From 300e38bda62002c2765b8f0836b6fb61addbc105 Mon Sep 17 00:00:00 2001
From: Romane Carryn <romane.carryn@student.uclouvain.be>
Date: Tue, 26 Aug 2025 15:36:52 +0200
Subject: [PATCH 1/2] github button

---
 _templates/my_header.html                     |   9 ++
 .../SimpleDoseComputationAndOptOnCT.ipynb     |   4 +-
 auto_community/Template/run_template.ipynb    |   4 +-
 .../DICOMExample/create3DSeqFromDicom.ipynb   |   4 +-
 .../DICOMExample/create3DSeqFromImages.ipynb  |   4 +-
 .../createDynamic3DModelFromDicomFields.ipynb |   4 +-
 .../createModelWithROIsFromDicomImages.ipynb  |   4 +-
 .../DICOMExample/crop3DDataAroundROI.ipynb    |   4 +-
 .../DICOMExample/exampleImageResampling.ipynb |   4 +-
 .../DICOMExample/generateDRRAndGTVMasks.ipynb |   4 +-
 .../run_generateRandomSamplesFromModel.ipynb  |   4 +-
 .../run_SimpleDoseCalculation.ipynb           |   4 +-
 .../run_UseOfRangeShifterForProtonPlan.ipynb  |   4 +-
 ...photonPlanCreationAndDoseCalculation.ipynb |   4 +-
 ...protonPlanCreationAndDoseCalculation.ipynb |   4 +-
 .../PlanDeliverySimulation.ipynb              |   4 +-
 .../run_PBSDeliveryTimings.ipynb              |   4 +-
 .../run_4DProtonOptimization.ipynb            |   4 +-
 .../run_4DprotonEvaluation.ipynb              |   4 +-
 .../run_SimpleOptimizationPhoton.ipynb        |   4 +-
 .../run_SimpleOptimizationProton.ipynb        |   4 +-
 .../run_beamletFreeOpti.ipynb                 |   4 +-
 .../run_boundConstraintsOpti.ipynb            |   4 +-
 .../run_evaluatePhotonRobustness.ipynb        |   4 +-
 .../run_evaluateProtonRobustness.ipynb        |   4 +-
 .../run_robustOptimizationProtons.ipynb       |   4 +-
 ..._simpleOptimization_createDicomStudy.ipynb |   6 +-
 .../Segmentation/run_Segmentation.ipynb       |   4 +-
 .../exampleInterFractionChanges.ipynb         |   4 +-
 ...run_exampleApplyBaselineShiftToModel.ipynb |   4 +-
 ...leDeformableBreathigDataAugmentation.ipynb |   4 +-
 ...run_exampleDeformationFromWeightMaps.ipynb |   4 +-
 .../dynamicData/run_exampleMidP.ipynb         |   4 +-
 .../run_exampleApplyBaselineShift.ipynb       |   4 +-
 .../run_exampleDilateBinaryMask.ipynb         |   4 +-
 .../run_exampleTransform3D.ipynb              |   4 +-
 .../multiplePythonEnv/backAndForthChild.ipynb |   4 +-
 .../run_backAndForthParent.ipynb              |   4 +-
 .../run_sharedMemoryParent.ipynb              |   4 +-
 .../multiplePythonEnv/sharedMemoryChild.ipynb |   4 +-
 .../registration/run_exampleMorphons.ipynb    |   4 +-
 .../registration/run_exampleRigid.ipynb       |   4 +-
 .../SimpleDoseComputationAndOptOnCT.py        |   2 -
 community/Template/run_template.py            |   2 -
 examples/DICOMExample/create3DSeqFromDicom.py |   2 -
 .../DICOMExample/create3DSeqFromImages.py     |   2 -
 .../createDynamic3DModelFromDicomFields.py    |   2 -
 .../createModelWithROIsFromDicomImages.py     |   2 -
 examples/DICOMExample/crop3DDataAroundROI.py  |   2 -
 .../DICOMExample/exampleImageResampling.py    |   2 -
 .../DICOMExample/generateDRRAndGTVMasks.py    |   2 -
 .../run_generateRandomSamplesFromModel.py     |   2 -
 .../run_SimpleDoseCalculation.py              |   3 +-
 .../run_UseOfRangeShifterForProtonPlan.py     |   2 -
 ...un_photonPlanCreationAndDoseCalculation.py |   2 -
 ...un_protonPlanCreationAndDoseCalculation.py |   2 -
 .../PlanDeliverySimulation.py                 |   2 -
 .../run_PBSDeliveryTimings.py                 |   2 -
 .../run_4DProtonOptimization.py               |   4 +-
 .../run_4DprotonEvaluation.py                 |   2 -
 .../run_SimpleOptimizationPhoton.py           |   4 +-
 .../run_SimpleOptimizationProton.py           |   4 +-
 .../PlanOptimization/run_beamletFreeOpti.py   |   4 +-
 .../run_boundConstraintsOpti.py               |   4 +-
 .../run_evaluatePhotonRobustness.py           |   4 +-
 .../run_evaluateProtonRobustness.py           |   4 +-
 .../run_robustOptimizationProtons.py          |   4 +-
 ...run_simpleOptimization_createDicomStudy.py |   4 +-
 examples/Segmentation/run_Segmentation.py     |   4 +-
 .../exampleInterFractionChanges.py            |   4 +-
 .../run_exampleApplyBaselineShiftToModel.py   |   2 -
 ...ampleDeformableBreathigDataAugmentation.py |   2 -
 .../run_exampleDeformationFromWeightMaps.py   |   2 -
 examples/dynamicData/run_exampleMidP.py       |   2 -
 .../run_exampleApplyBaselineShift.py          |   2 -
 .../run_exampleDilateBinaryMask.py            |   4 +-
 .../imageProcessing/run_exampleTransform3D.py |   2 -
 .../multiplePythonEnv/backAndForthChild.py    |   3 +-
 .../run_backAndForthParent.py                 |   2 -
 .../run_sharedMemoryParent.py                 |   2 -
 .../multiplePythonEnv/sharedMemoryChild.py    |   2 -
 examples/registration/run_exampleMorphons.py  |   4 +-
 examples/registration/run_exampleRigid.py     |   4 +-
 sg_execution_times.rst                        | 122 +++++++++---------
 84 files changed, 169 insertions(+), 240 deletions(-)

