├── .gitignore ├── .readthedocs.yaml ├── README.md ├── README_qustllm.md ├── cci_datasets └── human_lr_pair.csv ├── docs ├── Makefile ├── alignments.rst ├── artifacts │ ├── fiji-align-stack-options.png │ ├── fiji-align-stack-results-annotated-cropped.png │ ├── fiji-align-stack-results-annotated.png │ ├── fiji-align-stack-results.png │ ├── fiji-align-stack-transformation-matrix.png │ ├── fiji-bioformats-import-options-dapi.png │ ├── fiji-bioformats-import-options.png │ ├── fiji-bioformats-series-options-dapi.png │ ├── fiji-bioformats-series-options.png │ ├── fiji-bunwrapj-options.png │ ├── fiji-bunwrapj-results-grids.png │ ├── fiji-bunwrapj-results-vectors.png │ ├── fiji-bunwrapj-results.png │ ├── fiji-bunwrapj-save-direct-transf.png │ ├── fiji-color-deconvolution-options.png │ ├── fiji-file-import-bioformats-dapi.png │ ├── fiji-file-import-bioformats.png │ ├── fiji-hematoxylin-DAPI-stack.png │ ├── fiji-hne-dapi-loaded.png │ ├── fiji-image-adjust-brightness-contrast.png │ ├── fiji-image-color-color-deconvolution.png │ ├── fiji-image-to-stack-option.png │ ├── fiji-image-type-rgb-color.png │ ├── fiji-stack-to-images.png │ ├── fiji-wsi-dapi-8bit.png │ ├── fiji-wsi-dapi-brightnesscontrast.png │ ├── fiji-wsi-dapi-equalized-gray.png │ ├── fiji-wsi-dapi-equalized.png │ ├── fiji-wsi-dapi.png │ ├── fiji-wsi-he-deconvoluted.png │ ├── fiji-wsi-he-stack.png │ ├── fiji-wsi-hematoxylin-inverted-cleaned-background-removed-equalized.png │ ├── fiji-wsi-hematoxylin-inverted-cleaned-background-removed.png │ ├── fiji-wsi-hematoxylin-invteted-cleaned.png │ ├── fiji-wsi-hematoxylin-invteted.png │ ├── fiji-wsi-hematoxylin.png │ ├── linear_registration_results.gif │ ├── nonlinear_registration_results.gif │ ├── quipath-hne.png │ ├── qupath-cell-detection.png │ ├── qupath-hne-pixel-size-calibration.png │ ├── qupath-xenium-loader-results.png │ ├── qupath-xenium-loader.png │ ├── qustllm_diagram1.png │ ├── qustllm_diagram2.png │ └── qustwsi_diagram.png ├── building.rst ├── conf.py ├── index.rst ├── installing.rst ├── make.bat ├── prerequisites.rst └── tutorial.rst ├── qupath-extension-qust-0.5.0.jar ├── qupath-extension-qust ├── .gradle │ ├── 8.5 │ │ ├── checksums │ │ │ └── checksums.lock │ │ ├── dependencies-accessors │ │ │ ├── 47ef54c758d61ca8f7eb2ed336d7c5c090eca25c │ │ │ │ ├── classes │ │ │ │ │ └── org │ │ │ │ │ │ └── gradle │ │ │ │ │ │ └── accessors │ │ │ │ │ │ └── dm │ │ │ │ │ │ ├── LibrariesForLibs$BioimageioLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$BundleAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$CommonmarkLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$CommonsLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$CudaLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$GroovyLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$IkonliLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$JunitLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$LicensePluginAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$LogviewerLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$OpencvBundleAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$OpencvLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$PluginAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$QupathLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$QupathVersionAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs$VersionAccessors.class │ │ │ │ │ │ ├── LibrariesForLibs.