| | --- |
| | license: cc-by-4.0 |
| | task_categories: |
| | - reinforcement-learning |
| | tags: |
| | - stem-microscopy |
| | - electron-microscopy |
| | - materials-science |
| | - gymnasium |
| | - benchmark |
| | - dose-efficiency |
| | pretty_name: STEMGym |
| | size_categories: |
| | - 1K<n<10K |
| | --- |
| | |
| | # STEMGym: Benchmark Data for Dose-Efficient Autonomous STEM Microscopy |
| |
|
| | This dataset accompanies the [STEMGym](https://github.com/KurbanIntelligenceLab/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 |
| |
|
| | ```bash |
| | # 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](https://creativecommons.org/licenses/by/4.0/) license. |
| |
|
| | ## Citation |
| |
|
| | ```bibtex |
| | @inproceedings{stemgym2026, |
| | title={STEMGym: A Benchmark for Dose-Efficient Autonomous STEM Microscopy}, |
| | author={Polat, John}, |
| | year={2026} |
| | } |
| | ``` |
| |
|
