diff --git a/Modules/Core/files.cmake b/Modules/Core/files.cmake
index e9f3daabdf..f1bd7b5ec4 100644
--- a/Modules/Core/files.cmake
+++ b/Modules/Core/files.cmake
@@ -1,329 +1,330 @@
 file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
 
 set(CPP_FILES
   mitkCoreActivator.cpp
   mitkCoreObjectFactoryBase.cpp
   mitkCoreObjectFactory.cpp
   mitkCoreServices.cpp
   mitkException.cpp
 
   Algorithms/mitkBaseDataSource.cpp
   Algorithms/mitkClippedSurfaceBoundsCalculator.cpp
   Algorithms/mitkCompareImageDataFilter.cpp
   Algorithms/mitkCompositePixelValueToString.cpp
   Algorithms/mitkConvert2Dto3DImageFilter.cpp
   Algorithms/mitkDataNodeSource.cpp
   Algorithms/mitkExtractSliceFilter.cpp
   Algorithms/mitkExtractSliceFilter2.cpp
   Algorithms/mitkHistogramGenerator.cpp
   Algorithms/mitkImageChannelSelector.cpp
   Algorithms/mitkImageSliceSelector.cpp
   Algorithms/mitkImageSource.cpp
   Algorithms/mitkImageTimeSelector.cpp
   Algorithms/mitkImageToImageFilter.cpp
   Algorithms/mitkImageToSurfaceFilter.cpp
   Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp
   Algorithms/mitkPlaneGeometryDataToSurfaceFilter.cpp
   Algorithms/mitkPointSetSource.cpp
   Algorithms/mitkPointSetToPointSetFilter.cpp
   Algorithms/mitkRGBToRGBACastImageFilter.cpp
   Algorithms/mitkSubImageSelector.cpp
   Algorithms/mitkSurfaceSource.cpp
   Algorithms/mitkSurfaceToImageFilter.cpp
   Algorithms/mitkSurfaceToSurfaceFilter.cpp
   Algorithms/mitkUIDGenerator.cpp
   Algorithms/mitkVolumeCalculator.cpp
   Algorithms/mitkTemporalJoinImagesFilter.cpp
 
   Controllers/mitkBaseController.cpp
   Controllers/mitkCallbackFromGUIThread.cpp
   Controllers/mitkCameraController.cpp
   Controllers/mitkCameraRotationController.cpp
   Controllers/mitkCrosshairManager.cpp
   Controllers/mitkLimitedLinearUndo.cpp
   Controllers/mitkOperationEvent.cpp
   Controllers/mitkPlanePositionManager.cpp
   Controllers/mitkProgressBar.cpp
   Controllers/mitkRenderingManager.cpp
   Controllers/mitkSliceNavigationController.cpp
   Controllers/mitkSliceNavigationHelper.cpp
   Controllers/mitkStatusBar.cpp
   Controllers/mitkStepper.cpp
   Controllers/mitkTestManager.cpp
   Controllers/mitkTimeNavigationController.cpp
   Controllers/mitkUndoController.cpp
   Controllers/mitkVerboseLimitedLinearUndo.cpp
   Controllers/mitkVtkLayerController.cpp
 
