diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp
index 565ecbd1da..b99c4c7b36 100644
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp
+++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp
@@ -1,129 +1,207 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 // Blueberry
 #include <berryISelectionService.h>
 #include <berryIWorkbenchWindow.h>
 
 // Qmitk
 #include "PAUSMotionCompensation.h"
 
 // Qt
 #include <QMessageBox>
 
 // mitk image
 #include <mitkImage.h>
 
 const std::string PAUSMotionCompensation::VIEW_ID = "org.mitk.views.pausmotioncompensation";
 
 void PAUSMotionCompensation::SetFocus()
 {
   m_Controls.buttonPerformImageProcessing->setFocus();
 }
 
 void PAUSMotionCompensation::CreateQtPartControl(QWidget *parent)
 {
   // create GUI widgets from the Qt Designer's .ui file
   m_Controls.setupUi(parent);
   connect(
     m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &PAUSMotionCompensation::DoImageProcessing);
+  connect(
+    m_Controls.buttonUpdateParameters, &QPushButton::clicked, this, &PAUSMotionCompensation::DoUpdateParameters);
 }
 
 void PAUSMotionCompensation::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
                                                 const QList<mitk::DataNode::Pointer> &nodes)
 {
+  // Clear the combo box where we choose the photoacoustic image
+  m_Controls.comboBoxPA->clear();
+
   // Make sure that there are exactle 2 nodes selected
-  if (nodes.size() == 2)
-  {
-    // iterate all selected objects, adjust warning visibility
-    foreach (mitk::DataNode::Pointer node, nodes)
-    {
-      if (node.IsNotNull() && dynamic_cast<mitk::Image *>(node->GetData()))
-      {
-        m_Controls.labelWarning->setVisible(false);
-        m_Controls.buttonPerformImageProcessing->setEnabled(true);
-        return;
-      }
+  if (nodes.size() != 2) {
+    m_Controls.labelWarning->setVisible(true);
+    m_Controls.buttonPerformImageProcessing->setEnabled(false);
+    return;
+  }
+
+  // Make sure that the image data is okay
+  foreach (mitk::DataNode::Pointer node, nodes) {
+    if (node.IsNull() || !dynamic_cast<mitk::Image *>(node->GetData())) {
+      m_Controls.labelWarning->setVisible(true);
+      m_Controls.buttonPerformImageProcessing->setEnabled(false);
+      return;
     }
+
+    // Add the image names to the combo box
+    m_Controls.comboBoxPA->addItem(QString::fromStdString(node->GetName()));
   }
-  m_Controls.labelWarning->setVisible(true);
-  m_Controls.buttonPerformImageProcessing->setEnabled(false);
+
+  m_Controls.labelWarning->setVisible(false);
+  m_Controls.buttonPerformImageProcessing->setEnabled(true);
+
 }
 
 void PAUSMotionCompensation::DoImageProcessing()
 {
   QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
 
   // Make sure that there are two images selected
   if (nodes.empty() || nodes.size() != 2)
   {
     QMessageBox::information(nullptr, "Warning", "Please select two images before starting image processing.");
     return;
   }
 
-  //TODO: I need to process two nodes and get the BaseData.
-  mitk::DataNode *node = nodes.front();
+  mitk::DataNode::Pointer paNode, usNode;
 
-  if (!node)
-  {
-    // Nothing selected. Inform the user and return
-    QMessageBox::information(nullptr, "Template", "Please load and select 2 images before starting image processing.");
+  foreach (mitk::DataNode::Pointer node, nodes) {
+    if(m_Controls.comboBoxPA->itemText(m_Controls.comboBoxPA->currentIndex()) == QString::fromStdString(node->GetName())) {
+      paNode = node;
+    } else {
+      usNode = node;
+    }
+  }
+
+  if(paNode.IsNull() || usNode.IsNull()) {
+    MITK_INFO << "One of the nodes is empty. This may happen, if the two images have the same name. Please rename one of them.";
+    QMessageBox::information(nullptr, "Template", "One of the nodes is empty. This may happen, if the two images have the same name. Please rename one of them.");
     return;
   }
 
