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Read and write TIFF(r) files

Project description

Tifffile is a Python library to

  1. store numpy arrays in TIFF (Tagged Image File Format) files, and
  2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, SGI, NIHImage, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, ZIF (Zoomable Image File Format), QPTIFF (QPI), NDPI, and GeoTIFF files.

Image data can be read as numpy arrays or zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Numpy arrays can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

A subset of the TIFF specification is supported, mainly 8, 16, 32 and 64-bit integer, 16, 32 and 64-bit float, grayscale and multi-sample images. Specifically, CCITT and OJPEG compression, chroma subsampling without JPEG compression, color space transformations, samples with differing types, or IPTC and XMP metadata are not implemented.

TIFF(r), the Tagged Image File Format, is a trademark and under control of Adobe Systems Incorporated. BigTIFF allows for files larger than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, QPTIFF, NDPI, SCN, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, PerkinElmer, Hamamatsu, Leica, and the Open Microscopy Environment consortium, respectively.

For command line usage run python -m tifffile --help

Author:Christoph Gohlke
Organization:Laboratory for Fluorescence Dynamics, University of California, Irvine
License:BSD 3-Clause
Version:2020.11.18

Requirements

This release has been tested with the following requirements and dependencies (other versions may work):

Revisions

2020.11.18
Pass 4363 tests. Support writing SEPARATED colorspace (#37). Use imagecodecs.deflate if available. Fix SCN and NDPI series with Z dimensions. Add TiffReader alias for TiffFile. TiffPage.is_volumetric returns True if ImageDepth > 1. Zarr store getitem returns numpy arrays instead of bytes.
2020.10.1
Formally deprecate unused TiffFile parameters (scikit-image #4996).
2020.9.30
Allow to pass additional arguments to compression codecs. Deprecate TiffWriter.save function (use TiffWriter.write). Deprecate TiffWriter.save compress parameter (use compression). Remove multifile parameter from TiffFile (breaking). Pass all is_flag arguments from imread to TiffFile. Do not byte-swap JPEG2000, WEBP, PNG, JPEGXR segments in TiffPage.decode.
2020.9.29
Fix reading files produced by ScanImage > 2015 (#29).
2020.9.28
Derive ZarrStore from MutableMapping. Support zero shape ZarrTiffStore. Fix ZarrFileStore with non-TIFF files. Fix ZarrFileStore with missing files. Cache one chunk in ZarrFileStore. Keep track of already opened files in FileCache. Change parse_filenames function to return zero-based indices. Remove reopen parameter from asarray (breaking). Rename FileSequence.fromfile to imread (breaking).
2020.9.22
Add experimental zarr storage interface (WIP). Remove unused first dimension from TiffPage.shaped (breaking). Move reading of STK planes to series interface (breaking). Always use virtual frames for ScanImage files. Use DimensionOrder to determine axes order in OmeXml. Enable writing striped volumetric images. Keep complete dataoffsets and databytecounts for TiffFrames. Return full size tiles from Tiffpage.segments. Rename TiffPage.is_sgi property to is_volumetric (breaking). Rename TiffPageSeries.is_pyramid to is_pyramidal (breaking). Fix TypeError when passing jpegtables to non-JPEG decode function (#25).
2020.9.3
Do not write contiguous series by default (breaking). Allow to write to SubIFDs (WIP). Fix writing F-contiguous numpy arrays (#24).
2020.8.25
Do not convert EPICS timeStamp to datetime object. Read incompletely written Micro-Manager image file stack header (#23). Remove tag 51123 values from TiffFile.micromanager_metadata (breaking).
2020.8.13
Use tifffile metadata over OME and ImageJ for TiffFile.series (breaking). Fix writing iterable of pages with compression (#20). Expand error checking of TiffWriter data, dtype, shape, and tile arguments.
2020.7.24
Parse nested OmeXml metadata argument (WIP). Do not lazy load TiffFrame JPEGTables. Fix conditionally skipping some tests.
2020.7.22
Do not auto-enable OME-TIFF if description is passed to TiffWriter.save. Raise error writing empty bilevel or tiled images. Allow to write tiled bilevel images. Allow to write multi-page TIFF from iterable of single page images (WIP). Add function to validate OME-XML. Correct Philips slide width and length.
2020.7.17
Initial support for writing OME-TIFF (WIP). Return samples as separate dimension in OME series (breaking). Fix modulo dimensions for multiple OME series. Fix some test errors on big endian systems (#18). Fix BytesWarning. Allow to pass TIFF.PREDICTOR values to TiffWriter.save.
2020.7.4
Deprecate support for Python 3.6 (NEP 29). Move pyramidal subresolution series to TiffPageSeries.levels (breaking). Add parser for SVS, SCN, NDPI, and QPI pyramidal series. Read single-file OME-TIFF pyramids. Read NDPI files > 4 GB (#15). Include SubIFDs in generic series. Preliminary support for writing packed integer arrays (#11, WIP). Read more LSM info subrecords. Fix missing ReferenceBlackWhite tag for YCbCr photometrics. Fix reading lossless JPEG compressed DNG files.
2020.6.3
Support os.PathLike file names (#9).
2020.5.30
Re-add pure Python PackBits decoder.
2020.5.25
Make imagecodecs an optional dependency again. Disable multi-threaded decoding of small LZW compressed segments. Fix caching of TiffPage.decode function. Fix xml.etree.cElementTree ImportError on Python 3.9. Fix tostring DeprecationWarning.
2020.5.11
Fix reading ImageJ grayscale mode RGB images (#6). Remove napari reader plugin.
2020.5.7
Add napari reader plugin (tentative). Fix writing single tiles larger than image data (#3). Always store ExtraSamples values in tuple (breaking).
2020.5.5
Allow to write tiled TIFF from iterable of tiles (WIP). Add function to iterate over decoded segments of TiffPage (WIP). Pass chunks of segments to ThreadPoolExecutor.map to reduce memory usage. Fix reading invalid files with too many strips. Fix writing over-aligned image data. Detect OME-XML without declaration (#2). Support LERC compression (WIP). Delay load imagecodecs functions. Remove maxsize parameter from asarray (breaking). Deprecate ijmetadata parameter from TiffWriter.save (use metadata).
2020.2.16
Add function to decode individual strips or tiles. Read strips and tiles in order of their offsets. Enable multi-threading when decompressing multiple strips. Replace TiffPage.tags dictionary with TiffTags (breaking). Replace TIFF.TAGS dictionary with TiffTagRegistry. Remove TIFF.TAG_NAMES (breaking). Improve handling of TiffSequence parameters in imread. Match last uncommon parts of file paths to FileSequence pattern (breaking). Allow letters in FileSequence pattern for indexing well plate rows. Allow to reorder axes in FileSequence. Allow to write > 4 GB arrays to plain TIFF when using compression. Allow to write zero size numpy arrays to nonconformant TIFF (tentative). Fix xml2dict. Require imagecodecs >= 2020.1.31. Remove support for imagecodecs-lite (breaking). Remove verify parameter to asarray function (breaking). Remove deprecated lzw_decode functions (breaking). Remove support for Python 2.7 and 3.5 (breaking).
2019.7.26

