├── .gitignore ├── AGLogo.png ├── AUTHORS ├── COPYING ├── ChangeLog ├── CommandLine.cpp ├── CommandLine.h ├── Direction.h ├── Doxyfile.in ├── GUIThread.cpp ├── GUIThread.h ├── INSTALL ├── InputStream.cpp ├── InputStream.h ├── Job.h ├── LengthUnit.h ├── Localization.cpp ├── Localization.h ├── Localization_decl.h ├── Makefile.am ├── Microscope.ico ├── ModuleLoader.cpp ├── ModuleLoader.h ├── NEWS ├── Pixel.cpp ├── Pixel.h ├── README.md ├── UnitEntries.cpp ├── UnitEntries.h ├── UnitEntries ├── ADC.h ├── FrameEntry.h ├── Hertz.h ├── Nanometre.h ├── PixelEntry.h ├── PixelSize.h ├── TemperatureEntry.h └── TimeEntry.h ├── alignment_fitter.cpp ├── alignment_fitter.h ├── aminclude.am ├── andor-sif ├── AndorSIF.cpp ├── AndorSIF.h ├── AndorSIF_OpenFile.cpp ├── AndorSIF_OpenFile.h ├── augment_config.cpp └── augment_config.h ├── base ├── Config.h └── Engine.h ├── binning ├── always_failing_binner.h ├── binning.cpp ├── binning.h ├── binning.hpp ├── binning_decl.h ├── config.cpp ├── config.h ├── constant_binner.cpp ├── constant_binner.h ├── dummy_binner.h ├── inversion.h ├── localization.h ├── localization_config.h ├── localization_config_impl.h └── localization_impl.h ├── boards ├── kokolorix.exp ├── rosaline.exp ├── standard.exp └── valgrind.exp ├── boost └── units │ ├── Eigen │ ├── Array │ └── Core │ ├── power10.hpp │ └── systems │ ├── base_units │ ├── frame.hpp │ └── pixel.hpp │ └── camera │ ├── area.hpp │ ├── base.hpp │ ├── frame_rate.hpp │ ├── intensity.hpp │ ├── intensity_dimension.hpp │ ├── length.hpp │ ├── resolution.hpp │ └── time.hpp ├── calibrate_3d ├── Config.cpp ├── Config.h ├── FormCalibrationConfig.cpp ├── FormCalibrationConfig.h ├── Output.cpp ├── Output.h ├── ParameterLinearizer.cpp ├── ParameterLinearizer.h ├── SigmaCurve.cpp ├── ZTruth.cpp ├── ZTruth.h ├── ZTruthConfig.cpp ├── ZTruthConfig.h ├── constant_parameter.hpp └── fwd.h ├── config.guess ├── config ├── unix.exp └── windows-telnet-and-netcat.exp ├── config_file.cpp ├── config_file.h ├── configure.ac ├── constant_background ├── fwd.hpp └── model.hpp ├── debug.h ├── dejagnu.h ├── density_map ├── Coordinates.h ├── CoordinatesFactory.cpp ├── CoordinatesFactory.h ├── DensityMap.h ├── DensityMap.hpp ├── DummyListener.cpp ├── DummyListener.h ├── GaussianSmoothing.cpp ├── GaussianSmoothing.h ├── GaussianSmoothing.hpp ├── Interpolator.h ├── InterpolatorChoice.cpp ├── InterpolatorChoice.h ├── InterpolatorChoice.hpp ├── InterpolatorFactory.h ├── LinearInterpolation.cpp ├── LinearInterpolation.h ├── LinearInterpolation.hpp ├── Listener.h ├── NearestNeighbourInterpolation.cpp ├── NearestNeighbourInterpolation.h ├── NearestNeighbourInterpolation.hpp ├── VirtualListener.cpp └── VirtualListener.h ├── display ├── DataSource.h ├── Manager.cpp ├── Manager.h ├── SharedDataSource.cpp ├── SharedDataSource.h ├── display_normalized.hpp ├── fwd.h ├── store_image.cpp └── store_image.h ├── doc ├── Makefile.am ├── bib4wbbt.bib ├── bibliography.xml ├── configure.ac ├── engine_options.xml ├── errors.xml ├── foprc.in ├── fundamentals.xml ├── input-options.xml ├── m4 │ └── .gitignore ├── make_titlepage.xsl ├── output-options.xml ├── polynomial_3d_holtzer_conversion.tex ├── polynomial_3d_parabolic_conversion.tex ├── polynomial_3d_psf.tex ├── rapidstorm-job-status.PNG ├── rapidstorm-output-box.PNG ├── rapidstorm-step-by-step-2.PNG ├── rapidstorm.xml ├── rapidstorm_fo.xsl ├── rapidstorm_guilabels.xsl ├── rapidstorm_html.xsl ├── rapidstorm_htmlhelp.xsl ├── rapidstorm_pre.xsl ├── spline-theory-example.pdf ├── spline-theory.tex ├── tex2im ├── titlepage.xml ├── ui.xml ├── usage-examples.xml ├── version.ent.in └── xml2db5.xsl ├── docs └── index.md ├── dstorm-config.txt ├── dstorm-unit-tests.sh ├── dstorm.00-pre ├── 00-dstorm.exp ├── 01-plugins-loaded.exp ├── 02-run-can-succeed.exp ├── 03-test-plugin-can-close-windows.exp └── 04-field-bounds-work.exp ├── dstorm.andorcam ├── compute-job.exp ├── infinite-acquisition.exp ├── live-view.exp ├── no-installed-cameras.exp └── two-successive-jobs.exp ├── dstorm.bugs ├── 106.exp ├── 110.exp ├── 132.exp ├── 133.exp ├── 139.exp ├── 148.exp ├── 165.exp ├── 177-2.exp ├── 178.exp ├── 179.exp ├── 186.exp ├── 188.exp ├── 190.exp ├── 197.exp ├── 202.exp ├── 206.exp ├── 212.exp ├── 218.exp ├── 228.exp ├── 3.exp ├── 43.exp ├── 48.exp ├── 51.exp ├── 62.exp ├── 63.exp ├── 66.exp ├── 74.exp ├── 75.exp ├── 75_stm.exp ├── 80.exp ├── 81.exp ├── 84.exp ├── 85.exp ├── 91.exp ├── 95.exp ├── 96.exp └── 99.exp ├── dstorm.cpp ├── dstorm.guf ├── andre-test-1.exp ├── error-check.exp ├── fixed-settings.exp ├── multi-plane-gui.exp ├── negative-alignment.exp ├── performance.exp ├── precision.exp └── two-plane-form-fitter.exp ├── dstorm.input ├── 00-input-file-is-recognized.exp ├── 01-txt-replay.exp ├── 02-errors.exp ├── 03-can-open-same-file-twice.exp ├── dual-view.exp ├── long-tif-file.exp ├── mirror.exp ├── new-stm-format.exp └── parallel-sif.exp ├── dstorm.outputs ├── drift-estimator.exp-disabled-pending-input-format-rework ├── emission-tracker.exp ├── expression-filter.exp ├── form-fitter.exp ├── linear-alignment.exp ├── localization-filter-can-remove-output.exp ├── localization-filter.exp ├── repeater.exp ├── save-image-to-nonexisting-location.exp ├── segmenter.exp ├── simple-filter.exp ├── viewer-closed-during-job.exp ├── viewer-supports-key-range-changes.exp └── viewer.exp ├── dstorm.test ├── alignment-fitter.exp ├── autoname.exp ├── can-compute-txt-file.exp ├── config-reset.exp ├── empty.stm ├── empty_input_file.exp ├── filenames.exp ├── job-removal.exp ├── load_tif_file.exp ├── median.exp ├── nojob.exp ├── output_exception.exp ├── remove-job.exp ├── serialization.exp ├── sif-computation.exp └── sif-shortjob.exp ├── dstorm.volker ├── fall_a.exp ├── fall_b.exp ├── fall_c.exp ├── fall_d.exp ├── fall_e.exp └── fall_f.exp ├── engine ├── Candidate.h ├── CandidateTree.cpp ├── CandidateTree.h ├── CandidateTree_decl.h ├── Candidate_decl.h ├── ChainLink.cpp ├── ChainLink.h ├── Config.cpp ├── Config.h ├── Config_decl.h ├── Engine.cpp ├── Engine.h ├── EngineDebug.h ├── EngineThread.cpp ├── EngineThread.h ├── FitJudger.cpp ├── FitJudger.h ├── FitJudgerFactory.h ├── FitPosition.h ├── FitPositionDeduplicater.h ├── FitPositionGenerator.cpp ├── FitPositionGenerator.h ├── FitPositionRoundRobin.h ├── Image.cpp ├── Image.h ├── Image_decl.h ├── Input.h ├── InputPlane.cpp ├── InputPlane.h ├── InputTraits.cpp ├── InputTraits.h ├── Input_decl.h ├── JobInfo.cpp ├── JobInfo.h ├── JobInfo_decl.h ├── PlaneSeparator.cpp ├── PlaneSeparator.h ├── SingleThreadedLocalizer.cpp ├── SingleThreadedLocalizer.h ├── Spot.h ├── SpotFinder.cpp ├── SpotFinder.h ├── SpotFinderBuilder.h ├── SpotFinder_decl.h ├── SpotFitter.h ├── SpotFitterFactory.cpp ├── SpotFitterFactory.h ├── SpotFitterFactory_decl.h └── SpotFitter_decl.h ├── engine_stm ├── ChainLink.cpp ├── ChainLink.h ├── LocalizationBuncher.cpp └── LocalizationBuncher.h ├── estimate_psf_form ├── Config.cpp ├── Config.h ├── Fitter.cpp ├── Fitter.h ├── GUI.cpp ├── GUI.h ├── Input.cpp ├── Input.h ├── LocalizationValueFinder.cpp ├── LocalizationValueFinder.h ├── Output.cpp ├── Output.h ├── Tile.h ├── VariableReduction.cpp ├── VariableReduction.h ├── VariableReduction_test.cpp ├── VariableReduction_test.h ├── decl.h ├── unit_test.cpp └── unit_test.h ├── expression ├── CommandLine.cpp ├── CommandLine.h ├── Config.cpp ├── Config.h ├── Config_decl.h ├── DynamicQuantity.h ├── Evaluator.h ├── Filter.cpp ├── Filter.h ├── LValue.cpp ├── LValue.h ├── Parser.cpp ├── Parser.h ├── Parser_test.cpp ├── QuantityDynamizer.h ├── QuantityDynamizer.hpp ├── SIPrefixes.h ├── SimpleFilters.cpp ├── SimpleFilters.h ├── Simplifier.h ├── Source.cpp ├── Source.h ├── Source_decl.h ├── UnitChecker.h ├── UnitTable.cpp ├── UnitTable.h ├── UnitTable_impl.h ├── Variable.h ├── VariableLValue.cpp ├── VariableLValue.h ├── localization_variable.cpp ├── localization_variable_decl.h ├── tokens.cpp ├── tokens.h ├── tokens_decl.h ├── types.cpp ├── types.h └── unit_test.cpp ├── fit_window ├── Config.cpp ├── Config.h ├── DataPoint.h ├── FitWindowCutter.cpp ├── FitWindowCutter.h ├── Optics.cpp ├── Optics.h ├── Plane.h ├── Spot.h ├── chunkify.h ├── chunkify.hpp ├── fit_position_out_of_range.cpp ├── fit_position_out_of_range.h ├── unit_tests.cpp └── unit_tests.h ├── gaussian_psf ├── Base3D.h ├── BaseEvaluator.cpp ├── BaseEvaluator.h ├── BaseExpression.h ├── DepthInfo3D.cpp ├── DepthInfo3D.h ├── DepthInfo3D_test.cpp ├── DepthInfo3D_test.h ├── DisjointEvaluator.h ├── JointEvaluator.h ├── No3D.cpp ├── No3D.h ├── No3D_test.cpp ├── No3D_test.h ├── PSF.tex ├── PSF.yacas ├── Polynomial3D.cpp ├── Polynomial3D.h ├── ReferenceEvaluation.h ├── check_evaluator.hpp ├── expressions.cpp ├── expressions.h ├── fixed_form.h ├── free_form.h ├── fwd.h ├── is_plane_dependent.h ├── make_psf.sh ├── mock_model.cpp ├── mock_model.h ├── parameters.h ├── polynomial_psf_generated_by_yacas.h ├── psf_document.tex ├── unit_test.cpp └── unit_test.h ├── guf ├── Config.cpp ├── Config.h ├── Config_decl.h ├── DistanceMetric.h ├── Factory.cpp ├── Factory.h ├── FitFunction.h ├── FitFunctionFactory.cpp ├── FitFunctionFactory.h ├── FitFunctionFactoryImplementation.h ├── FitFunctionFactoryImplementation.hpp ├── Fitter.cpp ├── Fitter.h ├── InitialValueFinder.cpp ├── InitialValueFinder.h ├── KernelCreator.cpp ├── KernelCreator.h ├── LocalizationChecker.cpp ├── LocalizationChecker.h ├── LocalizationCreator.cpp ├── LocalizationCreator.h ├── MultiKernelModel.h ├── NaiveFitter.cpp ├── NaiveFitter.h ├── PlaneFunction.h ├── PlaneFunction.hpp ├── Spot.h ├── TraitValueFinder.cpp ├── TraitValueFinder.h ├── create_evaluator.h ├── create_evaluator.hpp ├── instantiations │ ├── PlaneFunction.h │ ├── constant_background.h │ ├── create_evaluator.h │ ├── depthinfo3d_fixed_form_model.h │ ├── depthinfo3d_full_model.h │ ├── disjoint.h │ ├── double.h │ ├── float.h │ ├── joint_8.h │ ├── no3d_fixed_form_model.h │ ├── no3d_free_form_model.h │ └── no3d_full_model.h ├── unit_tests.cpp └── unit_tests.h ├── helpers ├── OutOfMemory.cpp ├── OutOfMemory.h ├── back_inserter.h ├── clone_ptr.hpp ├── default_on_copy.h ├── make_unique.hpp ├── nocopy_ptr.hpp ├── thread.cpp ├── thread.h └── virtual_clone_allocator.hpp ├── image ├── Box.cpp ├── Box.h ├── Box.hpp ├── Image.h ├── Image.hpp ├── MetaInfo.cpp ├── MetaInfo.h ├── MetaInfo.hpp ├── constructors.h ├── contains.h ├── convert.h ├── corners.h ├── crop.h ├── dilation.cpp ├── dilation.h ├── dilation_impl.h ├── extend.h ├── find_by_offset.hpp ├── fwd.h ├── instantiate.cpp ├── iterator.cpp ├── iterator.h ├── minmax.h ├── mirror.h ├── morphological_reconstruction.cpp ├── morphological_reconstruction.h ├── morphological_reconstruction.hpp ├── normalize.h ├── slice.cpp ├── slice.h ├── subtract.hpp └── unit_tests.cpp ├── input ├── AdapterSource.h ├── Choice.cpp ├── Choice.h ├── DefaultFilterTypes.h ├── FakeSource.h ├── FileInput.h ├── FilterFactory.h ├── FilterFactoryLink.hpp ├── Forwarder.cpp ├── Forwarder.h ├── InputMutex.cpp ├── InputMutex.h ├── Link.cpp ├── Link.h ├── MetaInfo.cpp ├── MetaInfo.h ├── Source.cpp ├── Source.h ├── Traits.h └── fwd.h ├── input_simulation ├── Fluorophore.cpp ├── Fluorophore.h ├── FluorophoreDistribution.h ├── FluorophoreDistributions.h ├── FluorophoreDistributions_Lattice.cpp ├── FluorophoreDistributions_Lines.cpp ├── FluorophoreDistributions_Random.cpp ├── NoiseGenerator.cpp ├── NoiseGenerator.h ├── NoiseSource.cpp ├── NoiseSource.h ├── pixelatedBessel.cpp └── pixelatedBessel.h ├── inputs ├── Basename.cpp ├── Basename.h ├── Buffer.cpp ├── Buffer.h ├── FileMethod.cpp ├── FileMethod.h ├── FileMethod_test.cpp ├── InputBase.cpp ├── InputBase.h ├── LocalizationFile.cpp ├── LocalizationFile.h ├── MedianFilter.cpp ├── MedianFilter.h ├── MedianFilter_test.cpp ├── PlaneFilter.cpp ├── PlaneFilter.h ├── ROIFilter.cpp ├── ROIFilter.h ├── ResolutionSetter.cpp ├── ResolutionSetter.h ├── ResolutionSetter_test.cpp ├── SampleInfo.cpp ├── SampleInfo.h ├── Splitter.cpp ├── Splitter.h ├── WarnAboutLocalizationFile.cpp ├── WarnAboutLocalizationFile.h ├── YMirror.cpp ├── YMirror.h ├── inputs.h ├── join.cpp ├── join.h ├── join │ ├── spatial.cpp │ ├── spatial.h │ ├── temporal.cpp │ └── temporal.h └── unit_tests.cpp ├── install-dirs.exp.in ├── job ├── Car.cpp ├── Car.h ├── Config.cpp ├── Config.h ├── Control.cpp ├── Control.h ├── OutputTreeRoot.cpp ├── OutputTreeRoot.h ├── Queue.cpp ├── Queue.h ├── Run.cpp └── Run.h ├── kalman_filter ├── EmissionTracker.cpp ├── EmissionTracker.h ├── EmissionTracker_test.cpp ├── EmissionTracker_test.h ├── KalmanTrace.cpp ├── KalmanTrace.h ├── NonlinearDriftEstimator.cpp ├── NonlinearDriftEstimator.h ├── unit_tests.cpp └── units.h ├── lib ├── dstorm.exp └── no-integration-tests.exp ├── librapidstormfile.pc.in ├── license_note_for_user ├── localization ├── Field.cpp ├── Field.h ├── Fields.cpp ├── Fields.h ├── Traits.cpp ├── Traits.h ├── Traits_decl.h ├── record.cpp ├── record.h └── record_decl.h ├── localization_file ├── converter.h ├── field.h ├── field_decl.h ├── fields.cpp ├── localization_field.h ├── localization_field_impl.h ├── reader.cpp ├── reader.h ├── unknown_field.h ├── writer.cpp └── writer.h ├── m4 └── .gitignore ├── namespaces.h ├── nonlinfit ├── AbstractFunction.h ├── Bind.h ├── DerivationSummand.h ├── Evaluation.h ├── Evaluation.hpp ├── Evaluator.h ├── FunctionConverter.h ├── InvalidPositionError.h ├── Lambda.h ├── Terminator.h ├── Xs.h ├── access_parameters.hpp ├── append.h ├── derive_by.hpp ├── functions │ ├── Constant.h │ ├── Polynom.h │ └── Zero.h ├── get_variable.hpp ├── index_of.h ├── levmar │ ├── Config.h │ ├── Fitter.cpp │ ├── Fitter.h │ └── exceptions.h ├── make_bitset.h ├── make_functor.hpp ├── parameter_is_negligible.hpp ├── plane │ ├── Disjoint.h │ ├── Disjoint.hpp │ ├── DisjointData.h │ ├── DisjointTermImplementation.h │ ├── Distance.h │ ├── Distance.hpp │ ├── GenericData.h │ ├── Joint.h │ ├── JointData.h │ ├── JointTermImplementation.h │ ├── Term.h │ ├── check_evaluator.hpp │ ├── create_term.hpp │ ├── fwd.h │ └── sum_matrix_rows.h ├── set_variable.hpp ├── sum │ ├── AbstractFunction.cpp │ ├── AbstractFunction.h │ ├── VariableMap.cpp │ ├── VariableMap.h │ ├── VariableMap.hpp │ └── unit_test.cpp ├── terminators │ └── StepLimit.h ├── unit_test.cpp └── unit_test.h ├── output ├── Basename.cpp ├── Basename.h ├── BasenameAdjustedFileEntry.cpp ├── BasenameAdjustedFileEntry.h ├── BasenameAdjustedFileEntry_decl.h ├── Basename_decl.h ├── Config.cpp ├── Config.h ├── FileOutputBuilder.h ├── Filter.cpp ├── Filter.h ├── FilterBuilder.h ├── FilterBuilder_impl.h ├── FilterSource.cpp ├── FilterSource.h ├── LocalizedImage.cpp ├── LocalizedImage.h ├── LocalizedImage_decl.h ├── LocalizedImage_traits.cpp ├── LocalizedImage_traits.h ├── Output.cpp ├── Output.h ├── OutputBuilder.h ├── OutputBuilder_impl.h ├── OutputSource.cpp ├── OutputSource.h ├── Output_decl.h ├── SourceFactory.cpp ├── SourceFactory.h ├── SourceFactory_decl.h ├── Traits.cpp ├── Traits.h └── Traits_decl.h ├── outputs ├── AverageImage.cpp ├── AverageImage.h ├── BasicTransmissions.cpp ├── BasicTransmissions.h ├── Crankshaft.cpp ├── Crankshaft.h ├── DriftRemover.cpp ├── DriftRemover.h ├── LinearAlignment.cpp ├── LinearAlignment.h ├── LocalizationCounter.cpp ├── LocalizationCounter.h ├── MemoryCache.cpp ├── MemoryCache.h ├── MemoryCache_Cache.cpp ├── MemoryCache_Cache.h ├── NullOutput.h ├── PrecisionEstimator.cpp ├── PrecisionEstimator.h ├── ProgressMeter.cpp ├── ProgressMeter.h ├── RegionOfInterest.cpp ├── RegionOfInterest.h ├── RegionSegmenter.cpp ├── RegionSegmenter.h ├── SigmaDiff3D.cpp ├── SigmaDiff3D.h ├── Slicer.cpp ├── Slicer.h ├── SpotMeter.cpp ├── SpotMeter.h ├── TraceFilter.cpp ├── TraceFilter.h ├── VarianceEstimator.cpp └── VarianceEstimator.h ├── polynomial_3d.h ├── rapidstorm.desktop.in ├── release ├── .gitignore ├── Makefile.in ├── README ├── create-dependencies.sh ├── create-release.sh.in ├── debian │ ├── changelog │ ├── compat │ ├── control │ ├── copyright │ ├── rapidstorm-dev-doc.docs │ ├── rapidstorm-doc.docs │ ├── rapidstorm-doc.install │ ├── rapidstorm.docs │ ├── rapidstorm.install │ ├── rapidstorm.menu │ ├── rapidstorm.preinst │ ├── rules │ └── source │ │ └── format └── pbuilder │ ├── hook │ ├── A01augment-mingw-i586 │ ├── B70dpkg-cross │ ├── C10shell │ ├── D01apt-ftparchive │ ├── F01apt-ftparchive │ └── add-to-changes.pl │ ├── pbuilder-satisfydepends-i586 │ └── pbuilderrc.in ├── ripley_k ├── DistanceHistogram.cpp ├── DistanceHistogram.h ├── RipleyK.cpp └── fwd.h ├── shell ├── JobFactory.h ├── JobMetaFactory.h ├── JobStarter.cpp ├── JobStarter.h ├── ReplayJob.cpp ├── ReplayJob.h └── Shell.cpp ├── signals └── InputFileNameChange.h ├── simparm ├── Attribute.cpp ├── Attribute.h ├── Attribute.hpp ├── BaseAttribute.h ├── BasicEntry.cpp ├── BasicEntry.h ├── BoostOptional.h ├── BoostUnits.h ├── Choice.h ├── ChoiceEntry.cpp ├── ChoiceEntry.h ├── Eigen.h ├── Eigen_decl.h ├── Entry.cpp ├── Entry.h ├── Entry.hpp ├── FileEntry.cpp ├── FileEntry.h ├── GUILabelTable.cpp ├── GUILabelTable.h ├── Group.cpp ├── Group.h ├── ManagedChoiceEntry.h ├── Menu.h ├── Message.cpp ├── Message.h ├── NEWS ├── Node.cpp ├── Node.h ├── NodeHandle.h ├── Object.cpp ├── Object.h ├── ObjectChoice.h ├── ProgressEntry.cpp ├── ProgressEntry.h ├── ProtocolNode.cpp ├── ProtocolNode.h ├── README ├── TabGroup.cpp ├── TabGroup.h ├── TreeEntry.cpp ├── TreeEntry.h ├── TreeRoot.cpp ├── TreeRoot.h ├── TriggerEntry.cpp ├── TriggerEntry.h ├── UserLevel.cpp ├── UserLevel.h ├── cmdline_ui │ ├── ChoiceNode.h │ ├── EntryNode.h │ ├── Node.cpp │ ├── Node.h │ ├── OptionTable.cpp │ ├── OptionTable.h │ ├── ProgressNode.cpp │ ├── ProgressNode.h │ ├── RootNode.cpp │ └── RootNode.h ├── dummy_ui │ ├── fwd.cpp │ └── fwd.h ├── exceeds.hpp ├── falls_below.hpp ├── iostream.h ├── is_numerical.hpp ├── text_stream │ ├── BackendRoot.cpp │ ├── BackendRoot.h │ ├── ChildrenList.h │ ├── EntryNode.h │ ├── FrontendNode.h │ ├── InnerBackendNode.cpp │ ├── InnerBackendNode.h │ ├── Launcher.cpp │ ├── Launcher.h │ ├── NoOpNode.h │ ├── Node.cpp │ ├── Node.h │ ├── NodeBackend.cpp │ ├── NodeBackend.h │ ├── RootNode.cpp │ ├── RootNode.h │ ├── TabNode.h │ ├── image_window │ │ ├── MainThread.cpp │ │ ├── MainThread.h │ │ ├── Window.cpp │ │ ├── Window.h │ │ ├── md5.c │ │ └── md5.h │ ├── unit_tests.cpp │ └── unit_tests.h ├── typeName.h ├── unit_tests.cpp ├── unit_tests.h ├── windows_resources.rc.in └── wx_ui │ ├── App.cpp │ ├── App.h │ ├── AttributeHandle.h │ ├── CheckboxNode.cpp │ ├── CheckboxNode.h │ ├── ChoiceNode.cpp │ ├── ChoiceNode.h │ ├── GUIHandle.h │ ├── GroupNode.cpp │ ├── GroupNode.h │ ├── Launcher.cpp │ ├── Launcher.h │ ├── Microscope_16.xpm │ ├── Microscope_24.xpm │ ├── Microscope_32.xpm │ ├── Microscope_48.xpm │ ├── Microscope_64.xpm │ ├── Node.cpp │ ├── Node.h │ ├── OutputChoiceNode.cpp │ ├── OutputChoiceNode.h │ ├── ProgressNode.cpp │ ├── ProgressNode.h │ ├── RootNode.cpp │ ├── RootNode.h │ ├── ScrolledTabNode.cpp │ ├── ScrolledTabNode.h │ ├── ScrolledWindowNode.cpp │ ├── ScrolledWindowNode.h │ ├── Sizer.cpp │ ├── Sizer.h │ ├── TabNode.cpp │ ├── TabNode.h │ ├── TextfieldNode.cpp │ ├── TextfieldNode.h │ ├── TreePage.cpp │ ├── TreePage.h │ ├── TreeRepresentation.cpp │ ├── TreeRepresentation.h │ ├── TreeRoot.cpp │ ├── TreeRoot.h │ ├── TriggerNode.cpp │ ├── TriggerNode.h │ ├── VisibilityControl.cpp │ ├── VisibilityControl.h │ ├── VisibilityNode.cpp │ ├── VisibilityNode.h │ ├── Window.cpp │ ├── Window.h │ ├── WindowNode.cpp │ ├── WindowNode.h │ ├── gui_thread.cpp │ ├── gui_thread.h │ ├── image_window │ ├── Canvas.cpp │ ├── Canvas.h │ ├── Handle.cpp │ ├── Handle.h │ ├── ImageWindow.cpp │ ├── ImageWindow.h │ ├── Key.cpp │ ├── Key.h │ ├── ScaleBar.cpp │ ├── ScaleBar.h │ ├── SizeConvert.h │ ├── ZoomSlider.cpp │ ├── ZoomSlider.h │ ├── create.h │ ├── helpers.cpp │ └── helpers.h │ ├── lambda.h │ ├── no_main_window.cpp │ ├── no_main_window.h │ ├── stock-hchain-24-broken.xpm │ └── stock-hchain-24.xpm ├── spotFinders ├── ErosionSmoother.cpp ├── Fillhole.cpp ├── Fillhole.h ├── GaussSmoothing.cpp ├── MedianSmoother.cpp ├── Spaltbandpass.cpp ├── Spalttiefpass.cpp ├── averageSmooth.cpp ├── averageSmooth.h ├── spotFinders.cpp └── spotFinders.h ├── stack_realign.h ├── test-plugin ├── BasenamePrinter.cpp ├── BasenamePrinter.h ├── Delayer.h ├── DummyFileInput.cpp ├── DummyFileInput.h ├── Exception.h ├── RepeatTrigger.h ├── Verbose.h ├── cpu_time.cpp ├── cpu_time.h ├── plugin.cpp ├── plugin.h ├── xenophon.cpp └── xenophon.h ├── third_party ├── any_iterator.hpp └── detail │ ├── any_iterator_abstract_base.hpp │ ├── any_iterator_metafunctions.hpp │ └── any_iterator_wrapper.hpp ├── threed_info ├── Config.cpp ├── Config.h ├── DepthInfo.cpp ├── DepthInfo.h ├── Lens3D.cpp ├── Lens3D.h ├── No3D.cpp ├── No3D.h ├── Polynomial3D.cpp ├── Polynomial3D.h ├── Spline3D.cpp ├── Spline3D.h ├── fwd.h ├── look_up_sigma_diff.cpp ├── look_up_sigma_diff.h └── types.h ├── tiff ├── OpenFile.h ├── RawImageFile.cpp ├── RawImageFile.h ├── TIFF.cpp ├── TIFF.h ├── TIFFOperation.cpp ├── TIFFOperation.h └── TIFF_OpenFile.cpp ├── traits ├── AffineProjection.cpp ├── AffineProjection.h ├── Projection.cpp ├── Projection.h ├── ProjectionConfig.h ├── ProjectionFactory.h ├── ScaledProjection.cpp ├── ScaledProjection.h ├── SupportPointProjection.cpp ├── image_resolution.h ├── optics.cpp ├── optics.h ├── optics_config.cpp ├── optics_config.h └── unit_tests.cpp ├── tsf ├── Output.cpp ├── Output.h └── TSFProto.proto ├── types ├── fluorophore.h └── samplepos.h ├── ui └── serialization │ ├── Node.cpp │ ├── Node.h │ ├── deserialize.cpp │ ├── deserialize.h │ ├── serialize.cpp │ └── serialize.h ├── unit_interval.h ├── unit_tests.cpp ├── unit_tests.h ├── units ├── amplitude.h ├── camera_response.h ├── frame_count.h ├── icl.h ├── megafrequency.h ├── microlength.h ├── microtime.h ├── nanolength.h ├── nanoresolution.h ├── permicrolength.h └── units.cpp ├── version.txt.in ├── viewer ├── Backend.cpp ├── Backend.h ├── ColourScheme.h ├── ColourSchemeFactory.h ├── Config.cpp ├── Config.h ├── DensityMap.cpp ├── DensityMapConfig.cpp ├── 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