.gitattributes
.gitignore
AGENTS.md
CLAUDE.md
Dockerfile
LICENSE.md
README.md
SKILLS.md
environment.yml
mkdocs.yml
pixi.lock
pixi.toml
pyproject.toml
requirements.txt
.github/workflows/docker-image.yml
.github/workflows/publish.yml
docs/container.md
docs/convert.md
docs/index.md
docs/main.md
docs/overview.md
docs/references.md
docs/requirements.txt
docs/images/logo.png
metadata_output/Cikteq SEM4000x Automap.tiff.yaml
metadata_output/Cikteq SEM4000x Normal.tiff.yaml
metadata_output/DNAcropSmall.ome.tiff.yaml
metadata_output/Delmic FAST-EM.tiff.yaml
metadata_output/EM04573_01small.ome.tif.yaml
metadata_output/EMSIS Xarosa.tif.yaml
metadata_output/TFS Phenom Pharos.tiff.yaml
metadata_output/Zeiss Supra55 Fibics ATLAS.tif.yaml
notes/todo_known_issues.md
src/biomero_converter/DbReader.py
src/biomero_converter/DicomSource.py
src/biomero_converter/GenericSource.py
src/biomero_converter/ISyntaxSource.py
src/biomero_converter/ImageDbSource.py
src/biomero_converter/ImageSource.py
src/biomero_converter/IncucyteSource.py
src/biomero_converter/LeicaSource.py
src/biomero_converter/MiraxSource.py
src/biomero_converter/OmeTiffWriter.py
src/biomero_converter/OmeWriter.py
src/biomero_converter/OmeZarrSource.py
src/biomero_converter/OmeZarrWriter.py
src/biomero_converter/TiffSource.py
src/biomero_converter/Timer.py
src/biomero_converter/TreeBuilder.py
src/biomero_converter/WindowScanner.py
src/biomero_converter/__init__.py
src/biomero_converter/color_conversion.py
src/biomero_converter/converter.py
src/biomero_converter/helper.py
src/biomero_converter/main.py
src/biomero_converter/ome_tiff_util.py
src/biomero_converter/ome_zarr_util.py
src/biomero_converter/parameters.py
src/biomero_converter/rocrate_utils.py
src/biomero_converter/tiff_metadata.py
src/biomero_converter/util.py
src/biomero_converter/version.py
src/biomero_converter/zarr_extension.py
src/biomero_converter.egg-info/PKG-INFO
src/biomero_converter.egg-info/SOURCES.txt
src/biomero_converter.egg-info/dependency_links.txt
src/biomero_converter.egg-info/entry_points.txt
src/biomero_converter.egg-info/requires.txt
src/biomero_converter.egg-info/scm_file_list.json
src/biomero_converter.egg-info/scm_version.json
src/biomero_converter.egg-info/top_level.txt
test/analyse_rocrate.py
test/openslide_reading.py
test/test_convert.py
test/test_metadata.py
test/test_roundtrip.py