+  DataManagement/mitkAffineTransform3D.cpp
   DataManagement/mitkAnatomicalStructureColorPresets.cpp
   DataManagement/mitkArbitraryTimeGeometry.cpp
   DataManagement/mitkAbstractTransformGeometry.cpp
   DataManagement/mitkAnnotationProperty.cpp
   DataManagement/mitkApplicationCursor.cpp
   DataManagement/mitkApplyTransformMatrixOperation.cpp
   DataManagement/mitkBaseData.cpp
   DataManagement/mitkBaseGeometry.cpp
   DataManagement/mitkBaseProperty.cpp
   DataManagement/mitkChannelDescriptor.cpp
   DataManagement/mitkClippingProperty.cpp
   DataManagement/mitkColorProperty.cpp
   DataManagement/mitkCrosshairData.cpp
   DataManagement/mitkDataNode.cpp
   DataManagement/mitkDataStorage.cpp
   DataManagement/mitkEnumerationProperty.cpp
   DataManagement/mitkFloatPropertyExtension.cpp
   DataManagement/mitkGeometry3D.cpp
   DataManagement/mitkGeometryData.cpp
   DataManagement/mitkGeometryTransformHolder.cpp
   DataManagement/mitkGroupTagProperty.cpp
   DataManagement/mitkGenericIDRelationRule.cpp
   DataManagement/mitkIdentifiable.cpp
   DataManagement/mitkImageAccessorBase.cpp
   DataManagement/mitkImageCaster.cpp
   DataManagement/mitkImageCastPart1.cpp
   DataManagement/mitkImageCastPart2.cpp
   DataManagement/mitkImageCastPart3.cpp
   DataManagement/mitkImageCastPart4.cpp
   DataManagement/mitkImage.cpp
   DataManagement/mitkImageDataItem.cpp
   DataManagement/mitkImageDescriptor.cpp
   DataManagement/mitkImageReadAccessor.cpp
   DataManagement/mitkImageStatisticsHolder.cpp
   DataManagement/mitkImageVtkAccessor.cpp
   DataManagement/mitkImageVtkReadAccessor.cpp
   DataManagement/mitkImageVtkWriteAccessor.cpp
   DataManagement/mitkImageWriteAccessor.cpp
   DataManagement/mitkIntPropertyExtension.cpp
   DataManagement/mitkIPersistenceService.cpp
   DataManagement/mitkIPropertyAliases.cpp
   DataManagement/mitkIPropertyDescriptions.cpp
   DataManagement/mitkIPropertyDeserialization.cpp
   DataManagement/mitkIPropertyExtensions.cpp
   DataManagement/mitkIPropertyFilters.cpp
   DataManagement/mitkIPropertyOwner.cpp
   DataManagement/mitkIPropertyPersistence.cpp
   DataManagement/mitkIPropertyProvider.cpp
   DataManagement/mitkITKEventObserverGuard.cpp
   DataManagement/mitkLandmarkProjectorBasedCurvedGeometry.cpp
   DataManagement/mitkLandmarkProjector.cpp
   DataManagement/mitkLevelWindow.cpp
   DataManagement/mitkLevelWindowManager.cpp
   DataManagement/mitkLevelWindowPreset.cpp
   DataManagement/mitkLevelWindowProperty.cpp
   DataManagement/mitkLookupTable.cpp
   DataManagement/mitkLookupTableProperty.cpp
   DataManagement/mitkLookupTables.cpp
   DataManagement/mitkMaterial.cpp
   DataManagement/mitkMemoryUtilities.cpp
   DataManagement/mitkModalityProperty.cpp
   DataManagement/mitkModifiedLock.cpp
   DataManagement/mitkNodePredicateAnd.cpp
   DataManagement/mitkNodePredicateBase.cpp
   DataManagement/mitkNodePredicateCompositeBase.cpp
   DataManagement/mitkNodePredicateData.cpp
   DataManagement/mitkNodePredicateDataType.cpp
   DataManagement/mitkNodePredicateDataUID.cpp
   DataManagement/mitkNodePredicateDimension.cpp
   DataManagement/mitkNodePredicateFunction.cpp
   DataManagement/mitkNodePredicateGeometry.cpp
   DataManagement/mitkNodePredicateNot.cpp
   DataManagement/mitkNodePredicateOr.cpp
   DataManagement/mitkNodePredicateProperty.cpp
   DataManagement/mitkNodePredicateDataProperty.cpp
   DataManagement/mitkNodePredicateSubGeometry.cpp
   DataManagement/mitkNumericConstants.cpp
   DataManagement/mitkPlaneGeometry.cpp
   DataManagement/mitkPlaneGeometryData.cpp
   DataManagement/mitkPlaneOperation.cpp
   DataManagement/mitkPlaneOrientationProperty.cpp
   DataManagement/mitkPointOperation.cpp
   DataManagement/mitkPointSet.cpp
   DataManagement/mitkPointSetShapeProperty.cpp
   DataManagement/mitkProperties.cpp
   DataManagement/mitkPropertyAliases.cpp
   DataManagement/mitkPropertyDescriptions.cpp
   DataManagement/mitkPropertyDeserialization.cpp
   DataManagement/mitkPropertyExtension.cpp
   DataManagement/mitkPropertyExtensions.cpp
   DataManagement/mitkPropertyFilter.cpp
   DataManagement/mitkPropertyFilters.cpp
   DataManagement/mitkPropertyKeyPath.cpp
   DataManagement/mitkPropertyList.cpp
   DataManagement/mitkPropertyListReplacedObserver.cpp
   DataManagement/mitkPropertyNameHelper.cpp
   DataManagement/mitkPropertyObserver.cpp
   DataManagement/mitkPropertyPersistence.cpp
   DataManagement/mitkPropertyPersistenceInfo.cpp
   DataManagement/mitkPropertyRelationRuleBase.cpp
   DataManagement/mitkProportionalTimeGeometry.cpp
   DataManagement/mitkRenderingModeProperty.cpp
   DataManagement/mitkResliceMethodProperty.cpp
   DataManagement/mitkRestorePlanePositionOperation.cpp
   DataManagement/mitkRotationOperation.cpp
   DataManagement/mitkScaleOperation.cpp
   DataManagement/mitkSlicedData.cpp
   DataManagement/mitkSlicedGeometry3D.cpp
   DataManagement/mitkSmartPointerProperty.cpp
   DataManagement/mitkStandaloneDataStorage.cpp
   DataManagement/mitkStringProperty.cpp
   DataManagement/mitkSurface.cpp
   DataManagement/mitkSurfaceOperation.cpp
   DataManagement/mitkSourceImageRelationRule.cpp
   DataManagement/mitkThinPlateSplineCurvedGeometry.cpp
   DataManagement/mitkTimeGeometry.cpp
   DataManagement/mitkTransferFunction.cpp
   DataManagement/mitkTransferFunctionInitializer.cpp
   DataManagement/mitkTransferFunctionProperty.cpp
   DataManagement/mitkTemporoSpatialStringProperty.cpp
   DataManagement/mitkUIDManipulator.cpp
   DataManagement/mitkVectorProperty.cpp
   DataManagement/mitkVtkInterpolationProperty.cpp
   DataManagement/mitkVtkRepresentationProperty.cpp
   DataManagement/mitkVtkResliceInterpolationProperty.cpp
   DataManagement/mitkVtkScalarModeProperty.cpp
   DataManagement/mitkWeakPointerProperty.cpp
   DataManagement/mitkIPropertyRelations.cpp
   DataManagement/mitkPropertyRelations.cpp
 
