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These softwares can be linked to Cytomin in Cytomine by various waysmeans.

First, they can simply be executed through command lines (e.g. from a remote computer) and their parameter values can be saved to Cytomine-core database for reproducibility. To do this, you have to read our [HOWTO] How to add a new software (basic principles)

Softwares can also be executed through the "Job" panel in Cytomine-WebUI provided that Cytomine-Core is aware of their location and parameters (this rely on a message broker). For this, you have to read our [DEPRECATED] Guide: Adding a new software (and make it executable from Cytomine-WebUI).

Finally, your software can easily be applied by an end-user (without even knowing the software parameter values) on specific regions of interest of an image through the JobTemplate panel in the Cytomine-WebUI "Explore" image view. For this, you have to read our page on [HOWTO] How to add a shortcut for a software (JobTemplate).