Metadata-Version: 2.4
Name: biomero-converter
Version: 0.2.0
Summary: Convert source images to OME-TIFF or OME-Zarr, with RO-Crate metadata
Author-email: Joost de Folter <folterj@gmail.com>, Maarten Paul <maarten.paul@gmail.com>
License-Expression: Apache-2.0
Project-URL: Homepage, https://github.com/NL-BioImaging/biomero-converter
Project-URL: Repository, https://github.com/NL-BioImaging/biomero-converter
Project-URL: Documentation, https://nl-bioimaging.github.io/biomero-converter/
Keywords: OME-Zarr,OME-TIFF,RO-Crate,microscopy,bioimaging,conversion
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: numpy
Requires-Dist: ome-zarr<0.18,>=0.16.0
Requires-Dist: zarr>=3.2.0
Requires-Dist: tifffile>=2026.9.20
Requires-Dist: liffile
Requires-Dist: imagecodecs
Requires-Dist: imageio
Requires-Dist: scikit-image
Requires-Dist: dask[array]
Requires-Dist: ome-types>=0.6.2
Requires-Dist: rocrate>=0.15.0
Requires-Dist: psutil
Requires-Dist: pyisyntax
Requires-Dist: openslide-python
Requires-Dist: openslide-bin
Requires-Dist: pydicom
Requires-Dist: chardet
Requires-Dist: python-dateutil
Requires-Dist: pyyaml
Requires-Dist: imaging-metadata-converter>=2.0.0
Provides-Extra: test
Requires-Dist: pytest>=7.0; extra == "test"
Dynamic: license-file

# biomero-converter

Conversion from various formats to Ome-tiff and Ome-zarr

This tool can be used as biomero plugin, Docker container or stand-alone

## Features
- Extract and process image data including bioformats unsupported formats
  - OME-Zarr
  - (OME-) Tiff
  - Thermo Fisher tiff files
  - ImageXpress Pico
  - Molecular Devices
  - CellReporterXpress experiment
  - image db files (.db)
  - isyntax files (.isyntax)
  - Incucyte archives (.icharch)
  - 3DHistech files (.mrxs)
  - DICOM files
  - Leica files (.lif, .lof, .xlef, .xlcf, .xlif)
    - all images in a file, or a single image selected by UUID
    - RGB, multi-channel, Z-stack, time series and tile scans (stitched)
- Export to Ome formats
  - OME-Tiff
  - OME-Zarr
- Supporting
  - (Large) whole slide images
  - Screen Plate Well / High Content Screening format
- Compatible with Omero

## Documentation
### [nl-bioimaging.github.io/biomero-converter](https://nl-bioimaging.github.io/biomero-converter/)
### Generated: [deepwiki.com/NL-BioImaging/biomero-converter](https://deepwiki.com/NL-BioImaging/biomero-converter)
![logo](docs/images/logo.png)
