glencoesoftware / webinar-notebooks

Jupyter notebooks from our OMERO Plus for High Content Screening & Analysis webinar

OMERO Plus Jupyter notebooks

This repository contains a set of Jupyter notebooks that demonstrate various image and metadata workflows by utilising OMERO Plus API.

Notebook 0

This notebook demonstrates basic python API calls.

The notebook covers: server connection, image retrieval and query service.

Notebooks 1 - 3

Presented during OMERO Plus for High Content Screening & Analysis: The Gold Standard in Data Management & Integratio webinar.

These notebooks demonstrate how to access the analytical data stored in OMERO using OMERO.tables and file annotations.

The notebooks cover: data retrieval, visualisation, statistical analysis and machine learning.

Notebook 4

Preseted during Using PathViewer and Multiplexed Imaging to Advance Cancer Research webinar.

This notebook demonstrates how to read raw image pixels from OMERO Plus, perform image processing using scikit-image and save the analysis results to OMERO Plus. Objects identified by scikit-image algorithms are converted to OMERO region of interests (ROIs) and a set of key - value pairs describing each object.

The notebook covers: raw pixel retrieval, image processing, OMERO ROI creation and saving, OMERO key - value pair creation, saving and linking to ROIs.

Requirements

• OMERO.server,
• OMERO.tables,
• matplotlib,
• pandas,
• scikit-learn,
• scikit-image.