   Interactions/mitkAction.cpp
   Interactions/mitkBindDispatcherInteractor.cpp
   Interactions/mitkDataInteractor.cpp
   Interactions/mitkDispatcher.cpp
   Interactions/mitkDisplayActionEventBroadcast.cpp
   Interactions/mitkDisplayActionEventFunctions.cpp
   Interactions/mitkDisplayActionEventHandler.cpp
   Interactions/mitkDisplayActionEventHandlerDesynchronized.cpp
   Interactions/mitkDisplayActionEventHandlerStd.cpp
   Interactions/mitkDisplayActionEventHandlerSynchronized.cpp
   Interactions/mitkDisplayCoordinateOperation.cpp
   Interactions/mitkEventConfig.cpp
   Interactions/mitkEventFactory.cpp
   Interactions/mitkEventRecorder.cpp
   Interactions/mitkEventStateMachine.cpp
   Interactions/mitkInteractionEventConst.cpp
   Interactions/mitkInteractionEvent.cpp
   Interactions/mitkInteractionEventHandler.cpp
   Interactions/mitkInteractionEventObserver.cpp
   Interactions/mitkInteractionKeyEvent.cpp
   Interactions/mitkInteractionPositionEvent.cpp
   Interactions/mitkInteractionSchemeSwitcher.cpp
   Interactions/mitkInternalEvent.cpp
   Interactions/mitkMouseDoubleClickEvent.cpp
   Interactions/mitkMouseMoveEvent.cpp
   Interactions/mitkMousePressEvent.cpp
   Interactions/mitkMouseReleaseEvent.cpp
   Interactions/mitkMouseWheelEvent.cpp
   Interactions/mitkPointSetDataInteractor.cpp
   Interactions/mitkSinglePointDataInteractor.cpp
   Interactions/mitkStateMachineAction.cpp
   Interactions/mitkStateMachineCondition.cpp
   Interactions/mitkStateMachineContainer.cpp
   Interactions/mitkStateMachineState.cpp
   Interactions/mitkStateMachineTransition.cpp
   Interactions/mitkVtkEventAdapter.cpp
   Interactions/mitkVtkInteractorStyle.cxx
   Interactions/mitkXML2EventParser.cpp
 
