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. |
Attributes¶
- 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.