Making it installabel package and switching to segmentation mode

BUILD.md

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+# Building and Publishing Guide
+
+This guide explains how to build and publish the microscopy-object-detection package.
+
+## Prerequisites
+
+```bash
+pip install build twine
+```
+
+## Building the Package
+
+### 1. Clean Previous Builds
+
+```bash
+rm -rf build/ dist/ *.egg-info
+```
+
+### 2. Build Distribution Archives
+
+```bash
+python -m build
+```
+
+This will create both wheel (`.whl`) and source distribution (`.tar.gz`) in the `dist/` directory.
+
+### 3. Verify the Build
+
+```bash
+ls dist/
+# Should show:
+# microscopy_object_detection-1.0.0-py3-none-any.whl
+# microscopy_object_detection-1.0.0.tar.gz
+```
+
+## Testing the Package Locally
+
+### Install in Development Mode
+
+```bash
+pip install -e .
+```
+
+### Install from Built Package
+
+```bash
+pip install dist/microscopy_object_detection-1.0.0-py3-none-any.whl
+```
+
+### Test the Installation
+
+```bash
+# Test CLI
+microscopy-detect --version
+
+# Test GUI launcher
+microscopy-detect-gui
+```
+
+## Publishing to PyPI
+
+### 1. Configure PyPI Credentials
+
+Create or update `~/.pypirc`:
+
+```ini
+[pypi]
+username = __token__
+password = pypi-YOUR-API-TOKEN-HERE
+```
+
+### 2. Upload to Test PyPI (Recommended First)
+
+```bash
+python -m twine upload --repository testpypi dist/*
+```
+
+Then test installation:
+
+```bash
+pip install --index-url https://test.pypi.org/simple/ microscopy-object-detection
+```
+
+### 3. Upload to PyPI
+
+```bash
+python -m twine upload dist/*
+```
+
+## Version Management
+
+Update version in multiple files:
+- `setup.py`: Update `version` parameter
+- `pyproject.toml`: Update `version` field
+- `src/__init__.py`: Update `__version__` variable
+
+## Git Tags
+
+After publishing, tag the release:
+
+```bash
+git tag -a v1.0.0 -m "Release version 1.0.0"
+git push origin v1.0.0
+```
+
+## Package Structure
+
+The built package includes:
+- All Python source files in `src/`
+- Configuration files in `config/`
+- Database schema file (`src/database/schema.sql`)
+- Documentation files (README.md, LICENSE, etc.)
+- Entry points for CLI and GUI
+
+## Troubleshooting
+
+### Import Errors
+If you get import errors, ensure:
+- All `__init__.py` files are present
+- Package structure follows the setup configuration
+- Dependencies are listed in `requirements.txt`
+
+### Missing Files
+If files are missing in the built package:
+- Check `MANIFEST.in` includes the required patterns
+- Check `pyproject.toml` package-data configuration
+- Rebuild with `python -m build --no-isolation` for debugging
+
+### Version Conflicts
+If version conflicts occur:
+- Ensure version is consistent across all files
+- Clear build artifacts and rebuild
+- Check for cached installations: `pip list | grep microscopy`
+
+## CI/CD Integration
+
+### GitHub Actions Example
+
+```yaml
+name: Build and Publish
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        pip install build twine
+    - name: Build package
+      run: python -m build
+    - name: Publish to PyPI
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: twine upload dist/*
+```
+
+## Best Practices
+
+1. **Version Bumping**: Use semantic versioning (MAJOR.MINOR.PATCH)
+2. **Testing**: Always test on Test PyPI before publishing to PyPI
+3. **Documentation**: Update README.md and CHANGELOG.md for each release
+4. **Git Tags**: Tag releases in git for easy reference
+5. **Dependencies**: Keep requirements.txt updated and specify version ranges
+
+## Resources
+
+- [Python Packaging Guide](https://packaging.python.org/)
+- [setuptools Documentation](https://setuptools.pypa.io/)
+- [PyPI Publishing Guide](https://packaging.python.org/tutorials/packaging-projects/)