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CHANGELOG.md
INTERNAL_FORK.md
LICENSE.md
README.md
notes.org
package-lock.json
package.json
pyproject.toml
uv.lock
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docs/writing-a-reader-plugin.md
docs/adr/0001-reader-plugin-architecture.md
docs/adr/0002-layout-hint-reservation.md
docs/adr/0003-external-adapter-package-for-non-bioio-readers.md
docs/adr/0004-plate-output-design.md
docs/adr/0005-lif-mosaic-write-strategy.md
src/zarrmony/__init__.py
src/zarrmony/_storage.py
src/zarrmony/_validate.py
src/zarrmony/api.py
src/zarrmony/audit.py
src/zarrmony/cli.py
src/zarrmony/errors.py
src/zarrmony/naming.py
src/zarrmony/transforms.py
src/zarrmony.egg-info/PKG-INFO
src/zarrmony.egg-info/SOURCES.txt
src/zarrmony.egg-info/dependency_links.txt
src/zarrmony.egg-info/entry_points.txt
src/zarrmony.egg-info/requires.txt
src/zarrmony.egg-info/scm_file_list.json
src/zarrmony.egg-info/scm_version.json
src/zarrmony.egg-info/top_level.txt
src/zarrmony/metadata/__init__.py
src/zarrmony/metadata/_lif_scene.py
src/zarrmony/metadata/channel_colors.py
src/zarrmony/metadata/lif_channels.py
src/zarrmony/metadata/lif_tiles.py
src/zarrmony/readers/__init__.py
src/zarrmony/readers/czi.py
src/zarrmony/readers/default.py
src/zarrmony/readers/lif.py
src/zarrmony/readers/nd2.py
src/zarrmony/readers/plate.py
src/zarrmony/readers/plugin.py
src/zarrmony/writers/__init__.py
src/zarrmony/writers/bf2raw.py
src/zarrmony/writers/ome_xml.py
src/zarrmony/writers/per_scene.py
src/zarrmony/writers/plate.py
src/zarrmony/writers/pyramid.py
src/zarrmony/writers/scene.py
tests/__init__.py
tests/conftest.py
tests/test_api.py
tests/test_api_lif_wiring.py
tests/test_audit.py
tests/test_bf2raw.py
tests/test_channel_colors.py
tests/test_cli.py
tests/test_errors.py
tests/test_integration_ome_tiff.py
tests/test_layout_dispatch.py
tests/test_lif_channels.py
tests/test_lif_grid_stitch.py
tests/test_lif_per_tile.py
tests/test_lif_projections.py
tests/test_lif_stage_stitch.py
tests/test_lif_tiles.py
tests/test_naming.py
tests/test_ome_xml.py
tests/test_plate.py
tests/test_plugin_registry.py
tests/test_pyramid.py
tests/test_readers.py
tests/test_scene_writer.py
tests/test_smoke.py
tests/test_storage.py
tests/test_transforms.py
tests/test_validate.py
tests/fixtures/__init__.py
tests/fixtures/lif_confocal_7ch.xml
tests/fixtures/synthesize.py