This package can be used to read image data using BioFormats into numpy arrays. It was initially created to simplify reading CZI image files, but should work with many more image data files thanks to BioFormats.

Author

Sebastian Rhode

Version

2015.06.18

• CPython 2.7
• Numpy 1.8.2
• python-bioformats
• BioFormats package
• javabridge
• czifile

The package is still under development and was mainly tested with CZI files.

The python-bioformats package includes loci_tool.jar but it is also possible to use the latest bioformats_package.jar. Currently the 5.1.3 version of bioformats_package.jar is used. Update it to your needs.

• Christoph Gohlke from providing the czifily.py.
• The Cellprofiler team for providing python-bioformats
• The OME people for creating BioFormats

1. CZI - Image format for microscopes http://www.zeiss.com/czi
2. The OME-TIFF format. http://www.openmicroscopy.org/site/support/file-formats/ome-tiff
3. Read microscopy images to numpy array with python-bioformats. http://ilovesymposia.com/2014/08/10/read-microscopy-images-to-numpy-arrays-with-python-bioformats/