API#

Documentation Types#

PySNT provides two API documentation approaches:

Auto-Generated API Documentation - Python API reference with type hints and signatures
Method Index - Alphabetical index of all SNT methods
Class Index - Alphabetical index of all SNT classes
Constants Index - Index of public static fields (constants)

API Organization#

PySNT modules map directly into SNT’s Java API, so that e.g., pysnt.analysis() mirrors SNT’s sc.fiji.snt.analysis package.

SNT Module	Description	SNT API Match
pysnt package	main package interface with root classes and core functionality
pysnt.analysis package	neuronal morphology analysis tools and statistics
pysnt.analysis.graph package	handling neuronal reconstructions as graphs
pysnt.analysis.growth package	growth analysis of neurites across time
pysnt.analysis.sholl package	Sholl analysis
pysnt.annotation package	handling of neuropil annotations and atlases metadata
pysnt.io package	import of neuronal reconstructions from multiple sources
pysnt.tracing package	tracing tools
pysnt.util package	Utility classes and helper functions
pysnt.viewer package	2D and 3D visualization utilities

PySNT Module	Description
pysnt.config module	Configuration system for PySNT
pysnt.converters package	Converters that transform SNT Java objects into Python equivalents
pysnt.core module	Handles initialization and setup functions

pysnt.gui_utils module	GUI utilities for PySNT to handle threading and platform-specific issues.
pysnt.java_utils module	Java environment management utilities
pysnt.setup_utils module	Setup and configuration helpers

Quick Reference#

Essential Imports#

import pysnt
from pysnt import SNTService, Tree
from pysnt.analysis import TreeStatistics

Essential Functions#

pysnt.initialize()          # Start PySNT
pysnt.display(obj)          # Smart display any object
pysnt.list_classes()        # Explore available classes
pysnt.get_methods(cls)      # Explore class methods
pysnt.find_members(cls, kw) # Search for functionality

Memory Configuration#

pysnt.initialize(max_heap="8g")     # 8GB heap
pysnt.initialize(max_heap="16g", min_heap="4g")  # 16GB max, 4GB initial

Configuration#

pysnt.set_option('display.table_mode', 'pandasgui')
pysnt.set_option('display.chart_format', 'svg')

Initialization#

import pysnt
pysnt.initialize()
pysnt.initialize('/path/to/Fiji.app', max_heap='8g')

Important

Important: pysnt is only available after pysnt.initialize() is called.

Import Strategies#

Three ways to import SNT classes:

Method	Coverage	Use Case	Autocompletion	Comments
Direct Import	Restricted to curated classes	Common tasks	Detailed	Fast, convenient
`get_class()`	Discoverable classes	Advanced/uncommon tasks	Basic	Slower on first access, then cached
`scyjava.jimport()`	Any Java class	Expert usage	N/A	May require a priori knowledge of SNT’s architecture

Discovery of Classes#

import pysnt.analysis as analysis
import pysnt.util as util

# Discover what's available
print("Analysis classes:")
analysis.list_classes()
print("\nUtility classes:")
util.list_classes()

# Get class lists programmatically
analysis_classes = analysis.get_available_classes()
util_classes = util.get_available_classes()

# Get curated classes (always available for direct import)
curated = analysis.get_curated_classes()
print(f"Curated: {curated}")

# Get extended classes (available via get_class)
extended = analysis.get_extended_classes()
print(f"Extended: {extended}")

Discovery of Functions#

import pysnt
from pysnt.analysis import TreeStatistics
# Get all methods from TreeStatistics
methods = pysnt.get_methods(TreeStatistics)
# Find all members containing 'length'
results = pysnt.find_members(TreeStatistics, 'length')
# Get only static fields (constants)
constants = pysnt.get_fields(TreeStatistics, static_only=True)