Refer to the CHANGES file for older revisions.

Notes

The API is not stable yet and might change between revisions.

Tested on little-endian platforms only.

Python 32-bit versions are deprecated. Python <= 3.7 are no longer supported.

Tifffile relies on the imagecodecs package for encoding and decoding LZW, JPEG, and other compressed image segments.

Several TIFF-like formats do not strictly adhere to the TIFF6 specification, some of which allow file or data sizes to exceed the 4 GB limit:

  • BigTIFF is identified by version number 43 and uses different file header, IFD, and tag structures with 64-bit offsets. It adds more data types. Tifffile can read and write BigTIFF files.
  • ImageJ hyperstacks store all image data, which may exceed 4 GB, contiguously after the first IFD. Files > 4 GB contain one IFD only. The size (shape and dtype) of the up to 6-dimensional image data can be determined from the ImageDescription tag of the first IFD, which is Latin-1 encoded. Tifffile can read and write ImageJ hyperstacks.
  • OME-TIFF stores up to 8-dimensional data in one or multiple TIFF of BigTIFF files. The 8-bit UTF-8 encoded OME-XML metadata found in the ImageDescription tag of the first IFD defines the position of TIFF IFDs in the high dimensional data. Tifffile can read OME-TIFF files, except when the OME-XML metadata are stored in a separate file. Tifffile can write numpy arrays to single-file OME-TIFF.
  • LSM stores all IFDs below 4 GB but wraps around 32-bit StripOffsets. The StripOffsets of each series and position require separate unwrapping. The StripByteCounts tag contains the number of bytes for the uncompressed data. Tifffile can read large LSM files.
  • STK (MetaMorph Stack) contains additional image planes stored contiguously after the image data of the first page. The total number of planes is equal to the counts of the UIC2tag. Tifffile can read STK files.
  • NDPI uses some 64-bit offsets in the file header, IFD, and tag structures. Tag values/offsets can be corrected using high bits stored after IFD structures. JPEG compressed segments with dimensions >65536 or missing restart markers are not readable with libjpeg. Tifffile can read NDPI files > 4 GB. JPEG segments with restart markers and dimensions >65536 can be decoded with the imagecodecs library on Windows.
  • Philips TIFF slides store wrong ImageWidth and ImageLength tag values for tiled pages. The values can be corrected using the DICOM_PIXEL_SPACING attributes of the XML formatted description of the first page. Tifffile can read Philips slides.
  • ScanImage optionally allows corrupt non-BigTIFF files > 2 GB. The values of StripOffsets and StripByteCounts can be recovered using the constant differences of the offsets of IFD and tag values throughout the file. Tifffile can read such files if the image data are stored contiguously in each page.
  • GeoTIFF sparse files allow strip or tile offsets and byte counts to be 0. Such segments are implicitly set to 0 or the NODATA value on reading. Tifffile can read GeoTIFF sparse files.

