Read and write image data from and to TIFF files.
Project description
Read and write image data from and to TIFF files.
Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, SGI, ImageJ, MicroManager, FluoView, SEQ and GEL files. Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly used in bio-scientific imaging. Specifically, reading JPEG and CCITT compressed image data or EXIF, IPTC, GPS, and XMP metadata is not implemented. Only primary info records are read for STK, FluoView, MicroManager, and NIH image formats.
TIFF, the Tagged Image File Format, is under the control of Adobe Systems. BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, and the Open Microscopy Environment consortium respectively.
For command line usage run python tifffile.py --help
- Author:
- Organization:
Laboratory for Fluorescence Dynamics, University of California, Irvine
- Version:
2017.01.12
Requirements
Matplotlib 1.5 (optional for plotting)
Installation
If using conda, conda install tifffile -c conda-forge.
Otherwise, pip install tifffile.
Notes
This is a mirror of the code at http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html. For any development concerns, please email Christoph Gohlke at cgohlke at uci.edu.
The API is not stable yet and might change between revisions.
Tested on little-endian platforms only.
Other Python packages and modules for reading bio-scientific TIFF files:
PyMca.TiffIO.py (same as fabio.TiffIO)
Acknowledgements
Egor Zindy, University of Manchester, for cz_lsm_scan_info specifics.
Wim Lewis for a bug fix and some read_cz_lsm functions.
Hadrien Mary for help on reading MicroManager files.
References
TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated. http://partners.adobe.com/public/developer/tiff/
TIFF File Format FAQ. http://www.awaresystems.be/imaging/tiff/faq.html
MetaMorph Stack (STK) Image File Format. http://support.meta.moleculardevices.com/docs/t10243.pdf
Image File Format Description LSM 5/7 Release 6.0 (ZEN 2010). Carl Zeiss MicroImaging GmbH. BioSciences. May 10, 2011
File Format Description - LSM 5xx Release 2.0. http://ibb.gsf.de/homepage/karsten.rodenacker/IDL/Lsmfile.doc
The OME-TIFF format. http://www.openmicroscopy.org/site/support/file-formats/ome-tiff
UltraQuant(r) Version 6.0 for Windows Start-Up Guide. http://www.ultralum.com/images%20ultralum/pdf/UQStart%20Up%20Guide.pdf
Micro-Manager File Formats. http://www.micro-manager.org/wiki/Micro-Manager_File_Formats
Tags for TIFF and Related Specifications. Digital Preservation. http://www.digitalpreservation.gov/formats/content/tiff_tags.shtml
Examples
>>> data = numpy.random.rand(5, 301, 219) >>> imsave('temp.tif', data)
>>> image = imread('temp.tif') >>> numpy.testing.assert_array_equal(image, data)
>>> with TiffFile('temp.tif') as tif: ... images = tif.asarray() ... for page in tif: ... for tag in page.tags.values(): ... t = tag.name, tag.value ... image = page.asarray()
Known build errors
On Windows, the error Error:unable to find vcvarsall.bat means that distutils is not correctly configured to use the C compiler. Modify (or create, if not existing) the configuration file distutils.cfg (located for example at C:\Python27\Lib\distutils\distutils.cfg) to contain:
[build] compiler=mingw32
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