`tasks.curation`¶

Curation tasks.

Module Contents¶

Classes¶

`Collect`	Collect external dataset from .csv file.
`ExtractMarkers`	Extract marker information from the original morphology files, if any.
`PlotMarkers`	Plot markers on morphologies.
`CheckNeurites`	Detect which neurites are present in the morphology, and add soma if missing.
`Sanitize`	Sanitize the morphologies.
`Recenter`	Recenter morphologies.
`Orient`	Orient morphologies.
`Align`	Align morphologies.
`EnsureNeuritesOutsideSoma`	Fix radius of the soma of each morphology and cut the root section of neurites if needed.
`DetectErrors`	Detect and plot errors in reconstructions.
`ErrorsReport`	Save error report for all morphologies.
`Resample`	Resample morphologies.
`PlotMorphologies`	Plot curated morphologies.

Attributes¶

logger

tasks.curation.logger¶

class tasks.curation.Collect(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Collect external dataset from .csv file.

Original dataset has to have a ‘morph_name’ and ‘morph_path’ columns, with the name and path to the corresponding morphologies. Any other valid columns will be gathered as well. In addition, it will only collect morphologies with allowed extension: .asc, .h5, .swc.

class tasks.curation.ExtractMarkers(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Extract marker information from the original morphology files, if any.

Markers are additional spatial information contained in some reconstructed morphologies. Some can be read by MorphIO (https://github.com/BlueBrain/MorphIO/pull/186). The markers are stored in a custom API: morphology_workflows.marker_helper.

class tasks.curation.PlotMarkers(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Plot markers on morphologies.

Plot the markers extracted from tasks.curation.ExtractMarkers on the morphologies.

with_plotly¶

Use Plotly for plotting

Type:: bool
Default value:: True

class tasks.curation.CheckNeurites(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Detect which neurites are present in the morphology, and add soma if missing.

This task adds three important boolean flags:

has_axon
has_basal
has_apical

set to False if any are absent.

For the axon, if it only has fewer sections than axon_n_section_min, it will be considered as has_axon=False.

If soma is absent, a soma is added as a circle, with center the mean of the first points of root sections, and radius as standard deviation of these points around the center.

If the input dataset has columns use_axon or use_dendrites, our corresponding flags will match.

Todo

Set various levels, a one section neurite can be set to has_basal=False for example.

mock_soma_type¶

Add a soma if missing of the given type

Type:: str
Choices:: {spherical, contour}
Default value:: spherical

axon_n_section_min¶

Minimum number of sections in an axon to consider it valid

Type:: int
Default value:: 5

ensure_stub_axon¶

Add a stub axon if there is no axon on the morphology

Type:: bool
Default value:: False

ensure_single_axon¶

Keep only largest axon if multiple are present

Type:: bool
Default value:: True

ensure_axon_at_soma¶

Ensure all axons are connected to the soma, and not dendrites

Type:: bool
Default value:: True

remove_dummy_neurites¶

Remove neurites with two equal points

Type:: bool
Default value:: True

min_length_first_section¶

Resize the first section to be at least of the given size (do nothing if None is given)

Type:: float
Permitted values:: float in (0, inf)
Default value:: 0.0001

class tasks.curation.Sanitize(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Sanitize the morphologies.

Sanitization is done with neuror.sanitize.sanitize() and does the following:

ensures it can be loaded with MorphIO
raises if the morphology has no soma or of invalid format
removes unifurcations
set negative diameters to zero
raises if the morphology has a neurite whose type changes along the way
removes segments with near zero lengths (shorter than 1e-4)

Note that the tasks.curation.CheckNeurites task adds a soma if missing, so a failure here means that the soma does not have a valid type.

ensure_roots_at_soma¶

Reconnect root sections at soma if they are not

Type:: bool
Default value:: True

class tasks.curation.Recenter(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Recenter morphologies.

Often, morphologies do not have a soma centered at [0, 0, 0], so we recenter and save the original location, in case it is important to know where the morphology is located in atlas.

class tasks.curation.Orient(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, data_validation_framework.task.ElementValidationTask

Orient morphologies.

Sometimes, morphologies are oriented along non-standard axis. At BBP, the standard axis is

y for pia direction (apical trunk, minus main axon, etc…)
z is the slice direction is invitro
x the other direction

If y is provided (default value), no oriention will be applied. One can also use minus sign, as -y to flip y axis.

pia_direction¶

Axis of pia direction, x, y or z

Type:: str
Default value:: y

class tasks.curation.Align(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(True), data_validation_framework.task.ElementValidationTask

Align morphologies.

Sometimes, a morphology is not aligned with any consistent direction, so we can try here to align them using a various algorithms from morph_tool.transform.align_morphology().

method can be: whole, trunk, first_segment, first_section, custom

If method is custom, one must provide external orientation direction in a json file via the parameter custom_orientation_json_path.

TODO: implement the axon_collateral method (for thalamus or example), following https://bbpgitlab.epfl.ch/cells/archive/iavarone/thalamus_pipeline/-/blob/master/notebooks/cell_alignement/Rt_TC_rotations_AxonCollaterals_Releases2019.ipynb

By default, this task is skipped.

method¶

Method to align morphology

Type:: str
Choices:: {custom, first_section, first_segment, trunk, whole}
Default value:: whole

neurite_type¶

Neurite to use to align morphology

Type:: str
Default value:: apical

direction¶

custom_orientation_json_path¶

Path to json with custom orientations

Type:: str

class tasks.curation.EnsureNeuritesOutsideSoma(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(True), data_validation_framework.task.ElementValidationTask

Fix radius of the soma of each morphology and cut the root section of neurites if needed.

class tasks.curation.DetectErrors(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Detect and plot errors in reconstructions.

Reconstructions may contain errors, which are detected here. They are of the following type:

fat ends
z-jumps
narrow start
dangling branch
multifurcation
overlapping points
z-range (new error only present here, which check is the z thickness is larger than min_range)

This task uses neuror.sanitize.annotate_neurolucida(). This task creates new .asc file with error annotated so it can be red by Neurolucida, and a morphology_workflows.marker_helper.MarkerSet container of the errors, for later plotting.

min_range¶

Minimum z-range to be an error

Type:: float
Default value:: 50

overlapping_point_tolerance¶

Tolerance used to detect overlapping points.

Type:: float
Default value:: 1e-06

plot_errors¶

Plot the detected errors

Type:: bool
Default value:: True

class tasks.curation.ErrorsReport(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.SetValidationTask

Save error report for all morphologies.

From the detected errors in tasks.curation.DetectErrors, create a CSV report.

error_report_path¶

Path to error report file in .csv

Type:: str
Default value:: error_report.csv

class tasks.curation.Resample(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Resample morphologies.

This tasks ensures a constant sampling rate of points along all branches using the morph_tool.resampling.resample_linear_density() function.

linear_density¶

Density of points per micron

Type:: float
Default value:: 1.0

class tasks.curation.PlotMorphologies(*args, **kwargs)¶

Bases: morphology_workflows.utils.StrIndexMixin, SkippableMixin(), data_validation_framework.task.ElementValidationTask

Plot curated morphologies.

This tasks creates a single pdf with all morphologies to visualise them after curation.

The PDF file is created using the neurom.view.matplotlib_impl.plot_morph() function.

with_plotly¶

Use Plotly for plotting

Type:: bool
Default value:: False

with_realistic_diameters¶

Use realistic diameters for plotting (take more time to plot)

Type:: bool
Default value:: True

tasks.curation¶

Module Contents¶

Classes¶

Attributes¶

`tasks.curation`¶