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web-neuroimaging

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UpdatedMay 6, 2026 at 18:18

Web research for neuroimaging documentation, SimpleITK, nibabel, napari, BIDS specs, and neuroscience methods. TRIGGER when user asks to look up docs, find API references, or research neuroimaging methods.

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Related occupationsSOC

Based on SOC occupation classification

Biological Scientists, All OtherLife, Physical, and Social Science Occupations·SOC 19-1029

SKILL.md

readonly

name	web-neuroimaging
description	Web research for neuroimaging documentation, SimpleITK, nibabel, napari, BIDS specs, and neuroscience methods. TRIGGER when user asks to look up docs, find API references, or research neuroimaging methods.
user-invocable	false

Web Research for Neuroimaging

Priority Documentation Sources

Domain	URL	Use For
SimpleITK	simpleitk.readthedocs.io	Registration, filters, transforms
SimpleITK examples	simpleitk.org/SimpleITK-Notebooks	Jupyter notebooks with full pipelines
nibabel	nipy.org/nibabel	NIfTI I/O, affines, orientation
napari	napari.org/stable	Viewer API, layers, events
BIDS	bids-specification.readthedocs.io	Data format, iEEG extension
PySide6/Qt	doc.qt.io/qtforpython-6	Widget API, signals/slots
NumPy	numpy.org/doc/stable	Array operations
SciPy	docs.scipy.org/doc/scipy	Signal processing, ndimage

Search Strategy

Official docs first — use WebFetch on the URLs above
GitHub repos — SimpleITK/SimpleITK, nipy/nibabel, napari/napari
NeuroStars (neurostars.org) — neuroimaging-specific Q&A forum
PubMed/Scholar — methodology references, validation studies
Stack Overflow — general Python/Qt issues

Common Lookups

SimpleITK Registration

Registration method API: simpleitk.readthedocs.io/en/master/link_Registration_docs.html
Transform types: Euler3D, Affine, BSpline, Displacement
Metrics: MattesMutualInformation, Correlation, MeanSquares
Optimizers: GradientDescentLineSearch, LBFGSB, ConjugateGradient

nibabel

Affine handling: nipy.org/nibabel/coordinate_systems.html
Image types: Nifti1Image, Nifti2Image, MGHImage
Orientation codes: RAS, LAS, LPI, etc.

BIDS-iEEG Extension

Electrode files: *_electrodes.tsv with x,y,z,size,type columns
Coordinate systems: *_coordsystem.json specifying space (T1w, MNI152NLin2009aSym, etc.)
Channel files: *_channels.tsv with name,type,units,sampling_frequency

napari

Layer types: Image, Points, Shapes, Labels, Surface, Tracks, Vectors
Events: dims.events.current_step, mouse_drag_callbacks, mouse_move_callbacks
Rendering: mip, attenuated_mip, minip, translucent, iso

Version-Specific Notes

SimpleITK v2.x changed API significantly from v1.x — always check version
napari 0.5→0.6 had breaking changes in viewer embedding
PySide6 6.5+ required for latest Qt features
nibabel 5.0 deprecated some older image classes

When Reporting

Include direct URLs to relevant doc pages
Provide minimal code examples
Note any version-specific behavior
Flag deprecated APIs

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name	web-neuroimaging
description	Web research for neuroimaging documentation, SimpleITK, nibabel, napari, BIDS specs, and neuroscience methods. TRIGGER when user asks to look up docs, find API references, or research neuroimaging methods.
user-invocable	false

Web Research for Neuroimaging

Priority Documentation Sources

Domain	URL	Use For
SimpleITK	simpleitk.readthedocs.io	Registration, filters, transforms
SimpleITK examples	simpleitk.org/SimpleITK-Notebooks	Jupyter notebooks with full pipelines
nibabel	nipy.org/nibabel	NIfTI I/O, affines, orientation
napari	napari.org/stable	Viewer API, layers, events
BIDS	bids-specification.readthedocs.io	Data format, iEEG extension
PySide6/Qt	doc.qt.io/qtforpython-6	Widget API, signals/slots
NumPy	numpy.org/doc/stable	Array operations
SciPy	docs.scipy.org/doc/scipy	Signal processing, ndimage

Search Strategy

Official docs first — use WebFetch on the URLs above
GitHub repos — SimpleITK/SimpleITK, nipy/nibabel, napari/napari
NeuroStars (neurostars.org) — neuroimaging-specific Q&A forum
PubMed/Scholar — methodology references, validation studies
Stack Overflow — general Python/Qt issues

Common Lookups

SimpleITK Registration

Registration method API: simpleitk.readthedocs.io/en/master/link_Registration_docs.html
Transform types: Euler3D, Affine, BSpline, Displacement
Metrics: MattesMutualInformation, Correlation, MeanSquares
Optimizers: GradientDescentLineSearch, LBFGSB, ConjugateGradient

nibabel

Affine handling: nipy.org/nibabel/coordinate_systems.html
Image types: Nifti1Image, Nifti2Image, MGHImage
Orientation codes: RAS, LAS, LPI, etc.

BIDS-iEEG Extension

Electrode files: *_electrodes.tsv with x,y,z,size,type columns
Coordinate systems: *_coordsystem.json specifying space (T1w, MNI152NLin2009aSym, etc.)
Channel files: *_channels.tsv with name,type,units,sampling_frequency

napari

Layer types: Image, Points, Shapes, Labels, Surface, Tracks, Vectors
Events: dims.events.current_step, mouse_drag_callbacks, mouse_move_callbacks
Rendering: mip, attenuated_mip, minip, translucent, iso

Version-Specific Notes

SimpleITK v2.x changed API significantly from v1.x — always check version
napari 0.5→0.6 had breaking changes in viewer embedding
PySide6 6.5+ required for latest Qt features
nibabel 5.0 deprecated some older image classes

When Reporting

Include direct URLs to relevant doc pages
Provide minimal code examples
Note any version-specific behavior
Flag deprecated APIs