Other libraries for reading scientific TIFF files from Python:

Some libraries are using tifffile to write OME-TIFF files:

Other tools for inspecting and manipulating TIFF files:

References

Examples

Save a 3D numpy array to a multi-page, 16-bit grayscale TIFF file:

>>> data = numpy.random.randint(0, 2**12, (4, 301, 219), 'uint16')
>>> imwrite('temp.tif', data, photometric='minisblack')

Read the whole image stack from the TIFF file as numpy array:

>>> image_stack = imread('temp.tif')
>>> image_stack.shape
(4, 301, 219)
>>> image_stack.dtype
dtype('uint16')

Read the image from the first page in the TIFF file as numpy array:

>>> image = imread('temp.tif', key=0)
>>> image.shape
(301, 219)

Read images from a sequence of TIFF files as numpy array:

>>> image_sequence = imread(['temp.tif', 'temp.tif'])
>>> image_sequence.shape
(2, 4, 301, 219)

Save a numpy array to a single-page RGB TIFF file:

>>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8')
>>> imwrite('temp.tif', data, photometric='rgb')

Save a floating-point array and metadata, using zlib compression:

>>> data = numpy.random.rand(2, 5, 3, 301, 219).astype('float32')
>>> imwrite('temp.tif', data, compression='zlib', metadata={'axes': 'TZCYX'})

Save a volume with xyz voxel size 2.6755x2.6755x3.9474 micron^3 to an ImageJ formatted TIFF file:

>>> volume = numpy.random.randn(57*256*256).astype('float32')
>>> volume.shape = 1, 57, 1, 256, 256, 1  # dimensions in TZCYXS order
>>> imwrite('temp.tif', volume, imagej=True, resolution=(1./2.6755, 1./2.6755),
...         metadata={'spacing': 3.947368, 'unit': 'um'})

Get the shape and dtype of the volume stored in the TIFF file:

>>> tif = TiffFile('temp.tif')
>>> len(tif.pages)  # number of pages in the file
57
>>> page = tif.pages[0]  # get shape and dtype of the image in the first page
>>> page.shape
(256, 256)
>>> page.dtype
dtype('float32')
>>> page.axes
'YX'
>>> series = tif.series[0]  # get shape and dtype of the first image series
>>> series.shape
(57, 256, 256)
>>> series.dtype
dtype('float32')
>>> series.axes
'ZYX'
>>> tif.close()

Read hyperstack and metadata from the ImageJ file:

>>> with TiffFile('temp.tif') as tif:
...     imagej_hyperstack = tif.asarray()
...     imagej_metadata = tif.imagej_metadata
>>> imagej_hyperstack.shape
(57, 256, 256)
>>> imagej_metadata['slices']
57

Read the “XResolution” tag from the first page in the TIFF file:

>>> with TiffFile('temp.tif') as tif:
...     tag = tif.pages[0].tags['XResolution']
>>> tag.value
(2000, 5351)
>>> tag.name
'XResolution'
>>> tag.code
282
>>> tag.count
1
>>> tag.dtype
'2I'

Read images from a selected range of pages:

>>> image = imread('temp.tif', key=range(4, 40, 2))
>>> image.shape
(18, 256, 256)

Create an empty TIFF file and write to the memory-mapped numpy array:

>>> memmap_image = memmap('temp.tif', shape=(256, 256), dtype='float32')
>>> memmap_image[255, 255] = 1.0
>>> memmap_image.flush()
>>> del memmap_image

Memory-map image data of the first page in the TIFF file:

>>> memmap_image = memmap('temp.tif', page=0)
>>> memmap_image[255, 255]
1.0
>>> del memmap_image

Successively write the frames of one contiguous series to a TIFF file:

>>> data = numpy.random.randint(0, 255, (30, 301, 219), 'uint8')
>>> with TiffWriter('temp.tif') as tif:
...     for frame in data:
...         tif.write(frame, contiguous=True)

Successively append image series to a BigTIFF file, which can exceed 4 GB:

>>> data = numpy.random.randint(0, 255, (5, 2, 3, 301, 219), 'uint8')
>>> with TiffWriter('temp.tif', bigtiff=True) as tif:
...     for i in range(data.shape[0]):
...         tif.write(data[i], photometric='minisblack')

Append an image to the existing TIFF file:

>>> data = numpy.random.randint(0, 255, (301, 219, 3), 'uint8')
>>> imwrite('temp.tif', data, append=True)

Iterate over pages and tags in the TIFF file and successively read images:

>>> with TiffFile('temp.tif') as tif:
...     for page in tif.pages:
...         for tag in page.tags:
...             tag_name, tag_value = tag.name, tag.value
...         image = page.asarray()

Write two numpy arrays to a multi-series OME-TIFF file:

>>> data0 = numpy.random.randint(0, 255, (32, 32, 3), 'uint8')
>>> data1 = numpy.random.randint(0, 1023, (4, 256, 256), 'uint16')
>>> with TiffWriter('temp.ome.tif') as tif:
...     tif.write(data0, photometric='rgb')
...     tif.write(data1, photometric='minisblack',
...              metadata={'axes': 'ZYX', 'SignificantBits': 10,
...                        'Plane': {'PositionZ': [0.0, 1.0, 2.0, 3.0]}})

Read the second image series from the OME-TIFF file:

>>> series1 = imread('temp.ome.tif', series=1)
>>> series1.shape
(4, 256, 256)

Create a TIFF file from a generator of tiles:

>>> def tiles():
...     data = numpy.arange(3*4*16*16, dtype='uint16').reshape((3*4, 16, 16))
...     for i in range(data.shape[0]): yield data[i]
>>> imwrite('temp.tif', tiles(), dtype='uint16', shape=(48, 64), tile=(16, 16))

Write a tiled, multi-resolution, pyramidal OME-TIFF file using JPEG compression. Sub-resolution images are written to SubIFDs:

>>> data = numpy.arange(1024*1024*3, dtype='uint8').reshape((1024, 1024, 3))
>>> with TiffWriter('temp.ome.tif') as tif:
...     options = dict(tile=(256, 256), compression='jpeg')
...     tif.write(data, subifds=2, **options)
...     # save pyramid levels to the two subifds
...     # in production use resampling to generate sub-resolutions!
...     tif.write(data[::2, ::2], subfiletype=1, **options)
...     tif.write(data[::4, ::4], subfiletype=1, **options)

Access the image levels in the pyramidal OME-TIFF file:

>>> baseimage = imread('temp.ome.tif')
>>> second_level = imread('temp.ome.tif', series=0, level=1)
>>> with TiffFile('temp.ome.tif') as tif:
...     baseimage = tif.series[0].asarray()
...     second_level = tif.series[0].levels[1].asarray()

Iterate over and decode single JPEG compressed tiles in the TIFF file:

>>> with TiffFile('temp.ome.tif') as tif:
...     fh = tif.filehandle
...     for page in tif.pages:
...         for index, (offset, bytecount) in enumerate(
...             zip(page.dataoffsets, page.databytecounts)
...         ):
...             fh.seek(offset)
...             data = fh.read(bytecount)
...             tile, indices, shape = page.decode(
...                 data, index, jpegtables=page.jpegtables
...             )

Use zarr to access the tiled, pyramidal images in the TIFF file:

>>> import zarr
>>> store = imread('temp.ome.tif', aszarr=True)
>>> z = zarr.open(store, mode='r')
>>> z
<zarr.hierarchy.Group '/' read-only>
>>> z[0]  # base layer
<zarr.core.Array '/0' (1024, 1024, 3) uint8 read-only>
>>> store.close()

Read an image stack from a series of TIFF files with a file name pattern:

>>> imwrite('temp_C001T001.tif', numpy.random.rand(64, 64))
>>> imwrite('temp_C001T002.tif', numpy.random.rand(64, 64))
>>> image_sequence = TiffSequence('temp_C001*.tif', pattern='axes')
>>> image_sequence.shape
(1, 2)
>>> image_sequence.axes
'CT'
>>> data = image_sequence.asarray()
>>> data.shape
(1, 2, 64, 64)
>>> with image_sequence.aszarr() as store:
...     zarr.open(store, mode='r')
<zarr.core.Array (1, 2, 64, 64) float64 read-only>
>>> image_sequence.close()

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