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".
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)
Build from source
We recommend to use Linux for building from source, in theory building on Windows should work, but it is not tested.
- Java SE 8
- Fiji (ij, jsch, jhdf5, protobuf-java) https://fiji.sc/
- google protobuf compiler (protoc) https://github.com/protocolbuffers/protobuf/releases
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/Fiji.app
- 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/Fiji.app/plugins -DFIJI_BIN=/home/user/Fiji.app/ImageJ-linux64 .. make install