Simulated Stack to RELION Reconstruction

This experiment shows how to:

1. build a synthetic dataset with ASPIRE,

2. write the stack via ImageSource.save so RELION can consume it, and

3. call relion_reconstruct on the saved STAR file.

Imports

import logging
from pathlib import Path

import numpy as np

from aspire.downloader import emdb_2660
from aspire.noise import WhiteNoiseAdder
from aspire.operators import RadialCTFFilter
from aspire.source import Simulation

logger = logging.getLogger(__name__)

Configuration

We set a few parameters to initialize the Simulation. You can safely alter n_particles (or change the defocus values, etc.) when trying this interactively; the defaults here are chosen for demonstrative purposes.

output_dir = Path("relion_save_demo")
output_dir.mkdir(exist_ok=True)

n_particles = 512
snr = 0.5
defocus = np.linspace(
    15000, 25000, 7
)  # defocus values for the radial CTF filters (angstroms)
star_file = f"sim_n{n_particles}.star"
star_path = output_dir / star_file

Volume and Filters

Start from the EMDB-2660 ribosome map and build a small set of radial CTF filters that RELION will recover as optics groups.

vol = emdb_2660()
ctf_filters = [RadialCTFFilter(defocus=d) for d in defocus]

Simulate, Add Noise, Save

Initialize the Simulation: mix the CTFs across the stack, add white noise at a target SNR, and write the particles and metadata to a RELION-compatible STAR/MRC stack.

sim = Simulation(
    n=n_particles,
    vols=vol,
    unique_filters=ctf_filters,
    noise_adder=WhiteNoiseAdder.from_snr(snr),
)
sim.save(star_path, overwrite=True)

Running relion_reconstruct

relion_reconstruct is an external RELION command, so we just show the call. Run this, from the output directory, in a RELION-enabled shell after generating the STAR file above.

logger.info(f"relion_reconstruct --i {star_file} " f"--o 'relion_recon.mrc' --ctf")