Datasetpublic

Stemson-AI/atomagined

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… See the full description on the dataset page: https://huggingface.co/datasets/Stemson-AI/atomagined.

sourceHugging Facecc-by-4.0updated 5mo agoView on Hugging Face

0likes15downloads

Dataset Card

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

python

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