https://github.com/cgohlke/czifile

Read Carl Zeiss image files (CZI).

Science Score: 36.0%

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1 of 1 committers (100.0%) from academic institutions
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Low similarity (10.4%) to scientific vocabulary

Keywords

format-reader image life-sciences-image python zeiss zeiss-czi-files

Last synced: 5 months ago · JSON representation

Repository

Read Carl Zeiss image files (CZI).

Basic Info

Host: GitHub
Owner: cgohlke
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://pypi.org/project/czifile
Size: 44.9 KB

Statistics

Stars: 30
Watchers: 6
Forks: 9
Open Issues: 1
Releases: 1

Topics

format-reader image life-sciences-image python zeiss zeiss-czi-files

Created almost 6 years ago · Last pushed about 1 year ago

Metadata Files

Readme License

README.rst

Read Carl Zeiss Image (CZI) files
=================================

Czifile is a Python library to read Carl Zeiss Image (CZI) files, the native
file format of the ZEN software by Carl Zeiss Microscopy GmbH. CZI files
contain multidimensional images and metadata from microscopy experiments.

:Author: `Christoph Gohlke `_
:License: BSD 3-Clause
:Version: 2019.7.2.1

Requirements
------------
- `CPython 2.7 or 3.5+ `_
- `Numpy 1.14 `_
- `Tifffile 2019.7.2 `_
- `Imagecodecs 2019.5.22 `_
  (optional; used for decoding LZW, JPEG, and JPEG XR)

Revisions
---------
2019.7.2.1

- Fix broken and deprecated imports.
- Update copyright and package metadata.

2019.7.2

- Require tifffile 2019.7.2.

2019.6.18

- Add package main function to view CZI files.
- Fix BGR to RGB conversion.
- Fix czi2tif conversion on Python 2.

2019.5.22

- Fix czi2tif conversion when CZI metadata contain non-ASCII characters.
- Use imagecodecs_lite as a fallback for imagecodecs.
- Make CziFile.metadata a function (breaking).
- Make scipy an optional dependency; fallback on ndimage or fail on zoom().

2019.1.26

- Fix czi2tif console script.
- Update copyright year.

2018.10.18

- Rename zisraw package to czifile.

2018.8.29

- Move czifile.py and related modules into zisraw package.
- Move usage examples to main docstring.
- Require imagecodecs package for decoding JpegXrFile, JpgFile, and LZW.

2018.6.18

- Save CZI metadata to TIFF description in czi2tif.
- Fix AttributeError using max_workers=1.
- Make Segment.SID and DimensionEntryDV1.dimension str types.
- Return metadata as XML unicode string or dict, not etree.
- Return timestamps, focus positions, events, and luts as tuple or ndarray

2017.7.21

- Use multi-threading in CziFile.asarray to decode and copy segment data.
- Always convert BGR to RGB. Remove bgr2rgb options.
- Decode JpegXR directly from byte arrays.

2017.7.13

- Add function to convert CZI file to memory-mappable TIFF file.

2017.7.11

- Add 'out' parameter to CziFile.asarray.
- Remove memmap option from CziFile.asarray (breaking).
- Change spline interpolation order to 0 (breaking).
- Make axes return a string.
- Require tifffile 2017.7.11.

2014.10.10

- Read data into a memory mapped array (optional).

2013.12.4

- Decode JpegXrFile and JpgFile via _czifle extension module.
- Attempt to reconstruct tiled mosaic images.

2013.11.20

- Initial release.

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

Python 2.7 and 3.4 are deprecated.

"ZEISS" and "Carl Zeiss" are registered trademarks of Carl Zeiss AG.

The ZISRAW file format design specification [1] is confidential and the
license agreement does not permit to write data into CZI files.

Only a subset of the 2016 specification is implemented. Specifically,
multifile images, image pyramids, and topography images are not yet supported.

Tested on Windows with a few example files only.

Czifile relies on the `imagecodecs `_
package for decoding LZW, JPEG, and JPEG XR compressed images. Alternatively,
the `imagecodecs_lite `_ package
can be used for decoding LZW compressed images.