   // here we have a valid mitk::DataNode
 
   // a node itself is not very useful, we need its data item (the image)
-  mitk::BaseData *data = node->GetData();
-  if (data)
+  mitk::BaseData *paData = paNode->GetData();
+  mitk::BaseData *usData = usNode->GetData();
+  if (paData && usData)
   {
     // test if this data item is an image or not (could also be a surface or something totally different)
-    mitk::Image *image = dynamic_cast<mitk::Image *>(data);
-    if (image)
+    mitk::Image *paImage = dynamic_cast<mitk::Image *>(paData);
+    mitk::Image *usImage = dynamic_cast<mitk::Image *>(usData);
+    if (paImage && usImage)
     {
       std::stringstream message;
       std::string name;
-      message << "Performing image processing for image ";
-      if (node->GetName(name))
+      message << "Performing motion compensation for image ";
+      if (paNode->GetName(name))
       {
         // a property called "name" was found for this DataNode
         message << "'" << name << "'";
       }
+      message << " and ";
+      if (usNode->GetName(name)) {
+        message << "'" << name << "'";
+      }
       message << ".";
       MITK_INFO << message.str();
 
       // actually do something here...
-      m_Filter->SetInput(0, image);
-      m_Filter->SetInput(1, image);
+      m_Filter->SetPaInput(paImage);
+      m_Filter->SetUsInput(usImage);
       m_Filter->Update();
-      // node->SetData(m_Filter->GetOutput(0));
-      // mitk::Image *test = m_Filter->GetOutput(0);
-      m_Filter->GetOutput(0);
-      m_Filter->GetOutput(1);
-      // node->SetData(test);
+      mitk::Image::Pointer paOutput = m_Filter->GetPaOutput();
+      mitk::Image::Pointer usOutput = m_Filter->GetUsOutput();
+
+      auto paOutNode = mitk::DataNode::New();
+      paOutNode->SetData(paOutput);
+      paOutNode->SetName(paNode->GetName() + " compensated");
 
-      MITK_INFO << "We are back in the plugin.";
+      this->GetDataStorage()->Add(paOutNode);
 
-      auto newNode = mitk::DataNode::New();
-      // newNode->SetData(test);
-      newNode->SetName("Test");
+      auto usOutNode = mitk::DataNode::New();
+      usOutNode->SetData(usOutput);
+      usOutNode->SetName(usNode->GetName() + " compensated");
 
-      this->GetDataStorage()->Add(newNode);
+      this->GetDataStorage()->Add(usOutNode);
 
       mitk::RenderingManager::GetInstance()->RequestUpdateAll();
     }
   }
 }
+
+void PAUSMotionCompensation::DoUpdateParameters() {
+
+  bool ok;
+
+  unsigned int batchSize = m_Controls.lineBatchSize->text().toInt(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetBatchSize(batchSize);
+
+  double pyrScale = m_Controls.linePyrScale->text().toDouble(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetPyrScale(pyrScale);
+
+  unsigned int levels = m_Controls.lineLevels->text().toInt(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetLevels(levels);
+
+  unsigned int winSize = m_Controls.lineWinSize->text().toInt(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetWinSize(winSize);
+
+  unsigned int iterations = m_Controls.lineIterations->text().toInt(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetIterations(iterations);
+
+  unsigned int polyN = m_Controls.linePolyN->text().toInt(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetPolyN(polyN);
+
+  double polySigma = m_Controls.linePolySigma->text().toDouble(&ok);
+  if(!ok) {
+    QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
+    return;
+  }
+  m_Filter->SetPolySigma(polySigma);
+}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h
index d04a194bee..d47836b4b1 100644
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h
+++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h
@@ -1,62 +1,62 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 
 #ifndef PAUSMotionCompensation_h
 #define PAUSMotionCompensation_h
 
 #include <berryISelectionListener.h>
 
 #include <QmitkAbstractView.h>
 
 #include "ui_PAUSMotionCompensationControls.h"
 
 #include "mitkPhotoacousticMotionCorrectionFilter.h"
 
