External Software and OMERO

Here we describe how to use third party tools to analyze data stored in OMERO. We provide installation instructions, step-by-step workflow either to use the User Interface or the API of those tools.

	CellProfiler	CellProfiler is a free open-source software for quantitative analysis of biological images. We demonstrate how to integrate CellProfiler and OMERO using the CellProfiler Python API and the OMERO Python API. For more details, visit the CellProfiler website. Follow the instructions in the README.md file to run the notebooks either locally or on mybinder.org.
	Fiji	Fiji is a popular free open-source image processing package based on ImageJ, https://imagej.net/Fiji. We demonstrate how to use Fiji User Interface and OMERO and we also demonstrate how to analyze data in OMERO using Fiji scripting facility.
	ilastik	ilastik is a free open-source interactive learning and segmentation toolkit, with which can be used to leverage machine learning algorithms to easily segment, classify, track and count cells or other experimental data. For more details go to see https://www.ilastik.org/. We will show how to analyze data stored in OMERO, using the ilastik user interface, Fiji and the OMERO ImageJ plugin. We will then also show how to analyze images using the ilastik API and OMERO.py API.
	Orbit	Orbit is a free open-source software with the focus on quantification of big images like whole slide scans. It offers sophisticated image analysis algorithms. Of those, tissue quantification using machine learning techniques, object/cell segmentation, and object classification are the basic ones. We demonstrate how to integrate Orbit and OMERO using both the User Interface and the API. For more details, go to http://www.orbit.bio/
	QuPath
	TrackMate	TrackMate is Fiji plugin for single-particle tracking. We demonstrate how to use TrackMate and OMERO using both the User Interface and the API.