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+# AGENTS.md
+
+This file provides detailed guidance to Claude Code agents when working with code in this repository.
+
+## Project Overview
+
+VisCy is a PyTorch Lightning-based deep learning pipeline for image-based phenotyping at single-cell resolution. It supports three main tasks:
+
+1. **Image Translation (Virtual Staining)** - Robust virtual staining using Cytoland models (VSCyto2D, VSCyto3D, VSNeuromast)
+2. **Representation Learning** - Self-supervised learning via DynaCLR for cell dynamics
+3. **Semantic Segmentation** - Supervised learning of cell states
+
+## Development Commands
+
+### Environment Setup
+
+```sh
+# Development installation with all dependencies
+pip install -e ".[dev]"
+
+# Install pre-commit hooks
+pre-commit install
+
+# Run pre-commit manually
+pre-commit run  # on staged files only
+```
+
+### Testing and Linting
+
+```sh
+# Run all tests
+pytest -v
+
+# Run specific test file
+pytest tests/path/to/test_file.py -v
+
+# Lint and format code
+ruff check viscy
+ruff format viscy tests
+```
+
+### CLI Usage
+
+The main entry point is the `viscy` CLI command (defined in `viscy/cli.py`):
+
+```sh
+# View help
+viscy --help
+
+# Training (fit)
+viscy fit --config path/to/config.yaml
+
+# Prediction (predict)
+viscy predict --config path/to/config.yaml --ckpt_path path/to/checkpoint.ckpt
+
+# Validation (validate)
+viscy validate --config path/to/config.yaml --ckpt_path path/to/checkpoint.ckpt
+
+# Testing (test)
+viscy test --config path/to/config.yaml --ckpt_path path/to/checkpoint.ckpt
+
+# Preprocessing (compute dataset statistics for normalization)
+viscy preprocess --data_path path/to/data.zarr --channel_names channel1 channel2
+
+# Export model to ONNX
+viscy export --model.class_path VisCy.Model --ckpt_path checkpoint.ckpt --export_path model.onnx
+
+# Precompute normalized arrays
+viscy precompute --data_path input.zarr --output_path output.zarr --channel_names ch1 ch2
+
+# Convert embeddings to AnnData
+viscy convert_to_anndata --embeddings_path embeddings.zarr --output_anndata_path output.h5ad
+```
+
+## Architecture
+
+### High-Level Structure
+
+VisCy follows PyTorch Lightning patterns with a modular architecture:
+
+- **CLI Layer** (`viscy/cli.py`): Lightning CLI wrapper that extends `LightningCLI` with custom subcommands
+- **Trainer** (`viscy/trainer.py`): Custom `VisCyTrainer` extending `lightning.pytorch.Trainer` with preprocessing, export, and conversion methods
+- **Task Modules**: Task-specific `LightningModule` implementations:
+  - `viscy/translation/engine.py`: `VSUNet` for image translation/virtual staining
+  - `viscy/representation/engine.py`: `ContrastiveModule` for self-supervised contrastive learning
+  - `viscy/representation/vae.py`: Beta-VAE models for representation learning
+- **Data Modules** (`viscy/data/`): Task-specific `LightningDataModule` implementations
+- **Networks** (`viscy/unet/networks/`): Network architectures (UNeXt2, Unet2D, Unet25D, FCMAE)
+- **Transforms** (`viscy/transforms/`): Custom data augmentations built on MONAI
+
+### Data Flow
+
+1. **Input Format**: OME-Zarr datasets stored in HCS (High-Content Screening) layout via `iohub`
+2. **Preprocessing**: Compute channel-wise statistics (mean/std) stored as metadata in OME-Zarr attributes
+3. **Training**: Lightning reads configs (YAML), loads data via DataModules, trains models, logs to TensorBoard
+4. **Inference**: Load checkpoint, predict on new data, write results to OME-Zarr
+5. **Evaluation**: Compare predictions to ground truth using metrics in `viscy/translation/evaluation_metrics.py`
+6. **Export**: Models can be exported to ONNX format for deployment
+
+### Key Data Modules
+
+- `viscy/data/hcs.py`: HCS OME-Zarr dataset for high-content screening data
+- `viscy/data/triplet.py`: Triplet sampling for contrastive learning (anchor, positive, negative)
+- `viscy/data/cell_division_triplet.py`: Cell division-specific triplet sampling
+- `viscy/data/gpu_aug.py`: GPU-accelerated augmentation wrapper
+- `viscy/data/combined.py`: Multi-task combined data module
+
+### Task-Specific Engines
+
+**VSUNet** (Virtual Staining):
+- Loss: `MixedLoss` combining L1, L2, and MS-DSSIM
+- Architectures: UNeXt2 (default), Unet2D, Unet25D, FCMAE
+- Key metrics: SSIM, Pearson correlation, MSE, MAE
+
+**ContrastiveModule** (DynaCLR):
+- Loss: Triplet margin loss, cosine embedding loss, or NTXentLoss
+- Encoder + projection head architecture
+- Tracks embeddings and similarity metrics
+
+**BetaVae** (Variational Autoencoder):
+- Implementations: `BetaVae25D`, `BetaVaeMonai`
+- Specialized logging in `vae_logging.py`
+
+### Config System
+
+Uses `jsonargparse` for Lightning CLI configuration. Configs are YAML files specifying:
+- `model`: Model class and hyperparameters
+- `data`: DataModule class and data paths
+- `trainer`: Lightning Trainer settings (GPUs, precision, etc.)
