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Release v2025.1.10
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cgohlke committed Jan 10, 2025
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30 changes: 18 additions & 12 deletions README.rst
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Expand Up @@ -16,7 +16,7 @@ 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,
Image data can be read as NumPy arrays or Zarr 2 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
Expand All @@ -35,7 +35,7 @@ many proprietary metadata formats.

:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD 3-Clause
:Version: 2024.12.12
:Version: 2025.1.10
:DOI: `10.5281/zenodo.6795860 <https://doi.org/10.5281/zenodo.6795860>`_

Quickstart
Expand Down Expand Up @@ -72,24 +72,29 @@ This revision was tested with the following requirements and dependencies
(other versions may work):

- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.8, 3.13.1 64-bit
- `NumPy <https://pypi.org/project/numpy/>`_ 2.1.3
- `Imagecodecs <https://pypi.org/project/imagecodecs/>`_ 2024.9.22
- `NumPy <https://pypi.org/project/numpy/>`_ 2.2.1
- `Imagecodecs <https://pypi.org/project/imagecodecs/>`_ 2024.12.30
(required for encoding or decoding LZW, JPEG, etc. compressed segments)
- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.9.3
- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.0
(required for plotting)
- `Lxml <https://pypi.org/project/lxml/>`_ 5.3.0
(required only for validating and printing XML)
- `Zarr <https://pypi.org/project/zarr/>`_ 2.18.4
(required only for opening Zarr stores; Zarr 3 is not compatible)
- `Fsspec <https://pypi.org/project/fsspec/>`_ 2024.10.0
- `Fsspec <https://pypi.org/project/fsspec/>`_ 2024.12.0
(required only for opening ReferenceFileSystem files)

Revisions
---------

2024.12.12
2025.1.10

- Pass 5110 tests.
- Improve type hints.
- Deprecate Python 3.10.

2024.12.12

- Read PlaneProperty from STK UIC1Tag (#280).
- Allow 'None' as alias for COMPRESSION.NONE and PREDICTOR.NONE (#274).
- Zarr 3 is not supported (#272).
Expand All @@ -98,7 +103,7 @@ Revisions

- Fix writing colormap to ImageJ files (breaking).
- Improve typing.
- Remove support for Python 3.9.
- Drop support for Python 3.9.

2024.8.30

Expand Down Expand Up @@ -270,7 +275,7 @@ sizes to exceed the 4 GB limit of the classic TIFF:
Tifffile can read GeoTIFF sparse files.
- **Tifffile shaped** files store the array shape and user-provided metadata
of multi-dimensional image series in JSON format in the ImageDescription tag
of the first page of the series. The format allows for multiple series,
of the first page of the series. The format allows multiple series,
SubIFDs, sparse segments with zero offset and byte count, and truncated
series, where only the first page of a series is present, and the image data
are stored contiguously. No other software besides Tifffile supports the
Expand Down Expand Up @@ -308,6 +313,7 @@ References

- TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated.
https://www.adobe.io/open/standards/TIFF.html
https://download.osgeo.org/libtiff/doc/
- TIFF File Format FAQ. https://www.awaresystems.be/imaging/tiff/faq.html
- The BigTIFF File Format.
https://www.awaresystems.be/imaging/tiff/bigtiff.html
Expand Down Expand Up @@ -762,7 +768,7 @@ Open the fsspec ReferenceFileSystem as a Zarr group:
<zarr.hierarchy.Group '/' read-only>
Create an OME-TIFF file containing an empty, tiled image series and write
to it via the Zarr interface (note: this does not work with compression):
to it via the Zarr 2 interface (note: this does not work with compression):

.. code-block:: python
Expand Down Expand Up @@ -797,7 +803,7 @@ threads:
dtype('float64')
Read an image stack from a series of TIFF files with a file name pattern
as NumPy or Zarr arrays:
as NumPy or Zarr 2 arrays:

.. code-block:: python
Expand All @@ -821,7 +827,7 @@ Write the Zarr 2 store to a fsspec ReferenceFileSystem in JSON format:
>>> store = image_sequence.aszarr()
>>> store.write_fsspec('temp.json', url='file://')
Open the fsspec ReferenceFileSystem as a Zarr array:
Open the fsspec ReferenceFileSystem as a Zarr 2 array:

.. code-block:: python
Expand Down

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