pysnt.annotation package

This module provides convenient access to SNT’s annotation classes.

The annotation module contains utilities for working with anatomical annotations, brain atlases, and compartment-based analysis tools.

get_available_classes() → List[str]

Get list of all available classes.

This includes both curated classes (always loaded) and extended classes (loaded on-demand). Extended classes are discovered if not already loaded.

Returns:

List of available class names.

Return type:

List[str]

get_class(class_name: str) → Any

Get a specific class by name.

This method provides access to both curated and extended classes. Extended classes are discovered and loaded on first access.

Supports inner class access using dot notation (e.g., “CircularModels.VonMisesFit”).

Parameters:

class_name (str) – Name of the class to retrieve. Can include inner class notation using dots (e.g., “CircularModels.VonMisesFit”).

Returns:

The requested SNT class or inner class.

Return type:

Java class

Raises:

• KeyError – If the class is not available.

• RuntimeError – If the JVM has not been started.

Examples

>>> # Get a regular class
>>> CircModels = pysnt.analysis.get_class("CircularModels")

>>> # Get an inner class
>>> VonMisesFit = pysnt.analysis.get_class("CircularModels.VonMisesFit")

list_classes()

Print all available classes organized by tier.

get_curated_classes() → List[str]

Get list of curated classes that are always available for direct import.

Returns:

List of curated class names.

Return type:

List[str]

get_extended_classes() → List[str]

Get list of extended classes available via get_class().

This will trigger discovery if not already done.

Returns:

List of extended class names.

Return type:

List[str]

class AllenUtils(*args, **kwargs)

Bases: object

Utility methods for accessing/handling AllenCompartments

All Methods and Attributes: See AllenUtils detailed documentation.

class AllenCompartment(*args, **kwargs)

Bases: object

Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation. A Compartment is defined by either a UUID (as per MouseLight's database) or its unique integer identifier. To improve performance, a compartment's metadata (reference to its mesh, its aliases, etc.) are not loaded at initialization, but retrieved only when such getters are called.

All Methods and Attributes: See AllenCompartment detailed documentation.

class InsectBrainCompartment(*args, **kwargs)

Bases: object

SNT class with method signatures.

Available for direct import after JVM initialization. Call pysnt.initialize() before using this class.

All Methods and Attributes: See InsectBrainCompartment detailed documentation.

See InsectBrainCompartment JavaDoc.

class InsectBrainUtils(*args, **kwargs)

Bases: object

Utility methods for retrieving species, brain, and neuron data from the Insect Brain Database

All Methods and Attributes: See InsectBrainUtils detailed documentation.

class VFBUtils(*args, **kwargs)

Bases: object

Utility methods for accessing/handling Virtual Fly Brain (VFB) annotations

All Methods and Attributes: See VFBUtils detailed documentation.

class ZBAtlasUtils(*args, **kwargs)

Bases: object

Utility methods for accessing the Max Plank Zebrafish Brain Atlas (ZBA) at fishatlas.neuro.mpg.de.

All Methods and Attributes: See ZBAtlasUtils detailed documentation.