update claude config + README

CLAUDE.md

@@ -0,0 +1,100 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+`biahub` is a bioimage analysis hub for high-throughput data reconstruction on HPC clusters with Slurm workload management. It accelerates processing of mult`imodal microscopy datasets stored as OME-ZARR files.
+
+## Key Development Commands
+
+### Usage on HPC nodes login-01, login-01, gpu-*, cpu-*
+Use pre-built biautils environment.
+
+```bash
+module load comp_micro
+conda activate biautils
+```
+
+### Fresh installation
+```bash
+# Create conda environment and install
+conda create -n biahub python==3.11
+conda activate biahub
+pip install -e ".[dev]"
+```
+
+### Code Quality and Testing
+```bash
+# Format code
+make format              # Run black and isort formatters
+make check-format        # Check formatting without changing files
+
+# Linting and validation
+make lint                # Run flake8 linting
+make pre-commit          # Run all pre-commit hooks
+
+# Testing  
+make test                # Run pytest with warnings disabled
+python -m pytest . --disable-pytest-warnings
+```
+
+### Package Management
+```bash
+make setup-develop       # Install package in development mode
+make uninstall          # Uninstall the package
+```
+
+## Architecture Overview
+
+### Command Line Interface
+- **Entry point**: `biahub.cli.main:cli` - Main CLI command with lazy-loaded subcommands
+- **CLI structure**: Uses Click with `LazyCommand` pattern for performance - commands are only imported when invoked
+- **Available commands**: 20+ processing commands including deskew, register, stitch, deconvolve, stabilize, track, segment, etc.
+
+### Core Processing Modules
+Each processing operation has its own module with standardized structure:
+- `biahub/<operation>.py` - Core processing function
+- CLI wrapper at `biahub/<operation>/<operation>_cli.py`
+- Configuration handled via Pydantic settings classes in `biahub/settings.py`
+
+### Key Processing Categories
+1. **Image Correction**: deskew, stabilize, register, flip
+2. **Reconstruction**: deconvolve (with PSF), reconstruct (phase/birefringence)
+3. **Multi-image Operations**: concatenate, stitch  
+4. **Analysis**: segment, track, characterize-psf
+5. **Calibration**: estimate-* commands for parameter optimization
+
+### Configuration System
+- **Settings**: Comprehensive Pydantic models in `biahub/settings.py` with validation
+- **Config files**: YAML configuration files in `settings/` directory with examples
+- **Validation**: Strong typing and validation for all parameters including transforms, slices, file paths
+
+### Data Flow Architecture
+- **Input/Output**: OME-ZARR datasets enable efficient HPC parallelization
+- **Processing patterns**: Most operations work on `/*/*/* `position patterns for parallel processing
+- **Slurm integration**: Commands can launch Slurm jobs or run locally with `-l` flag
+
+### Key Dependencies
+- Contains vendored packages in `biahub/vendor/` directory
+- External stitching library: `stitch @ git+https://github.com/ahillsley/stitching@jen`
+- Uses iohub for zarr i/o: `https://github.com/czbiohub-sf/iohub/`
+- Uses PyTorch for GPU acceleration.
+
+## Code Formatting Standards
+- **Black**: Line length 95, skip string normalization, Python 3.10+ target
+- **isort**: Black-compatible profile, line length 95
+- **Exclusions**: scripts/, examples/, notebooks/, ignore/ directories excluded from formatting
+
+## Testing Structure
+- Tests located in `tests/` directory with CLI-specific tests in `test_cli/`
+- Uses pytest with importlib import mode
+- Includes configuration validation tests and CLI integration tests
+
+## Development Notes
+- Write docstrings in numpy style.
+- Prefer PyTorch for GPU acceleration over other libraries such as cupy.
+- Python 3.11+ required
+- GPU support available (CUDA) for relevant operations
+- Heavy use of scientific Python stack: numpy, scipy, torch, matplotlib
+- Microscopy-specific libraries: napari, iohub, waveorder, antspyx

README.md

@@ -1,8 +1,8 @@
 # biahub
 
-Bio-image analysis hub supporting high-throughput data reconstruction on HPC clusters with [Slurm](https://slurm.schedmd.com/documentation.html) workload management.
+biahub (bioimage analysis hub) is a pipeline to turn raw high throughput imaging data into AI ready nD datasets on HPC clusters running on [Slurm](https://slurm.schedmd.com/documentation.html) workload management.
 
-![acquisition and reconstruction schematic](https://github.com/czbiohub-sf/shrimPy/blob/main/docs/figure_3a.png)
+![biahub schematic](https://github.com/czbiohub-sf/shrimPy/blob/main/docs/figure_3a.png)
 
 `biahub` was originally developed to reconstruct data acquired on the [mantis](https://doi.org/10.1093/pnasnexus/pgae323) microscope using the [shrimPy](https://github.com/czbiohub-sf/shrimPy) acquisition engine, and has since been extended to process diverse multimodal datasets. `biahub` reconstruction workflows rely on OME-ZARR datasets (for example, as created with [iohub](https://github.com/czbiohub-sf/iohub)) which enable efficient parallelization across compute nodes. Available reconstruction routines are listed below; more information can be obtained with `biahub --help`.