   IO/mitkAbstractFileIO.cpp
   IO/mitkAbstractFileReader.cpp
   IO/mitkAbstractFileWriter.cpp
   IO/mitkCustomMimeType.cpp
   IO/mitkFileReader.cpp
   IO/mitkFileReaderRegistry.cpp
   IO/mitkFileReaderSelector.cpp
   IO/mitkFileReaderWriterBase.cpp
   IO/mitkFileWriter.cpp
   IO/mitkFileWriterRegistry.cpp
   IO/mitkFileWriterSelector.cpp
   IO/mitkGeometry3DToXML.cpp
   IO/mitkIFileIO.cpp
   IO/mitkIFileReader.cpp
   IO/mitkIFileWriter.cpp
   IO/mitkGeometryDataReaderService.cpp
   IO/mitkGeometryDataWriterService.cpp
   IO/mitkImageVtkLegacyIO.cpp
   IO/mitkImageVtkXmlIO.cpp
   IO/mitkIMimeTypeProvider.cpp
   IO/mitkIOConstants.cpp
   IO/mitkIOMimeTypes.cpp
   IO/mitkIOUtil.cpp
   IO/mitkItkImageIO.cpp
   IO/mitkItkLoggingAdapter.cpp
   IO/mitkLegacyFileReaderService.cpp
   IO/mitkLegacyFileWriterService.cpp
   IO/mitkLocaleSwitch.cpp
   IO/mitkLogBackend.cpp
   IO/mitkMimeType.cpp
   IO/mitkMimeTypeProvider.cpp
   IO/mitkOperation.cpp
   IO/mitkPixelType.cpp
   IO/mitkPointSetReaderService.cpp
   IO/mitkPointSetWriterService.cpp
   IO/mitkProportionalTimeGeometryToXML.cpp
   IO/mitkRawImageFileReader.cpp
   IO/mitkStandardFileLocations.cpp
   IO/mitkSurfaceStlIO.cpp
   IO/mitkSurfaceVtkIO.cpp
   IO/mitkSurfaceVtkLegacyIO.cpp
   IO/mitkSurfaceVtkXmlIO.cpp
   IO/mitkUtf8Util.cpp
   IO/mitkVtkLoggingAdapter.cpp
   IO/mitkPreferenceListReaderOptionsFunctor.cpp
   IO/mitkIOMetaInformationPropertyConstants.cpp
   IO/mitkIPreferences.cpp
   IO/mitkPreferences.cpp
   IO/mitkIPreferencesService.cpp
   IO/mitkPreferencesService.cpp
   IO/mitkIPreferencesStorage.cpp
   IO/mitkXMLPreferencesStorage.cpp
 
