Datasets:

johnpolat
/

STEMGym

Error code:   StreamingRowsError
Exception:    ValueError
Message:      Dataset 'overview' has length 256 but expected 4096
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 99, in get_rows_or_raise
                  return get_rows(
                         ^^^^^^^^^
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                         ^^^^^^^^^^^^^^^^^^^^^
                File "/src/services/worker/src/worker/utils.py", line 77, in get_rows
                  rows_plus_one = list(itertools.islice(ds, rows_max_number + 1))
                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2543, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2060, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2083, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 544, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 383, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 80, in _generate_tables
                  num_rows = _check_dataset_lengths(h5, self.info.features)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 359, in _check_dataset_lengths
                  raise ValueError(f"Dataset '{path}' has length {dset.shape[0]} but expected {num_rows}")
              ValueError: Dataset 'overview' has length 256 but expected 4096

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STEMGym: Benchmark Data for Dose-Efficient Autonomous STEM Microscopy

This dataset accompanies the STEMGym benchmark — a Gymnasium-based environment for evaluating autonomous dose-efficient scanning transmission electron microscopy (STEM) agents.

Dataset Description

STEMGym provides simulated STEM specimens as HDF5 world files. Each world contains:

Overview image: Low-magnification survey of the full specimen
Tile grid: High-resolution STEM images (128×128 px tiles, 4px overlap, stride=124) arranged in an 8×8 grid
Ground truth annotations: Atom positions, defect types, and phase maps for scoring
Metadata: Pixel size, accelerating voltage, detector geometry, material parameters

Materials

Material	Description	Defect Types
SrTiO₃	Perovskite oxide	O vacancies, Sr vacancies, Ti antisites
BaTiO₃	Ferroelectric perovskite	O vacancies, Ba vacancies, domain boundaries
SiGe	Semiconductor alloy	Ge substitutions, strain fields

Difficulty Levels

Each material is provided at three difficulty levels (easy, medium, hard) controlling defect density, noise level, and spatial distribution.

Files

Simulated Worlds (`worlds/`)

File	Material	Difficulty	Size
`test_world.h5`	Synthetic (Gaussian blobs)	—	~5 MB
`srtio3_easy.h5`	SrTiO₃	Easy	~50 MB
`srtio3_medium.h5`	SrTiO₃	Medium	~50 MB
`srtio3_hard.h5`	SrTiO₃	Hard	~50 MB
`batio3_easy.h5`	BaTiO₃	Easy	~50 MB
`batio3_medium.h5`	BaTiO₃	Medium	~50 MB
`batio3_hard.h5`	BaTiO₃	Hard	~50 MB
`sige_easy.h5`	SiGe	Easy	~50 MB
`sige_medium.h5`	SiGe	Medium	~50 MB
`sige_hard.h5`	SiGe	Hard	~50 MB

Model Checkpoints (`checkpoints/`)

File	Model	Description	Size
`atom_finder.pt`	AtomFinderUNet	Atomic column detection ensemble (3 members)	~88 MB
`defect_classifier.pt`	DefectClassifierCNN	Defect type classification	~1.4 MB
`phase_identifier.pt`	PhaseIdentifierResNet	Material phase identification	~7.4 MB

HDF5 World Format

Each world file follows this layout:

/metadata/
    pixel_size_nm          # Physical pixel size
    tile_size_px           # Tile dimensions (128)
    tile_overlap_px        # Overlap between tiles (4)
    grid_rows, grid_cols   # Grid dimensions
    accelerating_voltage   # Beam energy (keV)
    convergence_angle      # Probe convergence (mrad)
    detector_inner/outer   # HAADF detector angles (mrad)
/overview                  # Low-magnification survey image
/tiles/{row}_{col}         # High-resolution tile images
/ground_truth/
    atom_positions         # (N, 3) array: x, y, atomic_number
    defect_types           # (M, 4) array: x, y, type_id, severity
    phase_map              # 2D array: phase labels per pixel
/valid_region              # Boolean mask of valid scan area

Usage

# Install STEMGym
pip install -e .

# Download this data
python scripts/download_data.py

# Run a benchmark
stemgym run --agent raster_equipped --task defect_census --world srtio3_medium --seeds 3

License

This dataset is released under the CC-BY-4.0 license.

Citation

@inproceedings{stemgym2026,
  title={STEMGym: A Benchmark for Dose-Efficient Autonomous STEM Microscopy},
  author={Polat, John},
  year={2026}
}

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