├── CMakeLists.txt ├── COPYING.txt ├── README.md ├── caffe └── caffe.proto ├── plugins.config ├── protobuf-java-3.3.1.jar ├── resources └── README.html ├── src └── de │ └── unifreiburg │ └── unet │ ├── ApplyDeformationLayer.java │ ├── Blob.java │ ├── BlobException.java │ ├── ByteBlob.java │ ├── CaffeBlob.java │ ├── CaffeJob.java │ ├── ConcatAndCropLayer.java │ ├── ConnectedComponentLabeling.java │ ├── ConvolutionLayer.java │ ├── CreateBlobsJob.java │ ├── CreateDeformationLayer.java │ ├── DataLayer.java │ ├── DetectionJob.java │ ├── DistanceTransform.java │ ├── DropoutLayer.java │ ├── FinetuneJob.java │ ├── FinetuneJobException.java │ ├── FloatBlob.java │ ├── HostConfigurationPanel.java │ ├── ImagePlusListView.java │ ├── IncompatibleImagesException.java │ ├── IntBlob.java │ ├── Job.java │ ├── JobManager.java │ ├── JobManagerPlugin.java │ ├── JobTableModel.java │ ├── MaskEmbedder.java │ ├── MaskExtractor.java │ ├── ModelDefinition.java │ ├── ModelDefinitionEditor.java │ ├── MyUserInfo.java │ ├── Net.java │ ├── NetworkLayer.java │ ├── NotImplementedException.java │ ├── Pair.java │ ├── PoolingLayer.java │ ├── ProcessResult.java │ ├── ProgressMonitor.java │ ├── ReLULayer.java │ ├── ResumeFinetuning.java │ ├── SegmentationJob.java │ ├── SftpFileIO.java │ ├── ShortBlob.java │ ├── SoftmaxLayer.java │ ├── SoftmaxWithLossLayer.java │ ├── SplitLayer.java │ ├── Tools.java │ ├── TrainImagePair.java │ ├── TrainImagePairException.java │ ├── TrainImagePairListView.java │ ├── TrainingSample.java │ ├── TrainingSampleException.java │ ├── URLOpener.java │ ├── UpConvolutionLayer.java │ ├── ValueAugmentationLayer.java │ └── ValueTransformationLayer.java └── test └── TestNetworkAnalyzer.java /CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/CMakeLists.txt -------------------------------------------------------------------------------- /COPYING.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/COPYING.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/README.md -------------------------------------------------------------------------------- /caffe/caffe.proto: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/caffe/caffe.proto -------------------------------------------------------------------------------- /plugins.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/plugins.config -------------------------------------------------------------------------------- /protobuf-java-3.3.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/protobuf-java-3.3.1.jar -------------------------------------------------------------------------------- /resources/README.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/resources/README.html -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ApplyDeformationLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ApplyDeformationLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/Blob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/Blob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/BlobException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/BlobException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ByteBlob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ByteBlob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/CaffeBlob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/CaffeBlob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/CaffeJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/CaffeJob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ConcatAndCropLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ConcatAndCropLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ConnectedComponentLabeling.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ConnectedComponentLabeling.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ConvolutionLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ConvolutionLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/CreateBlobsJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/CreateBlobsJob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/CreateDeformationLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/CreateDeformationLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/DataLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/DataLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/DetectionJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/DetectionJob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/DistanceTransform.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/DistanceTransform.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/DropoutLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/DropoutLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/FinetuneJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/FinetuneJob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/FinetuneJobException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/FinetuneJobException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/FloatBlob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/FloatBlob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/HostConfigurationPanel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/HostConfigurationPanel.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ImagePlusListView.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ImagePlusListView.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/IncompatibleImagesException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/IncompatibleImagesException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/IntBlob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/IntBlob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/Job.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/Job.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/JobManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/JobManager.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/JobManagerPlugin.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/JobManagerPlugin.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/JobTableModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/JobTableModel.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/MaskEmbedder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/MaskEmbedder.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/MaskExtractor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/MaskExtractor.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ModelDefinition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ModelDefinition.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ModelDefinitionEditor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ModelDefinitionEditor.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/MyUserInfo.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/MyUserInfo.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/Net.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/Net.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/NetworkLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/NetworkLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/NotImplementedException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/NotImplementedException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/Pair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/Pair.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/PoolingLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/PoolingLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ProcessResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ProcessResult.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ProgressMonitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ProgressMonitor.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ReLULayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ReLULayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ResumeFinetuning.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ResumeFinetuning.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/SegmentationJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/SegmentationJob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/SftpFileIO.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/SftpFileIO.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ShortBlob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ShortBlob.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/SoftmaxLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/SoftmaxLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/SoftmaxWithLossLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/SoftmaxWithLossLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/SplitLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/SplitLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/Tools.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/Tools.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/TrainImagePair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/TrainImagePair.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/TrainImagePairException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/TrainImagePairException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/TrainImagePairListView.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/TrainImagePairListView.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/TrainingSample.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/TrainingSample.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/TrainingSampleException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/TrainingSampleException.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/URLOpener.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/URLOpener.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/UpConvolutionLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/UpConvolutionLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ValueAugmentationLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ValueAugmentationLayer.java -------------------------------------------------------------------------------- /src/de/unifreiburg/unet/ValueTransformationLayer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/src/de/unifreiburg/unet/ValueTransformationLayer.java -------------------------------------------------------------------------------- /test/TestNetworkAnalyzer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lmb-freiburg/Unet-Segmentation/HEAD/test/TestNetworkAnalyzer.java --------------------------------------------------------------------------------