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Install

ImageJ update site

The CSBDeep plugin can be installed from the ImageJ update site 1. See the CSBDeep Wiki Pages for more details.

From source

  1. Clone this repository.
  2. Run the following command from inside the repo:

mvn -Dimagej.app.directory=/path/to/Fiji.app/ -Ddelete.other.versions=true

Run demos

  1. Download the exemplary image data
  2. Open Fiji.
  3. Open an example image, e.g. tribolium.tif.
  4. Run the plugin via PluginsCSBDeepDemo.
  5. Run the plugin by pressing Ok.

If all goes well, an image will be displayed representing the result of the model execution.

See the CSBDeep Wiki Pages for more details.

Run your own model

  1. Use the python code to train your network with your data. Export it as ZIP.
  2. Open Fiji.
  3. Open an image.
  4. Run the plugin for any network via PluginsCSBDeepRun your network.
  5. Load your exported network by pressing Browse on the Import model (.zip) line.
  6. Run the plugin by pressing Ok.

If all goes well, an image will be displayed representing the result of the model execution.

See the CSBDeep Wiki Page for more details.

GPU support

Please read this page for GPU support.

License

This project is licensed under the BSD 2-clause “Simplified” License – see the LICENSE.txt file for details.