L1_hard_limit', axon_hard_limit='L1_axon_hard_limit')

Compute hard limits.

morphology_workflows.annotation.plot_hard_limits(row, data_dir, with_plotly=True)

Plotting placement annotations on morphologies.

TODO: update the plotting without plotly.

morphology_workflows.annotation.find_apical_point(row, data_dir, tuft_percent=20)

Find apical point.

morphology_workflows.annotation.plot_apical_point(row, data_dir, with_plotly=True)

Plotting apical points on morphologies.

morphology_workflows.annotation.detect_cut_leaves(row, data_dir, bin_width=15, percentile_threshold=75)

Detect cut leaves and save status in df.

morphology_workflows.annotation.plot_cut_leaves(row, data_dir, with_plotly=True)

Plotting cut leaves on morphologies.