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.

	QuPath	QuPath is a free open-source cross-platform software application designed for bioimage analysis - and specifically to meet the needs of whole slide image analysis and digital pathology. We demonstrate how to integrate QuPath and OMERO using the User Interface.
	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.