Usage

Usage

This library includes examples for generating single structures and running batch simulations. You can find them in the examples/ directory.

Generating Single Structures

To generate a single structure, you can run the corresponding script from the examples/ directory.

Microtubules

python examples/generate_microtubules.py

Mitochondria

python examples/generate_mitochondria.py

Nuclear Pore Complex (NPC)

# Generate a single NPC centered at the origin
python examples/generate_npc.py

# Generate multiple NPCs on a nuclear envelope
python examples/generate_npc_nucleus.py

The output, including the point cloud (CSV), rendered images (PNG/TIFF), and masks, will be saved in the outputs/ directory.

Batch Generation

For generating a large dataset, the batch_generate.py script allows running multiple simulations in parallel.

# Run 4 parallel simulations for microtubules
python examples/batch_generate.py microtubule -n 4 -w 4

# Run 8 parallel simulations for mitochondria
python examples/batch_generate.py mitochondria -n 8 -w 4

# Run 10 single NPC simulations with 4 workers
python examples/batch_generate.py npc -n 10 -w 4

# Run 5 nucleus (multiple NPCs) simulations with 4 workers
python examples/batch_generate.py nucleus -n 5 -w 4

You can specify the structure type (microtubule, mitochondria, npc, or nucleus), the total number of simulations (-n), and the number of parallel workers (-w). The results will be saved in subdirectories within outputs/batch_simulation/.

Structure Types

Type	Description	Example Script
microtubule	Cylindrical filaments using B-splines	generate_microtubules.py
mitochondria	Tubular organelles using random walk	generate_mitochondria.py
npc	Single Nuclear Pore Complex	generate_npc.py
nucleus	Multiple NPCs on nuclear envelope	generate_npc_nucleus.py