philipp-pelz/public-4dstem

ECLIPSE-Lab public 4D-STEM hub

Published, experimental 4D-STEM datasets from other groups, re-hosted in one uniform, lossless-compressed HDF5 format (e4d) with complete, verified calibration metadata, for benchmarking reconstruction, compression and denoising methods across a wide dose range (ptychography and nanobeam diffraction). Every dataset remains the work of its original authors: please cite the original publication (see Citations below).

What every file guarantees

• Lossless: the cube equals the original raw data after the declared transforms (listed per dataset in cards/<id>.yaml, e.g. axis flips, EMPAD row crop); total counts are checked equal.
• Calibration (energy, convergence semi-angle, scan step, detector sampling dk, scan–detector rotation, defocus) with a per-field source (file, paper or fit). Checked against the data with scatterem diagnostics: the bright-field disk radius must match α/dk within 5 %, and the centre-of-mass curl rotation must match within 3° wherever the data can determine it.
• Dose: stated (file / paper / estimate) and measured from the counts. signal says whether values are electron counts, raw detector units (ADU) or preprocessed (normalized) values.
• A fixed benchmark_roi per dataset for comparable benchmarks.

Catalogue

id	modality	tasks	variants	stated dose (e/Ų)	measured (e/Ų)	signal	detector	kV	licence	GB	original DOI
Strauch2021_STO	ptycho	ptycho	1	5.7e+06 (paper)	5.72e+06	counts	Merlin Medipix3RX	300	CC-BY-4.0	0.13	10.1017/S1431927621012423
Harikrishnan2025_NNO	ptycho	ptycho	1	2.2e+06 (paper)	2.01e+06	counts	EMPAD	300	CC-BY-4.0	0.88	10.5281/zenodo.14954707
Dong2024_La3Ni2O7	ptycho	ptycho	3	9e+05 (estimate)	7.49e+05–7.87e+05	counts	Gatan K3 (energy-filtered)	300	CC-BY-4.0	0.57	10.1038/s41586-024-07482-1
Riechers2026_PdCuSi	nbed	amorphous	2	3e+05 (estimate)	6.38e+05–7.28e+05	counts	Dectris ELA	200	CC-BY-4.0	2.87	10.1016/j.jallcom.2026.186631
Kang2025_polySi	ptycho	ptycho	1	7.5e+05 (estimate)	5.68e+05	counts	Gatan K3	300	CC-BY-4.0	0.39	10.26599/NR.2025.94907398
Shi2025_PdH	ptycho	ptycho	3	2e+05–5e+05 (estimate/file)	2.07e+05–5.28e+05	adu	EMPAD	300	CC-BY-4.0	7.42	10.48550/arXiv.2508.11142
Sadri2024_STO	ptycho	ptycho, virtual_imaging	2	6.39–3.5e+05 (paper)	6.35–3.7e+05	counts	EMPAD	300	CC0-1.0	0.58	10.1038/s41524-024-01428-x
KP2025_cepstral_SiGe	nbed	strain, virtual_imaging	6	6.24e+03–6.24e+04 (estimate)	–	adu	EMPAD	300	CC-BY-4.0	4.74	10.48550/arXiv.2509.08321
Chen2025_NVdiamond	ptycho	ptycho	2	2e+05 (paper)	1.25e+05–1.33e+05	counts	Gatan K3 (energy-filtered)	300	CC-BY-4.0	0.82	10.1016/j.xinn.2025.101043
MillsZeltmann2022_AlAu	nbed	strain, virtual_imaging	1	6.71e+04 (estimate)	–	adu	Gatan K2-IS	300	CC-BY-4.0	0.08	10.1016/j.actamat.2023.118721
Ribet2024_UCNP	ptycho	ptycho	2	5e+03 (paper)	4.27e+03–4.98e+03	counts	4D Camera	300	CC-BY-4.0	0.51	10.1063/5.0207212
Zhang2025_SAEP	ptycho	ptycho	3	44–1.2e+03 (estimate/paper)	111–2.97e+03	counts	MerlinEM	300	CC-BY-4.0	0.26	10.48550/arXiv.2504.17501
Balhorn2022_PBTTT	nbed	virtual_imaging	1	156 (file)	–	adu	Gatan CCD (TitanX / NCEM)	300	CC-BY-4.0	0.91	10.1073/pnas.2204346119
Thronsen2022_AlSPED	sped	phase_map, acom	1	1e+03 (estimate)	–	normalized	MerlinEM 1S (Quantum Detectors)	200	CC-BY-4.0	4.02	10.1016/j.ultramic.2023.113861
Li2025_MOF	ptycho	ptycho	3	100 (paper)	98.9–116	adu	EMPAD	300	CC-BY-4.0	11.93	10.1038/s41467-025-55827-9
Kucukoglu2024_apoF	ptycho	ptycho	3	34 (paper)	–	adu	Dectris ELA	300	CC0-1.0	4.35	10.1101/2024.02.12.579607
Yuan2025_MAPbI3	ptycho	ptycho	3	11 (paper)	11–11	counts	Timepix3	200	CC-BY-4.0	0.03	10.1038/s41586-025-09693-6
Mireles2025_MoS2MoSe2	nbed	strain, virtual_imaging	1	9.94 (paper)	9.68	adu	EMPAD	80	CC-BY-4.0	3.70	10.1126/sciadv.adz7908
Wu2025_Sb2S3	nbed	acom, virtual_imaging	2	6.23 (estimate)	2.63–2.64	counts	Dectris Quadro (TESCAN Tensor)	100	CC-BY-4.0	2.42	10.1021/acsnano.5c04342

