Awesome

NOTE: aicspylibczi This project has been forked and made into a much more general tool for reading czi files by developers at the Allen Institute for Cell Science at the Allen Institute. Please try this version with pip install aicspylibczi or visit the fork homepage.

pylibczi

Python module to expose libCZI functionality for reading (subset of) Zeiss CZI files and meta-data.

Installation

The preferred installation method is with pip install. This will intall the pylibczi python module and extension binaries (hosted on PyPI):

pip install pylibczi

Usage

For example usage, see sample.py. In the first example, replace test.czi with your own CZI file containing scenes. In the second example, replace test2.czi with your own CZI file containing grayscale or BGR48 image data. The latter is a more generic reader for reading and assembling all subblocks.

Documentation

Documentation is available on readthedocs.

Build

Use these steps to build and install pylibczi locally:

• Clone the repository including submodules (--recurse-submodules).
• Requirements:
  • libCZI requires a c++11 compatible compiler.
  • Development requirements are those required for libCZI: libpng, zlib
  • Install the python requirements:

    pip install -r requirements.txt
    pip install -r dev-requirements.txt
    

• Build and install:

  python setup.py install
  

  • libCZI is automatically built as a submodule and linked statically to pylibczi.