CSBDeep Fiji Plugin

Install

ImageJ update site

The CSBDeep plugin can be installed from the ImageJ update site http://sites.imagej.net/CSBDeep/. 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 examplary image data
2. Open Fiji.
3. Open an example image, e.g. tribolium.tif.
4. Run the plugin via Plugins > CSBDeep > Demo.
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 Plugins > CSBDeep > Run 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.

Develop

Code Style

If you use eclipse you can import our code formatter doc/eclipse-code-formatter.xml, code cleanup (doc/eclipse-code-clean-up.xml) and import order (eclipse-import-order.importorder) settings.

GPU support

For GPU support we load the TensorFlow JNI with GPU support manually when a command is initialized. This means that the GPU version of the TensorFLow JNI must be accessible in the java library path (For example Fiji.app/lib/linux64 in a Fiji installation).

See the according CSBDeep Wiki page for a detailed installation guide.

Muliple GPUs

See the according CSBDeep Wiki page.

License

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