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$BioimageioLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$BundleAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$CommonmarkLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$CommonsLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$CudaLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$GroovyLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$IkonliLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$JunitLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$LicensePluginAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$LogviewerLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$OpencvBundleAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$OpencvLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$PluginAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$QupathLibraryAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$QupathVersionAccessors.class │ │ │ │ │ │ ├── LibrariesForLibsInPluginsBlock$VersionAccessors.class │ │ │ │ │ │ └── LibrariesForLibsInPluginsBlock.class │ │ │ │ └── sources │ │ │ │ │ └── org │ │ │ │ │ └── gradle │ │ │ │ │ └── accessors │ │ │ │ │ └── dm │ │ │ │ │ ├── LibrariesForLibs.java │ │ │ │ │ └── LibrariesForLibsInPluginsBlock.java │ │ │ ├── dependencies-accessors.lock │ │ │ ├── executionHistory.bin │ │ │ └── gc.properties │ │ ├── executionHistory │ │ │ ├── executionHistory.bin │ │ │ └── executionHistory.lock │ │ ├── fileChanges │ │ │ └── last-build.bin │ │ ├── fileHashes │ │ │ ├── fileHashes.bin │ │ │ ├── fileHashes.lock │ │ │ └── resourceHashesCache.bin │ │ └── gc.properties │ ├── buildOutputCleanup │ │ ├── buildOutputCleanup.lock │ │ ├── cache.properties │ │ └── outputFiles.bin │ ├── file-system.probe │ └── vcs-1 │ │ └── gc.properties ├── LICENSE ├── README.md ├── build.gradle ├── build │ └── classes │ │ └── java │ │ └── main │ │ └── qupath │ │ └── ext │ │ └── qust │ │ ├── AiDiaAnnotation$AnnotationLoader.class │ │ ├── AiDiaAnnotation.class │ │ ├── CellSpatialProfiling$AnnotationLoader.class │ │ ├── CellSpatialProfiling.class │ │ ├── CosmxAnnotation$AnnotationLoader.class │ │ ├── CosmxAnnotation.class │ │ ├── ObjectClassification$1.class │ │ ├── ObjectClassification$2.class │ │ ├── ObjectClassification$CellClassifier$1.class │ │ ├── ObjectClassification$CellClassifier$2.class │ │ ├── ObjectClassification$CellClassifier$3.class │ │ ├── ObjectClassification$CellClassifier.class │ │ ├── ObjectClassification.class │ │ ├── ObjectClassificationImageAcquisition$1.class │ │ ├── ObjectClassificationImageAcquisition$DetectedObjectImageSampling.class │ │ ├── ObjectClassificationImageAcquisition.class │ │ ├── QuSTExtension.class │ │ ├── QuSTSetup.class │ │ ├── RegionSegmentation$1.class │ │ ├── RegionSegmentation$2.class │ │ ├── RegionSegmentation$RegionSegmentationRunner$1.class │ │ ├── RegionSegmentation$RegionSegmentationRunner$2.class │ │ ├── RegionSegmentation$RegionSegmentationRunner$3.class │ │ ├── RegionSegmentation$RegionSegmentationRunner.class │ │ ├── RegionSegmentation.class │ │ ├── STAnnotation$AnnotationLoader.class │ │ ├── STAnnotation.class │ │ ├── SimpleTissueDetection2$GlobalThresholder.class │ │ ├── SimpleTissueDetection2.class │ │ ├── StarDistCellNucleusDetection$StarDistCellNucleusRunnable.class │ │ ├── StarDistCellNucleusDetection.class │ │ ├── VirtualEnvironmentRunner$1.class │ │ ├── VirtualEnvironmentRunner$2.class │ │ ├── VirtualEnvironmentRunner$EnvType.class │ │ ├── VirtualEnvironmentRunner.class │ │ ├── VirtualEnvironmentRunnerDialog$1.class │ │ ├── VirtualEnvironmentRunnerDialog$2.class │ │ ├── VirtualEnvironmentRunnerDialog$3.class │ │ ├── VirtualEnvironmentRunnerDialog$4.class │ │ ├── VirtualEnvironmentRunnerDialog$5.class │ │ ├── VirtualEnvironmentRunnerDialog$6.class │ │ ├── VirtualEnvironmentRunnerDialog.class │ │ ├── VisiumAnnotation$AnnotationLoader.class │ │ ├── VisiumAnnotation.class │ │ ├── XeniumPixelSizeCalibration$AnnotationLoader.class │ │ └── XeniumPixelSizeCalibration.class ├── gradle │ └── wrapper │ │ ├── gradle-wrapper.jar │ │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── java-hdf5 │ ├── META-INF │ │ └── MANIFEST.MF │ ├── hdf5.jar │ └── libhdf5_java.so ├── settings.gradle └── src │ └── main │ ├── java │ └── qupath │ │ └── ext │ │ └── qust │ │ ├── AiDiaAnnotation.java │ │ ├── BSplineModel.java │ │ ├── BestGPUSelector.java │ │ ├── BiHashMap.java │ │ ├── CellCellInteractionAnalysis.java │ │ ├── CellSpatialProfilingByClassification.java │ │ ├── CellSpatialProfilingByMeasurement.java │ │ ├── CosmxAnnotation.java │ │ ├── DBSCANCellX.java │ │ ├── DensityCellFunctionEnrichment.java │ │ ├── DetectionMeasurementToH5AD.java │ │ ├── DetectionObjectToOMECSV.java │ │ ├── MacenkoStainingNormalizer.java │ │ ├── MathTools.java │ │ ├── NeighborhoodCellFunctionEnrichment.java │ │ ├── NeighboringCellTypeComposition.java │ │ ├── ObjectClassification.java │ │ ├── ObjectClassificationDJL_MT.java │ │ ├── ObjectClassificationDJL_PC.java │ │ ├── ObjectClassificationDJL_PC_mGPU.java │ │ ├── ObjectClassificationImageAcquisition.java │ │ ├── PetesSimpleTissueDetection.java │ │ ├── ProgramDirectoryUtilities.java │ │ ├── PseudoVisiumSpotGeneration.java │ │ ├── QuSTExtension.java │ │ ├── QuSTLLMCKG.java │ │ ├── QuSTLLMHKG.java │ │ ├── QuSTLLMREQ.java │ │ ├── QuSTSetup.java │ │ ├── RegionSegmentation.java │ │ ├── RegionSegmentationImageAcquisition.java │ │ ├── STAnnotation.java │ │ ├── StarDistCellNucleusDetection.java │ │ ├── VirtualEnvironmentRunner.java │ │ ├── VirtualEnvironmentRunnerDialog.java │ │ ├── VisiumAnnotation.java │ │ ├── VisiumAnnotationImageRegistrationParameters.java │ │ ├── XeniumAnnotation.java │ │ └── XeniumAnnotationImageRegistrationParameters.java │ └── resources │ ├── META-INF │ └── services │ │ └── qupath.lib.gui.extensions.QuPathExtension │ └── native │ └── linux │ └── libhdf5_java.so ├── qust_scripts ├── classification.py ├── config.py ├── gene_result.txt ├── genes_ncbi_homo_sapiens_proteincoding.py ├── go-basic.obo ├── llm.py ├── requirements.txt ├── result.csv ├── train.py └── vit_pytorch │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── cct.cpython-310.pyc │ ├── dino.cpython-310.pyc │ ├── mae.cpython-310.pyc │ ├── simple_vit.cpython-310.pyc │ └── vit.cpython-310.pyc │ ├── ats_vit.py │ ├── cait.py │ ├── cct.py │ ├── cct_3d.py │ ├── cross_vit.py │ ├── crossformer.py │ ├── cvt.py │ ├── deepvit.py │ ├── dino.py │ ├── distill.py │ ├── efficient.py │ ├── es_vit.py │ ├── extractor.py │ ├── learnable_memory_vit.py │ ├── levit.py │ ├── local_vit.py │ ├── mae.py │ ├── max_vit.py │ ├── max_vit_with_registers.py │ ├── mobile_vit.py │ ├── mp3.py │ ├── mpp.py │ ├── na_vit.py │ ├── nest.py │ ├── parallel_vit.py │ ├── pit.py │ ├── recorder.py │ ├── regionvit.py │ ├── rvt.py │ ├── scalable_vit.py │ ├── sep_vit.py │ ├── simmim.py │ ├── simple_flash_attn_vit.py │ ├── simple_vit.py │ ├── simple_vit_1d.py │ ├── simple_vit_3d.py │ ├── simple_vit_with_fft.py │ ├── simple_vit_with_patch_dropout.py │ ├── simple_vit_with_qk_norm.py │ ├── simple_vit_with_register_tokens.py │ ├── t2t.py │ ├── twins_svt.py │ ├── vit.py │ ├── vit_1d.py │ ├── vit_3d.py │ ├── vit_for_small_dataset.py │ ├── vit_with_patch_dropout.py │ ├── vit_with_patch_merger.py │ ├── vivit.py │ └── xcit.py ├── tutorial.md └── user_guide └── 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