Other libraries for reading CZI files (all GPL licensed):

- `libCZI `_
- `Python-bioformats `_
- `Pylibczi `_

References
----------
1) ZISRAW (CZI) File Format Design Specification Release Version 1.2.2.
   CZI 07-2016/CZI-DOC ZEN 2.3/DS_ZISRAW-FileFormat.pdf (confidential).
   Documentation can be requested at
   ``_

Examples
--------

Read image data from a CZI file as numpy array:

>>> image = imread('test.czi')
>>> image.shape
(3, 3, 3, 250, 200, 3)
>>> image[0, 0, 0, 0, 0]
array([10, 10, 10], dtype=uint8)

Owner

Name: Christoph Gohlke
Login: cgohlke
Kind: user
Location: Irvine, California

Website: https://www.cgohlke.com
Repositories: 52
Profile: https://github.com/cgohlke

GitHub Events

Total

Create event: 1
Release event: 1
Issues event: 5
Watch event: 5
Issue comment event: 4
Push event: 2
Fork event: 1

Last Year

Create event: 1
Release event: 1
Issues event: 5
Watch event: 5
Issue comment event: 4
Push event: 2
Fork event: 1

Name	Email	Commits
Christoph Gohlke	c**e@u**u	35

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 13
Total pull requests: 0
Average time to close issues: 5 months
Average time to close pull requests: N/A
Total issue authors: 13
Total pull request authors: 0
Average comments per issue: 1.46
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: about 2 hours
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

yyyzzzhao (1)
arielleleon (1)
snowformatics (1)
erikogabrielsson (1)
haesleinhuepf (1)
pnewstein (1)
brainfo (1)
horsto (1)
shenxiaochenn (1)
Czaki (1)
amichaut (1)
WinterPan2017 (1)
andreasg123 (1)

Pull Request Authors

Top Labels

Issue Labels

enhancement (1) question (1)

Pull Request Labels

Packages

Total packages: 4
Total downloads:
- pypi 14,361 last-month
Total docker downloads: 310

Total dependent packages: 33
(may contain duplicates)
Total dependent repositories: 48
(may contain duplicates)
Total versions: 17
Total maintainers: 1

pypi.org: czifile

Read Carl Zeiss Image (CZI) files

Homepage: https://www.cgohlke.com
Documentation: https://czifile.readthedocs.io/
License: BSD
Latest release: 2019.7.2
published over 6 years ago

Versions: 13
Dependent Packages: 29
Dependent Repositories: 46
Downloads: 14,347 Last month
Docker Downloads: 310

Rankings

Dependent packages count: 0.5%

Average: 1.9%

Dependent repos count: 2.2%

Docker downloads count: 2.3%

Downloads: 2.5%

Maintainers (1)

cgohlke

Last synced: 5 months ago

Czifile is a Python library to read Carl Zeiss Image (CZI) files, the native file format of the ZEN(r) software by Carl Zeiss Microscopy GmbH. CZI files contain multidimensional images and metadata from microscopy experiments.

Homepage: https://www.lfd.uci.edu/~gohlke/
License: BSD-3-Clause
Latest release: 2019.7.2
published almost 6 years ago

Versions: 1
Dependent Packages: 4
Dependent Repositories: 1

Rankings

Dependent packages count: 12.5%

Average: 18.4%

Dependent repos count: 24.3%

Last synced: 6 months ago

pypi.org: napari-czifile

A napari plugin for reading files via czifile

Homepage: https://www.lfd.uci.edu/~gohlke/
Documentation: https://napari-czifile.readthedocs.io/
License: BSD
Latest release: 0.0.3
published about 4 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 14 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 11.9%

Stargazers count: 13.1%

Dependent repos count: 21.6%

Average: 26.5%

Downloads: 75.7%

Maintainers (1)

cgohlke

Last synced: 6 months ago

pypi.org: bioio-czifile

A bioio plugin for reading files via czifile

Homepage: https://pypi.org/project/{name}/
Documentation: https://bioio-czifile.readthedocs.io/
License: BSD
Latest release: 0.0.1
published over 2 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.6%

Average: 38.8%

Dependent repos count: 68.0%

Maintainers (1)

cgohlke

Last synced: 7 months ago

Dependencies

setup.py pypi

imagecodecs >=2019.5.22
numpy >=1.11.3
scipy >=1.1
tifffile >=2019.7.2

https://github.com/cgohlke/czifile

Science Score: 36.0%

Keywords

Repository

Basic Info

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Metadata Files

README.rst

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pypi.org: czifile

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conda-forge.org: czifile

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pypi.org: napari-czifile

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pypi.org: bioio-czifile

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Dependencies