Changelog

Changelog¶

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

NPCGenerator for simulating single Nuclear Pore Complex (NPC) point clouds.
NucleusGenerator for simulating multiple NPCs distributed on a nuclear envelope (ellipsoid surface).
NPC geometry model with preset NUP configurations (nup107, nup133, nup96, nup160) and custom parameter support.
Error models for NPC simulation:
Localization uncertainty with constant or Poisson-Uniform distribution
Linker error (antibody arm) with Normal or Stick models
Binding site jitter for structural heterogeneity
Optional random z-axis rotation for single NPC generation.
Example scripts: generate_npc.py and generate_npc_nucleus.py.
Configuration files: config_npc.py and config_nucleus.py.
NPC documentation: docs/npc.md.
Batch generation support for npc and nucleus structure types.

Initial release of biolocsim.
Core framework for SMLM point cloud simulation.
MicrotubuleGenerator for simulating microtubule structures using B-splines.
MitochondriaGenerator for simulating mitochondria using a persistent random walk model.
Functions to render point clouds into 2D images with PSF simulation.
Utilities for generating and saving various types of masks (centerlines, volumes, surfaces).
Export functionality for point clouds (CSV) and configurations (YAML).
Example scripts for generating single structures and running batch simulations.
Command-line interface for batch processing.