Getting started designing image processing workflows with the CLIJ2 Assistant

Open your 3D+channel+time data set. It’s recommended to start the assistant from a file that has been loaded from or saved to disk. Afterwards, activate CLIJx-Assistant by clicking on its tool icon.


Building workflows - step by step

CLIJx-Assistant has a built-in suggestions of what to do next: Just right click in any image that has the assistant attached.

Image [Image data source: Irene Seijo Barandiaran, Grapin-Botton lab, MPI CBG]

Consider the suggestions but also explore the categories of all available operations.

Image [Image data source: Irene Seijo Barandiaran, Grapin-Botton lab, MPI CBG]

You also find all CLIJx-Assistant operations in Fijis search bar. They have their own category to not be mixed up with CLIJ2 operations:


Interoperability with classical ImageJ and Fiji operations

As CLIJx-Assistant runs in classical ImageJ windows, you can use ImageJ operations on the shown images. However, they may be overwritten as soon as CLIJx-Assistant recomputes its results. Thus, it is recommended to duplicate an image before applying classical functions to it. You can use ImageJ’s Duplicate... menu or the built in menu:


The assistant in action

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If you want to keep an eye on memory usage in the GPU, the menu Plugins > ImageJ on GPU (CLIJx) > Memory Display allows you to overview available memory and memory consumption while building your workflow.


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