tasks.annotation¶
Annotation tasks.
Attributes¶
Classes¶
Collect curated dataset to work with on this phase. |
|
Assign mtypes to morphologies. |
|
Compute hard limits. |
|
Plot the hard limits. |
|
Detect apical point. |
|
Plot apical point. |
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Detect the cut leaves. |
|
Plot the cut leaves. |
Module Contents¶
- tasks.annotation.logger¶
- class tasks.annotation.CollectCurated(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,data_validation_framework.task.ElementValidationTask
Collect curated dataset to work with on this phase.
- class tasks.annotation.MType(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,data_validation_framework.task.ElementValidationTask
Assign mtypes to morphologies.
Currently, we only check if the mtype corresponds to the provided list of regex. If the list of regex is empty, we let all the morphologies pass (equivalent to skip).
If they do not, we invalidate the morphologies.
- mtype_regex¶
- class tasks.annotation.HardLimit(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,data_validation_framework.task.ElementValidationTask
Compute hard limits.
Hard limits are markers used to place morphologies in a circuit. They can be automatically computed as min and max extent of axon and dendrites.
Todo
There can be more such markers, manually placed with
nse-tools/placement-annotator
internal tool.- dendrite_hard_limit¶
Name of the dendrite hard limit annotation
- Type:
- Default value:
L1_hard_limit
- class tasks.annotation.PlotHardLimit(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,SkippableMixin
(),data_validation_framework.task.ElementValidationTask
Plot the hard limits.
Plot hard limits as lines on morphologies with plotly.
- class tasks.annotation.ApicalPoint(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,SkippableMixin
(),data_validation_framework.task.ElementValidationTask
Detect apical point.
For morphologies with apical dendrites we estimate the location of the apical point with the automatic tool
morph_tool.apical_point.apical_point_position()
.
- class tasks.annotation.PlotApicalPoint(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,SkippableMixin
(),data_validation_framework.task.ElementValidationTask
Plot apical point.
Plot apical point as a single scatter point on a morphology with plotly.
- class tasks.annotation.CutLeaves(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,data_validation_framework.task.ElementValidationTask
Detect the cut leaves.
Cut leaves are considered to represent boundaries of slices of in-vitro reconstructions. See
neuror.cut_plane.cut_leaves.find_cut_leaves()
for more details on the algorithm and its parameters.
- class tasks.annotation.PlotCutLeaves(*args, **kwargs)¶
Bases:
morphology_workflows.utils.StrIndexMixin
,SkippableMixin
(),data_validation_framework.task.ElementValidationTask
Plot the cut leaves.
We plot the cut-leaves as scatter markers, as the terminal points on dendrites intersecting the cut plane.