+
+Example structure:
+```yaml
+model:
+  class_path: viscy.translation.engine.VSUNet
+  init_args:
+    architecture: UNeXt2
+    loss_function:
+      l1_alpha: 0.5
+      ms_dssim_alpha: 0.5
+
+data:
+  class_path: viscy.data.hcs.HCSDataModule
+  init_args:
+    data_path: /path/to/data.zarr
+    source_channel: ["Phase"]
+    target_channel: ["Nuclei", "Membrane"]
+
+trainer:
+  max_epochs: 50
+  devices: [0]
+```
+
+#### Common Config Issues
+
+**Missing `class_path` error**: If you see an error like:
+```
+error: Parser key "model":
+  Does not validate against any of the Union subtypes
+  - Problem with given class_path 'lightning.LightningModule':
+      Validation failed: Key 'model_config.in_channels' is not expected
+```
+
+This means the config file is missing the `class_path` key. Old configs may have parameters directly under `model:` without specifying the class. Fix by restructuring:
+
+```yaml
+# OLD (incorrect):
+model:
+  model_config:
+    in_channels: 1
+    out_channels: 2
+  lr: 0.0002
+
+# NEW (correct):
+model:
+  class_path: viscy.translation.engine.VSUNet  # or appropriate model class
+  init_args:
+    architecture: UNeXt2
+    model_config:
+      in_channels: 1
+      out_channels: 2
+    lr: 0.0002
+```
+
+**Determining the correct `class_path`**:
+- For virtual staining: `viscy.translation.engine.VSUNet`
+- For contrastive learning: `viscy.representation.engine.ContrastiveModule`
+- For VAE: `viscy.representation.vae.BetaVae25D` or `viscy.representation.vae.BetaVaeMonai`
+- For classification: `viscy.representation.classification.ContrastiveClassifier`
+
+Look at the parameters to identify the model type:
+- `architecture`, `loss_function` → VSUNet
+- `encoder`, `loss_function` (with triplet/contrastive) → ContrastiveModule
+- `model_config.encoder_blocks`, `model_config.dims` → UNeXt2-based models
+
+### Transforms and Augmentations
+
+Custom transforms in `viscy/transforms/` extend MONAI's dictionary transforms:
+- Support for 2.5D (volumetric time-lapse) data
+- GPU-accelerated transforms when used with `GPUTransformDataModule`
+- Batched random transforms: elastic deformation, histogram shift, local pixel shuffling, z-stack shift
+
+## File Organization
+
+Data hierarchy follows the structure documented in `viscy/data_organization.md`:
+
+```
+project_root/
+├── datasets/
+│   ├── train/
+│   │   └── *.zarr  # Training OME-Zarr datasets
+│   └── test/
+│       └── *.zarr  # Test datasets
+└── models/
+    └── experiment_name/
+        ├── config.yaml  # Training config
+        └── lightning_logs/
+            └── version_*/
+                ├── checkpoints/*.ckpt
+                └── config.yaml  # Auto-saved full config
+```
+
+## Testing
+
+Tests mirror the source structure in `tests/`:
+- Unit tests for data modules, transforms, models
+- Fixtures defined in `tests/conftest.py`
+- Run specific test modules: `pytest tests/data/test_hcs.py -v`
+
+## Dependencies
+
+Core dependencies:
+- `torch>=2.4.1`: PyTorch framework
+- `lightning>=2.3`: PyTorch Lightning
+- `iohub[tensorstore]>=0.3a2`: OME-Zarr I/O with HCS layout
+- `monai>=1.4`: Medical image transforms and networks
+- `kornia`: Differentiable computer vision
+- `pytorch-metric-learning>2`: Contrastive learning losses
+- `timm>=0.9.5`: Vision model architectures
+
+Optional extras:
+- `[metrics]`: Cellpose, torchmetrics, UMAP for evaluation
+- `[visual]`: Visualization tools (torchview, plotly, dash)
+- `[examples]`: Jupyter, napari for interactive examples
+- `[dev]`: All dependencies + pytest, ruff, hypothesis
+
+## CI/Pre-commit
+
+Pre-commit hooks (`.pre-commit-config.yaml`):
+- `ruff-check` and `ruff-format` for linting/formatting
+- `pyproject-fmt` for pyproject.toml formatting
+- Standard hooks: detect-private-key, check-ast, trailing-whitespace, etc.
+
+Formatting configuration in `pyproject.toml`:
+- Line length: 88
+- Import sorting via ruff with `viscy` as first-party
+
+## Notes
+
+- GPU required for training (tested on NVIDIA Ampere/Hopper with CUDA 12.6)
+- Set `VISCY_LOG_LEVEL` environment variable to control logging
+- Default random seed is 42 for reproducibility
+- TF32 precision enabled by default for performance
+- Mixed precision training available via Lightning Trainer flags
diff --git a/CLAUDE.md b/CLAUDE.md
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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+@AGENTS.md