   Rendering/mitkAbstractAnnotationRenderer.cpp
   Rendering/mitkAnnotationUtils.cpp
   Rendering/mitkBaseRenderer.cpp
   Rendering/mitkBaseRendererHelper.cpp
   Rendering/mitkCrosshairVtkMapper2D.cpp
   Rendering/mitkGradientBackground.cpp
   Rendering/mitkImageVtkMapper2D.cpp
   Rendering/mitkMapper.cpp
   Rendering/mitkAnnotation.cpp
   Rendering/mitkPlaneGeometryDataMapper2D.cpp
   Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp
   Rendering/mitkPointSetVtkMapper2D.cpp
   Rendering/mitkPointSetVtkMapper3D.cpp
   Rendering/mitkRenderWindowBase.cpp
   Rendering/mitkRenderWindow.cpp
   Rendering/mitkRenderWindowFrame.cpp
   Rendering/mitkSurfaceVtkMapper2D.cpp
   Rendering/mitkSurfaceVtkMapper3D.cpp
   Rendering/mitkVideoRecorder.cpp
   Rendering/mitkVtkEventProvider.cpp
   Rendering/mitkVtkMapper.cpp
   Rendering/mitkVtkPropRenderer.cpp
   Rendering/mitkVtkWidgetRendering.cpp
   Rendering/vtkMitkLevelWindowFilter.cpp
   Rendering/vtkMitkRectangleProp.cpp
   Rendering/vtkMitkRenderProp.cpp
   Rendering/vtkMitkThickSlicesFilter.cpp
   Rendering/vtkNeverTranslucentTexture.cpp
 )
 
 set(RESOURCE_FILES
 Interactions/globalConfig.xml
 Interactions/DisplayInteraction.xml
 Interactions/DisplayConfigMITKBase.xml
 Interactions/DisplayConfigPACSBase.xml
 Interactions/DisplayConfigCrosshair.xml
 Interactions/DisplayConfigRotation.xml
 Interactions/DisplayConfigActivateCoupling.xml
 Interactions/DisplayConfigSwivel.xml
 Interactions/DisplayConfigPACSPan.xml
 Interactions/DisplayConfigPACSScroll.xml
 Interactions/DisplayConfigPACSZoom.xml
 Interactions/DisplayConfigPACSLevelWindow.xml
 Interactions/DisplayConfigBlockLMB.xml
 Interactions/PointSet.xml
 Interactions/PointSetConfig.xml
 
 mitkLevelWindowPresets.xml
 mitkAnatomicalStructureColorPresets.xml
 )
diff --git a/Modules/Core/include/mitkAffineTransform3D.h b/Modules/Core/include/mitkAffineTransform3D.h
index e6f535cd75..840fd8f6ac 100644
--- a/Modules/Core/include/mitkAffineTransform3D.h
+++ b/Modules/Core/include/mitkAffineTransform3D.h
@@ -1,24 +1,34 @@
 /*============================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center (DKFZ)
 All rights reserved.
 
 Use of this source code is governed by a 3-clause BSD license that can be
 found in the LICENSE file.
 
 ============================================================================*/
 
 #ifndef mitkAffineTransform3D_h
 #define mitkAffineTransform3D_h
 
 #include <mitkNumericConstants.h>
 #include <itkScalableAffineTransform.h>
+#include <nlohmann/json.hpp>
+#include <MitkCoreExports.h>
 
 namespace mitk
 {
   using AffineTransform3D = itk::ScalableAffineTransform<ScalarType, 3>;
+
+  /** \brief Write transform (4x4 matrix) as JSON array with 16 elements.
+   */
+  MITKCORE_EXPORT void ToJSON(nlohmann::json& j, AffineTransform3D::ConstPointer transform);
+
+  /** \brief Read transform from JSON array (16 elements, resp. 4x4 matrix).
+   */
+  MITKCORE_EXPORT void FromJSON(const nlohmann::json& j, AffineTransform3D::Pointer transform);
 }
 
