Documentation for deepImageJ

All the technical documentation can be found in deepImageJ's wiki. It will guide you through:

• Technical requirements to use deepImageJ.
• How to create or export deep learning PyTorch or TensorFlow models to be compatible with deepImageJ?
• How can I connect with a GPU?

How to run a model in deepImageJ?

• Click on DeepImageJ Install, and install one of the suggested models compatible with deepImageJ from the BioImage Model Zoo list. There's no need to restart Fiji once the model is installed.
• Once the model is installed (the installing pop up window closes), you can close the window.
• Click on DeepImageJ Run. Choose the recently installed model and click on Run on Test Image. To process and image, follow the same steps but click on Accept rather than on Run on a test image.

Try to install a model from a zip file.

Here we show an example with a model downloaded from the BioImage Model Zoo, but you can repeat the process with any other private model that follows the specifications of the zoo and is compatible with deepImageJ.

DeepImageJ Run is macro recordable!

• Start the macro recorder.
• Use DeepImageJ Run on an image.
• Copy the code line given by the macro recorder.
• Create a new ImageJ macro, paste the line and run it.

Practical introduction to deepImageJ 1

Workshop at SPAOM 2020: Practical Applications of Deep learning for Bioimage Analysis: Slides

User guide tutorial

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YAPIC models in deepImageJ

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NEUBIAS Academy @Home

Webinar Intro to Machine Learning-DeepLearning-DeepimageJ by Ignacio Arganda-Carreras