Layout

• data/<id>/<id>[_<variant>].h5 — the cube, (scan_y, scan_x, k_y, k_x), chunked per scan row, Blosc2 zstd + bitshuffle (needs hdf5plugin). Files above 45 GB are split along scan_y into .part-NN.h5.
• cards/<id>.yaml — the full metadata card (also embedded in each file as /metadata.attrs['card_json']).
• reports/<id>/ — verification report (JSON) and a preview (mean pattern, virtual BF / ADF).

Load with plain h5py

import json, h5py, hdf5plugin
with h5py.File('Strauch2021_STO.h5', 'r') as f:
    roi = f['data'][32:96, 32:96]              # reads only these chunks
    card = json.loads(f['metadata'].attrs['card_json'])

Load with scatterem

from scatterem.data.public.hub import Hub4DStem, list_datasets
ptycho_low_dose = list_datasets(task='ptycho', dose=(1, 1e3))
ds = Hub4DStem('Strauch2021_STO', roi='benchmark')  # Dataset4DStem

Variants

• Harikrishnan2025_NNO: fig_4b
• Dong2024_La3Ni2O7: region01, region02, region03
• Riechers2026_PdCuSi: FQ_locC_scan2, SQ_locA_scan3
• Shi2025_PdH: challenge, non_superlattice_500k, superlattice_200k
• Sadri2024_STO: highmag_hd, lowmag_highangle_hd
• KP2025_cepstral_SiGe: a0p75_1ms, a1p6_1ms, a1p6_10ms, a2_10ms, a3_1ms, a3_10ms
• Chen2025_NVdiamond: fig_3, fig_4
• MillsZeltmann2022_AlAu: au_beforeHT
• Ribet2024_UCNP: pristine, defect
• Zhang2025_SAEP: beta, mil101, uio66_first
• Li2025_MOF: fig2_zrbtb, fig3_moss6, fig4_moss6
• Kucukoglu2024_apoF: pos_16, pos_40, pos_51
• Yuan2025_MAPbI3: fig3_scan0, fig3_scan1, fig3_scan2
• Wu2025_Sb2S3: prec0, prec1

Citations (please cite the original work)

Strauch2021_STO

Strauch et al., Live processing of momentum-resolved STEM data for first moment imaging and ptychography, Microsc. Microanal. (2021)

DOI: 10.1017/S1431927621012423 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/5113449

Harikrishnan2025_NNO

Harikrishnan et al., Zenodo 14954707 (NNO multislice ptychography datasets)

DOI: 10.5281/zenodo.14954707 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/14954707

Dong2024_La3Ni2O7

Dong et al., Visualization of oxygen vacancies and self-doped ligand holes in La3Ni2O7-δ, Nature 630, 847–852 (2024)

DOI: 10.1038/s41586-024-07482-1 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/12807652

