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Scripting in Fiji

Using SciJava Ops within scripts unlocks the most powerful aspects of Ops. The following page will explain how you can write a script in Fiji's Script Editor that utilizes Ops for image processing.

Obtaining an OpEnvironment

To run Ops, scripts require an OpEnvironment. The easiest way to obtain an OpEnvironment with all available Ops is to declare an OpEnvironment as a script parameter:

#@ OpEnvironment ops

Obtaining inputs

Scripts using SciJava Ops obtain inputs like any other SciJava script, and the lines below will provide us with an Img input parameter and an Img output parameter.

#@ Img imgInput
#@output Img out

For more information on SciJava scripting parameters, please visit this page.

Calling Ops

The OpBuilder syntax should be used to retrieve and execute Ops from the OpEnvironment. The following line executes a Gaussian Blur on an input image using a filter.gauss Op:

out = ops.op("filter.gauss").input(imgInput, new Double(3.0)).apply()

Putting it all together

The below script can be pasted into the Script Editor. Ensure that the Script Editor is configured to run a Groovy script.

#@ OpEnvironment ops
#@ Img imgInput
#@output Img out

// Call some Ops!
out = ops.op("filter.gauss").input(imgInput, new Double(3.0)).apply()

Scripting in Fiji is a convenient gateway to accessing SciJava Ops. To see more, check out some examples, such as image deconvolution or FLIM analysis!