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This is the source of the U-Net Segmentation plugin for Fiji. You can obtain the latest stable version directly from the Fiji updater via update site "U-Net Segmentation".

For more details check our project page. Binary releases are available on our Fiji update site

The plugin requires connection to a Linux workstation (can be the local computer) running a special variant of caffe (caffe_unet).

U-Net Segmentation backend caffe_unet (binaries, source, docker)

Obtain the U-Net segmentation backend (caffe_unet) binaries and corresponding caffe source patch from the project page. Please also check our caffe-unet-docker repository.

Build from source

We recommend to use Linux for building from source, in theory building on Windows should work, but it is not tested.


ij.jar, jsch.jar and jhdf5.jar should be already included in an of-the-shelf Fiji installation. You can obtain protobuf-java from the U-Net update site.

General build instructions

Clone this repository, create a separate build directory, and run cmake using the cloned directory as source folder and the build directory as destination folder. Choose your Fiji plugins folder as install prefix.


  • Fiji is installed in /home/user/
  • You installed the protobuf compiler using your package management system (e.g. on debian-based systems using apt-get install protobuf-compiler)
  • You cloned this repository to /home/user/Unet-Segmentation

Then the following block should build and install the Unet-Segmentation plugin into Fiji. The API documentation can be found in /home/user/Unet-Segmentation/build/javadoc/doc/.

mkdir -p /home/user/Unet-Segmentation/build
cd /home/user/Unet-Segmentation/build
cmake -DCMAKE_INSTALL_PREFIX=/home/user/ -DFIJI_BIN=/home/user/  ..
make install