Riechers2026_PdCuSi

Riechers et al., Spatial distribution and connectivity of medium-range order signatures in a metallic glass probed with simulated and experimental 4DSTEM, J. Alloys Compd. (2026)

DOI: 10.1016/j.jallcom.2026.186631 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/18549114

Kang2025_polySi

Kang et al., Thermal cycle impact on polycrystalline silicon: Direct observation of electrical properties degradation and interfacial nanocrystalline grain defects, Nano Research (2025)

DOI: 10.26599/NR.2025.94907398 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/15089477

Shi2025_PdH

Shi et al., Electron Ptychography Images Hydrogen Atom Superlattices and 3D Inhomogeneities in Palladium Hydride Nanoparticles, arXiv:2508.11142 (2025)

DOI: 10.48550/arXiv.2508.11142 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/21363131

Sadri2024_STO

Sadri et al., Unsupervised deep denoising for four-dimensional scanning transmission electron microscopy, npj Comput. Mater. 10, 243 (2024)

DOI: 10.1038/s41524-024-01428-x · licence: CC0-1.0 · original data: https://doi.org/10.6084/m9.figshare.25815436

KP2025_cepstral_SiGe

Harikrishnan KP et al., Cepstral Strain Mapping for Small Pixel-Count Detectors, arXiv:2509.08321 (2025)

DOI: 10.48550/arXiv.2509.08321 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/18065811

Chen2025_NVdiamond

Chen et al., Visualizing the Atomic Structure of Nitrogen-vacancy Color Center in Diamond by Multislice Electron Ptychography, The Innovation 7, 101043 (2025)

DOI: 10.1016/j.xinn.2025.101043 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/14913471

MillsZeltmann2022_AlAu

Mills et al., Nanoscale mapping of point defect concentrations with 4D-STEM, Acta Materialia (2023)

DOI: 10.1016/j.actamat.2023.118721 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/7041997

Ribet2024_UCNP

Ribet et al., Uncovering the three-dimensional structure of upconverting core–shell nanoparticles with multislice electron ptychography, Appl. Phys. Lett. (2024)

DOI: 10.1063/5.0207212 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/10775819

Zhang2025_SAEP

Zhang et al., Surface morphology and thickness variation estimation of zeolites via electron ptychography, arXiv:2504.17501 (2025)

DOI: 10.48550/arXiv.2504.17501 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/17709147

Balhorn2022_PBTTT

Balhorn et al., Closing the loop between microstructure and charge transport in conjugated polymers by combining microscopy and simulation, Proc. Natl. Acad. Sci. U.S.A. 119, e2204346119 (2022)

DOI: 10.1073/pnas.2204346119 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/6585396

Thronsen2022_AlSPED

Thronsen et al., Scanning precession electron diffraction data analysis approaches for phase mapping of precipitates in aluminium alloys, Ultramicroscopy (2023)

DOI: 10.1016/j.ultramic.2023.113861 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/6645396

Li2025_MOF

Li et al., Atomically resolved imaging of radiation-sensitive metal-organic frameworks via electron ptychography, Nat. Commun. 16 (2025)

DOI: 10.1038/s41467-025-55827-9 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/13958144

Kucukoglu2024_apoF

Küçükoğlu et al., Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution, bioRxiv (2024)

DOI: 10.1101/2024.02.12.579607 · licence: CC0-1.0 · original data: https://www.ebi.ac.uk/empiar/EMPIAR-12236/

Yuan2025_MAPbI3

Yuan et al., Atomically resolved edges and defects in lead halide perovskites, Nature 647, 364–368 (2025)

DOI: 10.1038/s41586-025-09693-6 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/11482208

Mireles2025_MoS2MoSe2

Mireles et al., Strain mapping of three-dimensionally structured two-dimensional materials, Sci. Adv. (2026)

DOI: 10.1126/sciadv.adz7908 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/17246822

Wu2025_Sb2S3

Wu et al., Correlative and in situ microscopy investigation of phase transformation, crystal growth, and degradation of antimony sulfide thin films, ACS Nano (2025)

DOI: 10.1021/acsnano.5c04342 · licence: CC-BY-4.0 · original data: https://zenodo.org/records/15536234