 #endif
diff --git a/Modules/Core/src/DataManagement/mitkAffineTransform3D.cpp b/Modules/Core/src/DataManagement/mitkAffineTransform3D.cpp
new file mode 100644
index 0000000000..24677b60d7
--- /dev/null
+++ b/Modules/Core/src/DataManagement/mitkAffineTransform3D.cpp
@@ -0,0 +1,58 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include <mitkAffineTransform3D.h>
+
+void mitk::ToJSON(nlohmann::json& j, AffineTransform3D::ConstPointer transform)
+{
+  const auto& matrix = transform->GetMatrix().GetVnlMatrix();
+
+  for (int row = 0; row < 3; ++row)
+  {
+    for (int column = 0; column < 3; ++column)
+    {
+      j.push_back(matrix[row][column]);
+    }
+
+    j.push_back(0);
+  }
+
+  const auto& offset = transform->GetOffset();
+
+  for (int column = 0; column < 3; ++column)
+    j.push_back(offset[column]);
+
+  j.push_back(1);
+}
+
+void mitk::FromJSON(const nlohmann::json& j, AffineTransform3D::Pointer transform)
+{
+  size_t i = 0;
+  itk::Matrix<ScalarType, 3, 3> matrix;
+
+  for (int row = 0; row < 3; ++row)
+  {
+    for (int column = 0; column < 3; ++column)
+      j.at(i++).get_to(matrix[row][column]);
+
+    ++i;
+  }
+
+  transform->SetMatrix(matrix);
+
+  itk::Vector<ScalarType, 3> offset;
+
+  for (int column = 0; column < 3; ++column)
+    j.at(i++).get_to(offset[column]);
+
+  transform->SetOffset(offset);
+}
diff --git a/Modules/ROI/autoload/IO/src/mitkROIIO.cpp b/Modules/ROI/autoload/IO/src/mitkROIIO.cpp
index ade9c8016d..9817496d05 100644
--- a/Modules/ROI/autoload/IO/src/mitkROIIO.cpp
+++ b/Modules/ROI/autoload/IO/src/mitkROIIO.cpp
@@ -1,213 +1,236 @@
 /*============================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center (DKFZ)
 All rights reserved.
 
 Use of this source code is governed by a 3-clause BSD license that can be
 found in the LICENSE file.
 
 ============================================================================*/
 
 #include "mitkROIIO.h"
 #include <mitkProportionalTimeGeometry.h>
 #include <mitkROI.h>
 #include <mitkROIIOMimeTypes.h>
 
 #include <filesystem>
 #include <fstream>
 
 namespace
 {
   int CheckFileFormat(const nlohmann::json& json)
   {
     if ("MITK ROI" != json["FileFormat"].get<std::string>())
       mitkThrow() << "Unknown file format (expected \"MITK ROI\")!";
 
     auto version = json["Version"].get<int>();
 
-    if (1 != version)
-      mitkThrow() << "Unknown file format version (expected version 1)!";
+    if (version < 1 || version > 2)
+      mitkThrow() << "Unknown file format version (expected version 1 or 2)!";
 
     return version;
   }
 
   mitk::Vector3D GetSize(const mitk::BaseGeometry* geometry)
   {
     auto bounds = geometry->GetBounds();
 
     mitk::Vector3D result;
     result[0] = bounds[1];
     result[1] = bounds[3];
     result[2] = bounds[5];
 
     return result;
   }
 
   void SetSize(mitk::BaseGeometry* geometry, const mitk::Vector3D& size)
   {
     mitk::BaseGeometry::BoundsArrayType bounds({ 0.0, size[0], 0.0, size[1], 0.0, size[2] });
     geometry->SetBounds(bounds);
   }
 
-  mitk::TimeGeometry::Pointer ReadGeometry(const nlohmann::json& jGeometry)
+  mitk::TimeGeometry::Pointer ReadGeometry(const nlohmann::json& jGeometry, int version)
   {
     auto geometry = mitk::Geometry3D::New();
     geometry->ImageGeometryOn();
 
     if (!jGeometry.is_object())
       mitkThrow() << "Geometry is expected to be a JSON object.";
 
