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.

Switching the TensorFlow version

For supporting a model trained with a specific TensorFlow version or for GPU support, one has to install a specific native TensorFlow JNI. In order to achieve that, do the following:

1. Open Edit > Options > TensorFlow...
   • Choose the version matching your system / model
   • Wait until a message opens telling you that the library was installed
   • Restart Fiji

GPU support

For GPU support, two things have to be done:

• install CUDA and CuDNN and make sure Fiji knows about the installation paths
• install a TensorFlow version with GPU support (see section above)

For further details please refer to the CSBDeep Wiki page.

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.