├── .github ├── build.sh ├── get_jars_sizes.py ├── setup.sh └── workflows │ ├── build.yml │ ├── download_all_engines.yml │ ├── example_run_all_bmz_models.yml │ ├── example_run_pytorch1_2_model.yml │ ├── example_run_tf1_and_tf2_model.yml │ └── jar_sizes.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── download-engines.py ├── lib └── ShmCreate.c ├── pom.xml ├── python ├── op_environments │ ├── stardist_environment.yaml │ └── stardist_postprocessing.yaml └── ops │ ├── stardist_fine_tune │ └── stardist_fine_tune.py │ ├── stardist_inference │ └── stardist_inference.py │ └── stardist_postprocessing │ └── stardist_postprocessing.py ├── scripts ├── example-download-bmz-model.py ├── example-download-engine.py ├── example-run-pytorch-model-in-fiji.py └── example-run-tf2-model-in-fiji.py ├── src └── main │ ├── java │ └── io │ │ └── bioimage │ │ └── modelrunner │ │ ├── apposed │ │ └── appose │ │ │ ├── Appose.java │ │ │ ├── Builder.java │ │ │ ├── CondaException.java │ │ │ ├── Environment.java │ │ │ ├── FilePaths.java │ │ │ ├── Mamba.java │ │ │ ├── MambaInstallException.java │ │ │ ├── MambaInstallerUtils.java │ │ │ ├── Service.java │ │ │ ├── SharedMemory.java │ │ │ ├── TaskEvent.java │ │ │ └── Types.java │ │ ├── bioimageio │ │ ├── BioimageioDirectConnection.java │ │ ├── BioimageioRepo.java │ │ ├── description │ │ │ ├── Author.java │ │ │ ├── Axes.java │ │ │ ├── AxesV04.java │ │ │ ├── AxesV05.java │ │ │ ├── Axis.java │ │ │ ├── AxisSize.java │ │ │ ├── AxisV04.java │ │ │ ├── AxisV05.java │ │ │ ├── Badge.java │ │ │ ├── Cite.java │ │ │ ├── ExecutionConfig.java │ │ │ ├── ModelDescriptor.java │ │ │ ├── ModelDescriptorFactory.java │ │ │ ├── ModelDescriptorV04.java │ │ │ ├── ModelDescriptorV05.java │ │ │ ├── SampleImage.java │ │ │ ├── TensorSpec.java │ │ │ ├── TensorSpecV04.java │ │ │ ├── TensorSpecV05.java │ │ │ ├── TestArtifact.java │ │ │ ├── TransformSpec.java │ │ │ ├── cellpose │ │ │ │ ├── ModelDescriptorCellposeV04.java │ │ │ │ └── ModelDescriptorCellposeV05.java │ │ │ ├── deepimagej │ │ │ │ ├── DeepImageJExecutionConfig.java │ │ │ │ └── DeepImageJProcessing.java │ │ │ ├── exceptions │ │ │ │ └── ModelSpecsException.java │ │ │ ├── stardist │ │ │ │ ├── ModelDescriptorStardistV04.java │ │ │ │ └── ModelDescriptorStardistV05.java │ │ │ └── weights │ │ │ │ ├── KerasWeights.java │ │ │ │ ├── ModelArchitecture.java │ │ │ │ ├── ModelDependencies.java │ │ │ │ ├── ModelWeight.java │ │ │ │ ├── OnnxWeights.java │ │ │ │ ├── PytorchWeights.java │ │ │ │ ├── TfJsWeights.java │ │ │ │ ├── TfWeights.java │ │ │ │ ├── TorchscriptWeights.java │ │ │ │ └── WeightFormat.java │ │ ├── download │ │ │ └── DownloadModel.java │ │ └── tiling │ │ │ ├── ImageInfo.java │ │ │ ├── ImgLib2Utils.java │ │ │ ├── PatchSpec.java │ │ │ ├── TileCalculator.java │ │ │ ├── TileGrid.java │ │ │ ├── TileInfo.java │ │ │ └── TileMaker.java │ │ ├── download │ │ ├── FileDownloader.java │ │ └── MultiFileDownloader.java │ │ ├── engine │ │ ├── AbstractEngine.java │ │ ├── DeepLearningEngineInterface.java │ │ ├── EngineInfo.java │ │ ├── EngineLoader.java │ │ ├── ParentLastURLClassLoader.java │ │ ├── PythonEngine.java │ │ ├── engines │ │ │ ├── JaxEngine.java │ │ │ ├── KerasEngine.java │ │ │ ├── OnnxEngine.java │ │ │ ├── PytorchEngine.java │ │ │ └── TensorflowEngine.java │ │ └── installation │ │ │ └── EngineInstall.java │ │ ├── example │ │ ├── ExampleDownloadEngine.java │ │ ├── ExampleDownloadModel.java │ │ ├── ExampleLoadAndRunAllBmzModels.java │ │ ├── ExampleLoadAndRunModel.java │ │ ├── ExampleLoadPytorch1Pytorch2.java │ │ └── ExampleLoadTensorflow1Tensorflow2.java │ │ ├── exceptions │ │ ├── LoadEngineException.java │ │ ├── LoadModelException.java │ │ └── RunModelException.java │ │ ├── gui │ │ ├── ContentPanel.java │ │ ├── DefaultIcon.java │ │ ├── EnvironmentInstaller.java │ │ ├── Gui.java │ │ ├── GuiUtils.java │ │ ├── Header.java │ │ ├── HeaderGui.java │ │ ├── LogoPanel.java │ │ ├── ModelCard.java │ │ ├── ModelSelectionPanel.java │ │ ├── ModelSelectionPanelGui.java │ │ ├── SearchBar.java │ │ ├── YesNoDialog.java │ │ ├── adapter │ │ │ ├── GuiAdapter.java │ │ │ └── RunnerAdapter.java │ │ ├── custom │ │ │ ├── CellposePluginUI.java │ │ │ ├── ConsumerInterface.java │ │ │ ├── StarDistPluginUI.java │ │ │ └── gui │ │ │ │ ├── ButtonsPanel.java │ │ │ │ ├── CellposeGUI.java │ │ │ │ ├── FooterPanel.java │ │ │ │ ├── IntegerTextField.java │ │ │ │ ├── PlaceholderTextField.java │ │ │ │ ├── StarDistGUI.java │ │ │ │ ├── StarDistOptionalParams.java │ │ │ │ └── ThresholdSlider.java │ │ └── workers │ │ │ ├── ImageLoaderWorker.java │ │ │ ├── InstallEnvWorker.java │ │ │ └── ModelInfoWorker.java │ │ ├── model │ │ ├── BaseModel.java │ │ ├── java │ │ │ ├── BioimageIoModelJava.java │ │ │ └── DLModelJava.java │ │ ├── processing │ │ │ ├── Processing.java │ │ │ └── TransformationInstance.java │ │ ├── python │ │ │ ├── BioimageIoModelPytorch.java │ │ │ ├── BioimageIoModelPytorchProtected.java │ │ │ ├── DLModelPytorch.java │ │ │ └── DLModelPytorchProtected.java │ │ └── special │ │ │ ├── cellpose │ │ │ └── Cellpose.java │ │ │ └── stardist │ │ │ ├── Stardist2D.java │ │ │ ├── Stardist3D.java │ │ │ └── StardistAbstract.java │ │ ├── numpy │ │ ├── ByteArrayUtils.java │ │ ├── DecodeImgLib2.java │ │ └── DecodeNumpy.java │ │ ├── runmode │ │ ├── RunMode.java │ │ ├── RunModeScripts.java │ │ └── ops │ │ │ ├── CellposeFineTuneJdllOp.java │ │ │ ├── CellposeInferJdllOp.java │ │ │ ├── CellposeTrainJdllOp.java │ │ │ ├── GenericOp.java │ │ │ ├── OpInterface.java │ │ │ ├── StardistFineTuneJdllOp.java │ │ │ └── StardistInferJdllOp.java │ │ ├── system │ │ ├── PlatformDetection.java │ │ └── Version.java │ │ ├── tensor │ │ ├── ImgLib2ToArray.java │ │ ├── ListToImgLib2.java │ │ ├── Tensor.java │ │ ├── Utils.java │ │ └── shm │ │ │ ├── CLibrary.java │ │ │ ├── LibRt.java │ │ │ ├── MacosHelpers.java │ │ │ ├── SharedMemoryArray.java │ │ │ ├── SharedMemoryArrayLinux.java │ │ │ ├── SharedMemoryArrayMacOS.java │ │ │ ├── SharedMemoryArrayWin.java │ │ │ └── SharedMemoryFile.java │ │ ├── transformations │ │ ├── AbstractTensorPixelTransformation.java │ │ ├── AbstractTensorTransformation.java │ │ ├── BinarizeTransformation.java │ │ ├── ClipTransformation.java │ │ ├── EnsureDtypeTransformation.java │ │ ├── FixedZeroMeanUnitVarianceTransformation.java │ │ ├── PythonTransformation.java │ │ ├── ScaleLinearTransformation.java │ │ ├── ScaleRangeTransformation.java │ │ ├── SigmoidTransformation.java │ │ ├── TensorTransformation.java │ │ └── ZeroMeanUnitVarianceTransformation.java │ │ ├── utils │ │ ├── CommonUtils.java │ │ ├── Constants.java │ │ ├── FileUtils.java │ │ ├── IndexingUtils.java │ │ ├── JSONUtils.java │ │ ├── Log.java │ │ ├── YAMLUtils.java │ │ └── ZipUtils.java │ │ └── versionmanagement │ │ ├── AvailableEngines.java │ │ ├── DeepLearningVersion.java │ │ ├── InstalledEngines.java │ │ ├── JarInfo.java │ │ ├── SupportedVersions.java │ │ └── VersionStringUtils.java │ └── resources │ ├── .jdll_properties │ ├── ShmCreate.dylib │ ├── appose-python.zip │ ├── availableDLVersions.json │ ├── 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