Atomagined Dataset (WebDataset)

Simulated atomic-resolution HAADF-STEM images from the atomagined dataset. Each image is a 256x256 simulation of a unique ICSD crystal structure prototype viewed along a specific crystallographic direction, with various post-processing distortion conditions applied.

Dataset Description

This is a WebDataset conversion of the atomagined proxy dataset (subset available via GitHub). The full dataset (~67,871 images) is hosted on the Materials Data Facility. This version contains 299 samples from 61 unique structure/orientation combinations across three subsets: general simulations, retrieval targets, and retrieval choices.

Each h5 file in the original data contains multiple distortion variants of the same simulation. These have been flattened so that each (structure, distortion) pair is an individual sample.

Format

WebDataset format: 1 TAR shard, 76 MB total.

Each sample in the shard contains:

• {idx:06d}.npy — 256x256 float32 HAADF-STEM image
• {idx:06d}.json — metadata

Metadata Fields

Field	Type	Description
ref_id	string	Reference ID: {ICSD_CollCode}.{uvw_encoding}
subset	string	Dataset subset: general, targets, or choices
distortion	string	Distortion condition (e.g., raw, stem00-clean, stem00-blur1, stem00-cnts2)
width	int	Image width (256)
height	int	Image height (256)
min_value	float	Minimum pixel intensity
max_value	float	Maximum pixel intensity
mean_value	float	Mean pixel intensity
std_value	float	Standard deviation of pixel intensity
icsd_id	string	ICSD collection code
chemical_name	string	Systematic chemical name
chemical_formula	string	Structural chemical formula
structure_type	string	Crystal structure type
space_group	string	Space group name
space_group_number	string	International Tables space group number
uvw_orient	string	Viewing direction [u,v,w]
hkl_orient	string	Miller indices of the viewing plane
n_atoms_projected	int	Number of atom columns in the projection

Distortion Conditions

Code	Description
raw	Raw simulation output
stem00-clean	Clean (no distortion)
stem00-blur{1,2}	Gaussian blur (two levels)
stem00-cnts{1,2}	Count noise / Poisson noise
stem00-scan{1,2}	Scan distortion
stem00-bkgd{1,2}	Background noise
stem00-dfct{1,2}	Structural defects
stem00-blbk{1,2}	Blur + background combined
stem01-comb1	Combined distortion level 1
stem02-comb2	Combined distortion level 2

Usage

import webdataset as wds
import numpy as np
from torch.utils.data import DataLoader

url = "path/to/atomagined_wds/train-0000.tar"
dataset = wds.WebDataset(url).decode()
dataloader = DataLoader(dataset, batch_size=32, num_workers=2)

for sample in dataloader:
    image = sample[".npy"]      # 256x256 float32
    metadata = sample[".json"]  # dict with ICSD info, distortion type, etc.

Source

Original data from MaterialEyes/atomagined. Full dataset on Materials Data Facility.

Citation

Schwenker, E. et al. Image Matching for Computer Vision in Atomic-Resolution Electron Microscopy, 2020.

License

CC-BY-4.0