tasks.annotation
¶
Annotation tasks.
Module Contents¶
Classes¶
Collect curated dataset to work with on this phase. |
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Assign mtypes to morphologies. |
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Compute hard limits. |
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Plot the hard limits. |
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Detect apical point. |
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Plot apical point. |
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Detect the cut leaves. |
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Plot the cut leaves. |
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tasks.annotation.
logger
¶
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class
tasks.annotation.
CollectCurated
(*args, **kwargs)¶ Bases:
data_validation_framework.task.ElementValidationTask
Collect curated dataset to work with on this phase.
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class
tasks.annotation.
MType
(*args, **kwargs)¶ Bases:
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
None
, we let all the morphologies pass (equivalent to skip).If they do not, we unvalidate the morphologies.
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mtype_regex
¶
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class
tasks.annotation.
HardLimit
(*args, **kwargs)¶ Bases:
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
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class
tasks.annotation.
PlotHardLimit
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,data_validation_framework.task.ElementValidationTask
Plot the hard limits.
Plot hard limits as lines on morphologies with plotly.
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class
tasks.annotation.
ApicalPoint
(*args, **kwargs)¶ Bases:
data_validation_framework.task.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()
.
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class
tasks.annotation.
PlotApicalPoint
(*args, **kwargs)¶ Bases:
data_validation_framework.task.SkippableMixin()
,data_validation_framework.task.ElementValidationTask
Plot apical point.
Plot apical point as a single scatter point on a morphology with plotly.
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class
tasks.annotation.
CutLeaves
(*args, **kwargs)¶ Bases:
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()
for more details on the algorithm and its parameters.
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class
tasks.annotation.
PlotCutLeaves
(*args, **kwargs)¶ Bases:
data_validation_framework.task.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.