morphology_workflows.annotation
¶
Annotation functions.
Module Contents¶
Functions¶
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Assign mtype to morphologies. |
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Find min/max y value of morphology based on neurite_type. |
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Compute hard limits. |
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Plotting placement annotations on morphologies. |
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Find apical point. |
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Plotting apical points on morphologies. |
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Detect cut leaves and save status in df. |
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Plotting cut leaves on morphologies. |
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morphology_workflows.annotation.
logger
¶
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morphology_workflows.annotation.
assign_mtypes
(row, data_dir, mtype_regex=None)¶ Assign mtype to morphologies.
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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
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morphology_workflows.annotation.
SEGMENT_TO_NEURITE
¶
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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.
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morphology_workflows.annotation.
plot_hard_limits
(row, data_dir, with_plotly=True)¶ Plotting placement annotations on morphologies.
TODO: update the ploting without plotly.
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morphology_workflows.annotation.
find_apical_point
(row, data_dir, tuft_percent=20)¶ Find apical point.
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morphology_workflows.annotation.
plot_apical_point
(row, data_dir, with_plotly=True)¶ Plotting apical points on morphologies.
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morphology_workflows.annotation.
detect_cut_leaves
(row, data_dir, bin_width=15, percentile_threshold=75)¶ Detect cut leaves and save status in df.
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morphology_workflows.annotation.
plot_cut_leaves
(row, data_dir, with_plotly=True)¶ Plotting cut leaves on morphologies.