Metadata-Version: 2.1
Name: tllab-common
Version: 2023.3.1
Summary: Common code for the Lenstra lab.
Home-page: https://gitlab.rhpc.nki.nl/LenstraLab/tllab_common
Author: Lenstra lab NKI
Author-email: t.lenstra@nki.nl
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: untangle
Requires-Dist: pandas
Requires-Dist: psutil
Requires-Dist: numpy
Requires-Dist: tqdm
Requires-Dist: tifffile
Requires-Dist: czifile
Requires-Dist: pyyaml
Requires-Dist: dill
Requires-Dist: colorcet
Requires-Dist: multipledispatch
Requires-Dist: scipy
Requires-Dist: tiffwrite
Requires-Dist: roifile
Requires-Dist: ipython
Provides-Extra: bioformats
Requires-Dist: python-javabridge ; extra == 'bioformats'
Requires-Dist: python-bioformats ; extra == 'bioformats'
Provides-Extra: transforms
Requires-Dist: SimpleITK-SimpleElastix ; extra == 'transforms'

# Common Code
Code that both LiveCellAnalysis and smFISH (or others) use and doesn't get major changes goes here. This code should be a submodule in smFISH and LiveCellAnalysis.

# Command line tools:
## wimread
    wimread imagefile
Displays information (pixel size, interval time etc.) about the image file.

# Installation (Ubuntu)
python-javabridge is required, which requires java, for ubuntu:

    sudo apt install openjdk-8-jdk-headless

Set java 8 as default java: 

    sudo update-alternatives --config java

Then this code can be installed as a package:

    sudo pip install git+https://gitlab.rhpc.nki.nl/LenstraLab/tllab_common.git

or editable:

    git clone https://gitlab.rhpc.nki.nl/LenstraLab/tllab_common.git 
    pip install -e tllab_common/ --user
