Preprint 🚨 GPU-accelerating ImageJ Macro image processing workflows using CLIJ

Hey fans of GPU-accelerated image processing,

my fantastic colleague Daniela Vorkel and myself wrote a book chapter about translating ImageJ Macros to GPU-accelerated #clij macros. We just put it online as preprint:

We would :heart: to get feedback from the community. Especially, clij beginners are welcome to share their experience and open questions. Yet we can incorporate them :wink:

Thanks for your support!

Cheers,
Dani & Robert

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Hi Robert, I am going to read this with great interest !

I’ ll send you my comments / remarks.

Fred

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Awesome chapter, very user-friendly. I made a few grammatical comments to improve readability. 2008.11799_TCF200828edit.pdf (2.1 MB)

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Hey @fadero,

thaaaaanks! Finally, a native speaker had a look at it. So cool :heart:

Have a great weekend!

Cheers,
Robert

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A post was split to a new topic: Bio-formats - clij compatibility

This is a great tool! Can CLIJ2 accelerate my customized plugins? Or only the functions currently inside the CLIJ2 package is accelerated by GPU?

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Hey @Kai_Z,

you can accelerate your custom plugins by building in clij. You need to translate your workflow from a CPU workflow to a GPU-accelerated workflow :wink:
You can learn how to do this in the article linked above and then switch programming language to the one your plugins are written in. Let me know if you need support! :slightly_smiling_face:

Cheers,
Robert

Hey Robert,

I was thinking about accelerating the deconvolution process using some existing plugins (such as the Deconvolutionlab2) or customized ones. Some methods, such as the Richardson–Lucy, take minutes to process a Z stack of 20-30 slices. This is almost impossible for me to process hundreds/thousands of Z stacks. At the same time, our workstation has a quite good GPU not being used by ImageJ/Fiji. So it will be great to apply clij to these computation intensive tasks. I found the clijplugin/PluginTemplate.java, is that what you referring to? Given the complexity of these deconvolution plugins, it is challenging for me to rewrite the code into clij version.

Kai

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Hey @Kai_Z,

I see. So we’re working on a deconvolution CLIJ plugin (mostly work by @bnorthan). There is a thread with an example script. All still a bit experimental though. But feel free to give it a try!

Thanks for the suggestion! As you can imagine, translating all plugins to make use of clij is not really possible. That’s why we need feedback like yours to concentrate on the important ones :slightly_smiling_face:

Cheers,
Robert

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That’s super cool!! I cannot wait to try it tomorrow!

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