+    bool hasTransform = false;
+
+    if (jGeometry.contains("Transform"))
+    {
+      if (version < 2)
+        mitkThrow() << "Transforms are not supported in MITK ROI file format version 1.";
+
+      auto transform = mitk::AffineTransform3D::New();
+      mitk::FromJSON(jGeometry["Transform"], transform);
+      geometry->SetIndexToWorldTransform(transform);
+
+      hasTransform = true;
+    }
+
     if (jGeometry.contains("Origin"))
+    {
+      if (hasTransform)
+        mitkThrow() << "Origin is already defined by Transform.";
+
       geometry->SetOrigin(jGeometry["Origin"].get<mitk::Point3D>());
+    }
 
     if (jGeometry.contains("Spacing"))
+    {
+      if (hasTransform)
+        mitkThrow() << "Spacing is already defined by Transform.";
+
       geometry->SetSpacing(jGeometry["Spacing"].get<mitk::Vector3D>());
+    }
 
     if (jGeometry.contains("Size"))
       SetSize(geometry, jGeometry["Size"].get<mitk::Vector3D>());
 
     auto timeSteps = jGeometry.contains("TimeSteps")
       ? jGeometry["TimeSteps"].get<mitk::TimeStepType>()
       : 1;
 
     auto result = mitk::ProportionalTimeGeometry::New();
     result->Initialize(geometry, timeSteps);
 
     return result;
   }
 
   nlohmann::json WriteGeometry(const mitk::TimeGeometry* timeGeometry)
   {
     auto geometry = timeGeometry->GetGeometryForTimeStep(0);
 
-    nlohmann::json result = {
-      { "Origin", geometry->GetOrigin() },
-      { "Spacing", geometry->GetSpacing() },
-      { "Size", GetSize(geometry) }
-    };
+    nlohmann::json result;
+
+    mitk::ToJSON(result["Transform"], geometry->GetIndexToWorldTransform());
+    result["Size"] = GetSize(geometry);
 
     auto timeSteps = timeGeometry->CountTimeSteps();
 
     if (timeSteps > 1)
       result["TimeSteps"] = timeSteps;
 
     return result;
   }
 }
 
 mitk::ROIIO::ROIIO()
   : AbstractFileIO(ROI::GetStaticNameOfClass(), MitkROIIOMimeTypes::ROI_MIMETYPE(), "MITK ROI")
 {
   this->RegisterService();
 }
 
 std::vector<mitk::BaseData::Pointer> mitk::ROIIO::DoRead()
 {
   auto *stream = this->GetInputStream();
   std::ifstream fileStream;
 
   if (nullptr == stream)
   {
     auto filename = this->GetInputLocation();
 
     if (filename.empty() || !std::filesystem::exists(filename))
       mitkThrow() << "Invalid or nonexistent filename: \"" << filename << "\"!";
 
     fileStream.open(filename);
 
     if (!fileStream.is_open())
       mitkThrow() << "Could not open file \"" << filename << "\" for reading!";
 
     stream = &fileStream;
   }
 
   auto result = ROI::New();
 
   try
   {
     auto j = nlohmann::json::parse(*stream);
 
-    CheckFileFormat(j);
+    auto version = CheckFileFormat(j);
 
-    auto geometry = ReadGeometry(j["Geometry"]);
+    auto geometry = ReadGeometry(j["Geometry"], version);
     result->SetTimeGeometry(geometry);
 
     if (j.contains("Name"))
       result->SetProperty("name", mitk::StringProperty::New(j["Name"].get<std::string>()));
 
     if (j.contains("Caption"))
       result->SetProperty("caption", mitk::StringProperty::New(j["Caption"].get<std::string>()));
 
     for (const auto& roi : j["ROIs"])
       result->AddElement(roi.get<ROI::Element>());
   }
   catch (const nlohmann::json::exception &e)
   {
     mitkThrow() << e.what();
   }
 
   return { result };
 }
 
 void mitk::ROIIO::Write()
 {
   auto input = dynamic_cast<const ROI*>(this->GetInput());
 
   if (input == nullptr)
     mitkThrow() << "Invalid input for writing!";
 
   if (input->GetNumberOfElements() == 0)
     mitkThrow() << "No ROIs found!";
 
   auto* stream = this->GetOutputStream();
   std::ofstream fileStream;
 
   if (stream == nullptr)
   {
     auto filename = this->GetOutputLocation();
 
