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README.md

@@ -9,6 +9,7 @@ tags:
   - gymnasium
   - benchmark
   - dose-efficiency
+  - autonomous-microscopy
 pretty_name: STEMGym
 size_categories:
   - 1K<n<10K
@@ -16,28 +17,36 @@ size_categories:
 
 # 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.
+This dataset accompanies the [STEMGym](https://anonymous.4open.science/r/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
+- **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 | 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 |
+| 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 (easy, medium, hard) controlling defect density, noise level, and spatial distribution.
+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
 
@@ -45,24 +54,45 @@ Each material is provided at three difficulty levels (easy, medium, hard) contro
 
 | 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 |
+| `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 |
+| `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
 
@@ -72,18 +102,19 @@ 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
+    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, 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
+    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
@@ -93,10 +124,10 @@ Each world file follows this layout:
 pip install -e .
 
 # Download this data
-python scripts/download_data.py
+python stem_gym/scripts/download_data.py
 
 # Run a benchmark
-stemgym run --agent raster_equipped --task defect_census --world srtio3_medium --seeds 3
+stemgym run --agent raster_equipped --task defect_census --world srtio3_clustered_easy --seeds 3
 ```
 
 ## License
@@ -105,10 +136,4 @@ This dataset is released under the [CC-BY-4.0](https://creativecommons.org/licen
 
 ## Citation
 
-```bibtex
-@inproceedings{stemgym2026,
-  title={STEMGym: A Benchmark for Dose-Efficient Autonomous STEM Microscopy},
-  author={Polat, John},
-  year={2026}
-}
-```
+Citation will be provided after review.