Pipeline core

The core classes and methods for the python microfluidics, microscopy, and analysis pypline pipeline.

References

• OMERO python bindings
• Zeroc-ice python

Installation

How to set up access to OMERO from python:

• Install openssl headers version 1.0.2: sudo apt-get install libssl1.0-dev
• Install the corresponding openssl (as default is 1.1.1): conda install openssl==1.0.2k
• Install bzip headers : sudo apt-get install libbz2-dev
• Install zeroc-ice from PyPI, which includes Ice: pip install zeroc-ice==3.6.0
• Run connect_to_omero.py as a test (TODO TESTS)

Disclaimers

TLDR: Most of this stuff is depcrecated. Using OMERO 5.2.5 means that we need to use depreacted python 2.7 (EOL 2020.01.01), and we need to use zeroc-ice version 3.6 which is also dropped in the newer version of OMERO. The local version of openssl (conda) needs to fit the headers of libssl-dev (apt-get). By default conda will install OpenSSL version 1.1.1 as all the others are no longer maintained. However, using the headers of verions 1.0.2 means that we have to downgrade OpenSSL to version 1.0.2 also.

It is highly recommended that we upgrade OMERO to 5.6 in order to use Python 3, in which case it will even be possible to get OMERO.py directly from PyPI with easy installation, omero-py

Requirements

pyOmeroUpload: https://github.com/SynthSys/pyOmeroUpload.git

Clone the repository: git clone https://github.com/SynthSys/pyOmeroUpload.git Then install with pip install pyOmeroUpload

Local file Origanisation

If the experiment is saved locally, we expect the organisation to be as in this repository