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README.md

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+---
+license: cc-by-4.0
+task_categories:
+  - reinforcement-learning
+tags:
+  - stem-microscopy
+  - electron-microscopy
+  - materials-science
+  - gymnasium
+  - benchmark
+  - dose-efficiency
+  - autonomous-microscopy
+pretty_name: STEMGym Benchmark
+size_categories:
+  - 1K<n<10K
+---
+
+# STEMGym: A Gymnasium Environment for Benchmarking Dose-Efficient Autonomous Scanning Transmission Electron Microscopy
+
+A Gymnasium-based benchmark 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-HAADF images (128x128 px tiles, 4px overlap, stride=124) arranged in an 8x8 grid
+- **Ground truth annotations**: Atom positions, defect types, and phase maps for scoring
+- **Metadata**: Pixel size, accelerating voltage, detector geometry, material parameters
+
+### Materials
+
+| Material | Zone Axis | FOV | Defect Types | Task |
+|----------|-----------|-----|-------------|------|
+| SrTiO3 | [001] | ~100 nm | O vacancies clustered along grain boundary | Defect Census |
+| BaTiO3 | [001] | ~100 nm | Cubic/tetragonal phase boundaries + O vacancies | Phase Mapping + Defect Census |
+| SiGe | [110] | ~50 nm | Ge substitutions concentrated in one quadrant | Targeted Characterization |
+| GaN | [11-20] | ~80 nm | InGaN quantum-well substitutions | Defect Census |
+| Pt nanoparticles | — | ~60 nm | Pt nanoparticles on amorphous carbon | Particle Census |
+
+### Difficulty Levels
+
+Each material is provided at three difficulty levels:
+
+| Level | Vacancy Rate | Phonon Configs | Dose (e-/A^2) |
+|-------|-------------|----------------|---------------|
+| Easy | 5% | 4 | 1e4 |
+| Medium | 3% | 8 | 5e3 |
+| Hard | 1% | 16 | 1e3 |
+
+## Files
+
+### Simulated Worlds (`worlds/`)
+
+| File | Material | Difficulty | Size |
+|------|----------|-----------|------|
+| `test_world.h5` | Synthetic (Gaussian blobs) | — | 9.7 MB |
+| `replay_world.h5` | Synthetic (replay validation) | — | 2.5 MB |
+| `srtio3_clustered_easy.h5` | SrTiO3 | Easy | 884 MB |
+| `srtio3_clustered_medium.h5` | SrTiO3 | Medium | 884 MB |
+| `srtio3_clustered_hard.h5` | SrTiO3 | Hard | 885 MB |
+| `batio3_interface_easy.h5` | BaTiO3 | Easy | 911 MB |
+| `batio3_interface_medium.h5` | BaTiO3 | Medium | 911 MB |
+| `batio3_interface_hard.h5` | BaTiO3 | Hard | 911 MB |
+| `sige_gradient_clustered_easy.h5` | SiGe | Easy | 150 MB |
+| `sige_gradient_clustered_medium.h5` | SiGe | Medium | 148 MB |
+| `sige_gradient_clustered_hard.h5` | SiGe | Hard | 147 MB |
+| `gan_easy.h5` | GaN | Easy | 451 MB |
+| `gan_medium.h5` | GaN | Medium | 449 MB |
+| `gan_hard.h5` | GaN | Hard | 448 MB |
+| `pt_nanoparticles_easy.h5` | Pt | Easy | 129 MB |
+| `pt_nanoparticles_medium.h5` | Pt | Medium | 129 MB |
+| `pt_nanoparticles_hard.h5` | Pt | Hard | 129 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 |
+| `dqn_agent.zip` | DQN (SB3) | RL navigation baseline | 0.8 MB |
+| `ppo_agent.zip` | PPO (SB3) | RL navigation baseline | 1.0 MB |
+| `sac_agent.zip` | SAC (SB3) | RL navigation baseline | 8.4 MB |
+
+### Transfer Checkpoints (`checkpoints/transfer/`)
+
+Material-specific analyst models trained on individual materials for transfer experiments:
+
+| Directory | Contents |
+|-----------|----------|
+| `transfer/srtio3/` | atom_finder.pt, defect_classifier.pt, phase_identifier.pt, training_metadata.json |
+| `transfer/batio3/` | atom_finder.pt, defect_classifier.pt, phase_identifier.pt, training_metadata.json |
+| `transfer/sige/` | atom_finder.pt, defect_classifier.pt, phase_identifier.pt, training_metadata.json |
+| `transfer/gan/` | atom_finder.pt, defect_classifier.pt, phase_identifier.pt, training_metadata.json |
+
+## HDF5 World Format
+
+Each world file follows this layout:
+
+```
+/metadata/
+    pixel_size_nm          # Physical pixel size
+    tile_size_px           # Tile dimensions (128)
+    grid_shape             # Grid dimensions (rows, cols)
+    fov_nm                 # Field of view in nm
+    scenario               # Material/scenario name
+    difficulty             # easy / medium / hard
+/overview                  # (H, W) low-res overview image
+/tiles/{row}_{col}         # (128, 128) float32 normalized HAADF tiles
+/ground_truth/
+    atom_positions         # (N, 2) in nm
+    atom_types             # (N,) int [0=pristine, 1=vacancy, 2=substitution]
+    defect_mask            # (N,) bool
+    defect_types           # (N,) str ["pristine"/"vacancy"/"substitution"]
+    phase_map              # (H, W) int32, optional
+/valid_region              # (H, W) bool
+```
+
+## Usage
+
+```bash
+pip install -e .
+python stem_gym/scripts/download_data.py
+stemgym run --agent raster_equipped --task defect_census --world srtio3_clustered_easy --seeds 3
+```
+
+## License
+
+This dataset is released under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
+
+## Citation
+
+```bibtex
+@inproceedings{anonymous2026stemgym,
+  title={STEMGym: A Gymnasium Environment for Benchmarking Dose-Efficient Autonomous Scanning Transmission Electron Microscopy},
+  author={Anonymous},
+  year={2026}
+}
+```