     if (filename.empty())
       mitkThrow() << "Neither an output stream nor an output filename was specified!";
 
     fileStream.open(filename);
 
     if (!fileStream.is_open())
       mitkThrow() << "Could not open file \"" << filename << "\" for writing!";
 
     stream = &fileStream;
   }
 
   if (!stream->good())
     mitkThrow() << "Stream for writing is not good!";
 
   nlohmann::ordered_json j = {
     { "FileFormat", "MITK ROI" },
-    { "Version", 1 }
+    { "Version", 2 }
   };
 
   if (auto name = input->GetProperty("name"); name.IsNotNull())
     j["Name"] = name->GetValueAsString();
 
   j["Geometry"] = WriteGeometry(input->GetTimeGeometry());
 
   auto caption = input->GetConstProperty("caption");
 
   if (caption.IsNotNull())
     j["Caption"] = caption->GetValueAsString();
 
   nlohmann::json rois;
 
   for (const auto& roi : *input)
     rois.push_back(roi.second);
 
   j["ROIs"] = rois;
 
   *stream << std::setw(2) << j << std::endl;
 }
 
 mitk::ROIIO* mitk::ROIIO::IOClone() const
 {
   return new ROIIO(*this);
 }
diff --git a/Modules/ROI/autoload/IO/src/mitkROIIOMimeTypes.cpp b/Modules/ROI/autoload/IO/src/mitkROIIOMimeTypes.cpp
index 91b8032fe5..40d8697186 100644
--- a/Modules/ROI/autoload/IO/src/mitkROIIOMimeTypes.cpp
+++ b/Modules/ROI/autoload/IO/src/mitkROIIOMimeTypes.cpp
@@ -1,75 +1,77 @@
 /*============================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center (DKFZ)
 All rights reserved.
 
 Use of this source code is governed by a 3-clause BSD license that can be
 found in the LICENSE file.
 
 ============================================================================*/
 
 #include <mitkROIIOMimeTypes.h>
 #include <mitkIOMimeTypes.h>
 
 #include <filesystem>
 #include <fstream>
 
 #include <nlohmann/json.hpp>
 
 mitk::MitkROIIOMimeTypes::MitkROIMimeType::MitkROIMimeType()
   : CustomMimeType(ROI_MIMETYPE_NAME())
 {
   this->AddExtension("json");
   this->SetCategory("MITK ROI");
   this->SetComment("MITK ROI");
 }
 
 bool mitk::MitkROIIOMimeTypes::MitkROIMimeType::AppliesTo(const std::string& path) const
 {
   bool result = CustomMimeType::AppliesTo(path);
 
   if (!std::filesystem::exists(path)) // T18572
     return result;
 
   std::ifstream file(path);
 
   if (!file.is_open())
     return false;
 
   auto json = nlohmann::json::parse(file, nullptr, false);
 
   if (json.is_discarded() || !json.is_object())
     return false;
 
   if ("MITK ROI" != json.value("FileFormat", ""))
     return false;
 
-  if (1 != json.value<int>("Version", 0))
+  auto version = json.value<int>("Version", 0);
+
+  if (version < 1 || version > 2)
     return false;
 
   return true;
 }
 
 mitk::MitkROIIOMimeTypes::MitkROIMimeType* mitk::MitkROIIOMimeTypes::MitkROIMimeType::Clone() const
 {
   return new MitkROIMimeType(*this);
 }
 
 mitk::MitkROIIOMimeTypes::MitkROIMimeType mitk::MitkROIIOMimeTypes::ROI_MIMETYPE()
 {
   return MitkROIMimeType();
 }
 
 std::string mitk::MitkROIIOMimeTypes::ROI_MIMETYPE_NAME()
 {
   return IOMimeTypes::DEFAULT_BASE_NAME() + ".roi";
 }
 
 std::vector<mitk::CustomMimeType*> mitk::MitkROIIOMimeTypes::Get()
 {
   std::vector<CustomMimeType*> mimeTypes;
   mimeTypes.push_back(ROI_MIMETYPE().Clone());
   return mimeTypes;
 }