 /**
   \brief PAUSMotionCompensation
 
   Photoacoustic and ultrasound image motion correction can be performed with this plugin. Internally OpenCV2 calc OpticalFlowFarneback is used.
   \sa QmitkAbstractView
   \ingroup ${plugin_target}_internal
 */
 class PAUSMotionCompensation : public QmitkAbstractView
 {
   // this is needed for all Qt objects that should have a Qt meta-object
   // (everything that derives from QObject and wants to have signal/slots)
   Q_OBJECT
 
 public:
   static const std::string VIEW_ID;
 
 protected:
   virtual void CreateQtPartControl(QWidget *parent) override;
 
   virtual void SetFocus() override;
 
   /// \brief called by QmitkFunctionality when DataManager's selection has changed
   virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
                                   const QList<mitk::DataNode::Pointer> &nodes) override;
 
   /// \brief Called when the user clicks the GUI button
   void DoImageProcessing();
+  void DoUpdateParameters();
 
   Ui::PAUSMotionCompensationControls m_Controls;
-  
   mitk::PhotoacousticMotionCorrectionFilter::Pointer m_Filter = mitk::PhotoacousticMotionCorrectionFilter::New();
 };
 
 #endif // PAUSMotionCompensation_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui
index 72f68af55b..8afd79a28c 100644
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui
+++ b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui
@@ -1,162 +1,179 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <ui version="4.0">
  <class>PAUSMotionCompensationControls</class>
  <widget class="QWidget" name="PAUSMotionCompensationControls">
   <property name="geometry">
    <rect>
     <x>0</x>
     <y>0</y>
     <width>242</width>
-    <height>391</height>
+    <height>555</height>
    </rect>
   </property>
   <property name="minimumSize">
    <size>
     <width>0</width>
     <height>0</height>
    </size>
   </property>
   <property name="windowTitle">
    <string>QmitkTemplate</string>
   </property>
   <layout class="QVBoxLayout" name="verticalLayout">
    <item>
     <widget class="QLabel" name="labelWarning">
      <property name="styleSheet">
       <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
      </property>
      <property name="text">
       <string>Please select 2 images!</string>
      </property>
     </widget>
    </item>
+   <item>
+    <widget class="QLabel" name="label_8">
+     <property name="text">
+      <string>Photoacoustic image</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QComboBox" name="comboBoxPA"/>
+   </item>
+   <item>
+    <widget class="QPushButton" name="buttonPerformImageProcessing">
+     <property name="toolTip">
+      <string>Do image processing</string>
+     </property>
+     <property name="text">
+      <string>Start processing</string>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="QLabel" name="label_7">
      <property name="text">
       <string>Batch size</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="lineBatchSize">
      <property name="text">
       <string>5</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label">
      <property name="text">
       <string>Pyramid scale:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="linePyrScale">
      <property name="text">
       <string>0.5</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label_2">
      <property name="text">
       <string>Levels:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="lineLevels">
      <property name="text">
       <string>3</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label_3">
      <property name="text">
       <string>Averaging window size:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="lineWinSize">
      <property name="text">
       <string>15</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label_4">
      <property name="text">
       <string>Iterations:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="lineIterations">
      <property name="text">
       <string>3</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label_5">
      <property name="text">
       <string>Pixel neighborhood for poly-expan:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="linePolyN">
      <property name="text">
       <string>5</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLabel" name="label_6">
      <property name="text">
       <string>Standard deviation:</string>
      </property>
     </widget>
    </item>
    <item>
     <widget class="QLineEdit" name="linePolySigma">
      <property name="text">
       <string>1.1</string>
      </property>
     </widget>
    </item>
    <item>
-    <widget class="QPushButton" name="buttonPerformImageProcessing">
-     <property name="toolTip">
-      <string>Do image processing</string>
-     </property>
+    <widget class="QPushButton" name="buttonUpdateParameters">
      <property name="text">
-      <string>Start processing</string>
+      <string>Update Parameters</string>
      </property>
     </widget>
    </item>
    <item>
     <spacer name="spacer1">
      <property name="orientation">
       <enum>Qt::Vertical</enum>
      </property>
      <property name="sizeType">
       <enum>QSizePolicy::Expanding</enum>
      </property>
      <property name="sizeHint" stdset="0">
       <size>
        <width>20</width>
        <height>220</height>
       </size>
      </property>
     </spacer>
    </item>
   </layout>
  </widget>
  <layoutdefault spacing="6" margin="11"/>
  <resources/>
  <connections/>
 </ui>