Bump tifffile from 2023.4.12 to 2025.10.16

[dependabot]

Bumps tifffile from 2023.4.12 to 2025.10.16.

Release notes

Sourced from tifffile's releases.

v2025.10.16

Read and write TIFF files

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, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, Philips DP, and ThermoFisher EER formatted 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.

Image data 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.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

Changes

• Add option to decode EER super-resolution sub-pixels (breaking, #313).
• Parse EER metadata to dict (breaking).

v2025.10.4

Read and write TIFF files

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, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, and Philips DP formatted 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.

Image data 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.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

Changes

• Fix parsing SVS description ending with "|".

v2025.9.30

Read and write TIFF files

Tifffile is a Python library to

... (truncated)

Changelog

Sourced from tifffile's changelog.

2025.10.16

• Pass 5124 tests.
• Add option to decode EER super-resolution sub-pixels (breaking, #313).
• Parse EER metadata to dict (breaking).

2025.10.4

• Fix parsing SVS description ending with "|".

2025.9.30

• Fix reading NDTiff series with unordered axes in index (#311).

2025.9.20

• Derive TiffFileError from ValueError.
• Natural-sort files in glob pattern passed to imread by default (breaking).
• Fix optional sorting of list of files passed to FileSequence and imread.

2025.9.9

• Consolidate Nuvu camera metadata.

2025.8.28

• Support DNG DCP files (#306).

2025.6.11

• Fix reading images with dimension length 1 through Zarr (#303).

2025.6.1

• Add experimental option to write iterator of bytes and bytecounts (#301).

2025.5.26

• Use threads in Zarr stores.

2025.5.24

• Fix incorrect tags created by Philips DP v1.1 (#299).
• Make Zarr stores partially listable.

2025.5.21

• Move Zarr stores to tifffile.zarr namespace (breaking).
• Require Zarr 3 for Zarr stores and remove support for Zarr 2 (breaking).
• Drop support for Python 3.10.

... (truncated)

Commits

• 79e27e8 Release v2025.10.16
• 7735380 Update CHANGES.rst
• d27561e Update tests/test_tifffile.py
• 04b59cc Update tifffile/tifffile.py
• b1d9cba Update tifffile/zarr.py
• b5c7ba2 Release v2025.10.4
• 83401a7 Update CHANGES.rst
• 3d8bcca Update tifffile/tifffile.py
• 74e52bc Update tifffile/zarr.py
• ae08cad Update tests/test_tifffile.py
• Additional commits viewable in compare view

You can trigger a rebase of this PR by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

Note
Automatic rebases have been disabled on this pull request as it has been open for over 30 days.