diff --git a/_templates/my_header.html b/_templates/my_header.html
index d874661..4662911 100644
--- a/_templates/my_header.html
+++ b/_templates/my_header.html
@@ -17,6 +17,15 @@
   </span>
 </button>
 
+<button class="btn btn-sm" id="github-button" style="display: inline-block;"
+          data-bs-placement="bottom" data-bs-toggle="tooltip" title="Open on GitHub">
+    <span class="btn__icon-container">
+      <a id="github-link" href="https://github.com/OpenTPS/examples.git" target="_blank" style="color: inherit;">
+        <i class="fa-brands fa-github"></i>
+      </a>
+    </span>
+  </button>
+
 
 <button onclick="toggleFullScreen()"
   class="btn btn-sm btn-fullscreen-button"
diff --git a/auto_community/CommunityExample/SimpleDoseComputationAndOptOnCT.ipynb b/auto_community/CommunityExample/SimpleDoseComputationAndOptOnCT.ipynb
index c9547ee..5950f7f 100644
--- a/auto_community/CommunityExample/SimpleDoseComputationAndOptOnCT.ipynb
+++ b/auto_community/CommunityExample/SimpleDoseComputationAndOptOnCT.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_community/Template/run_template.ipynb b/auto_community/Template/run_template.ipynb
index 5e47a29..6d06694 100644
--- a/auto_community/Template/run_template.ipynb
+++ b/auto_community/Template/run_template.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/create3DSeqFromDicom.ipynb b/auto_examples/DICOMExample/create3DSeqFromDicom.ipynb
index cacb09d..f9245e5 100644
--- a/auto_examples/DICOMExample/create3DSeqFromDicom.ipynb
+++ b/auto_examples/DICOMExample/create3DSeqFromDicom.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/create3DSeqFromImages.ipynb b/auto_examples/DICOMExample/create3DSeqFromImages.ipynb
index 8126ebd..9d5e3a1 100644
--- a/auto_examples/DICOMExample/create3DSeqFromImages.ipynb
+++ b/auto_examples/DICOMExample/create3DSeqFromImages.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/createDynamic3DModelFromDicomFields.ipynb b/auto_examples/DICOMExample/createDynamic3DModelFromDicomFields.ipynb
index 9aa5e55..195220f 100644
--- a/auto_examples/DICOMExample/createDynamic3DModelFromDicomFields.ipynb
+++ b/auto_examples/DICOMExample/createDynamic3DModelFromDicomFields.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/createModelWithROIsFromDicomImages.ipynb b/auto_examples/DICOMExample/createModelWithROIsFromDicomImages.ipynb
index 9c1c990..b38a74d 100644
--- a/auto_examples/DICOMExample/createModelWithROIsFromDicomImages.ipynb
+++ b/auto_examples/DICOMExample/createModelWithROIsFromDicomImages.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/crop3DDataAroundROI.ipynb b/auto_examples/DICOMExample/crop3DDataAroundROI.ipynb
index 9174893..580bdcb 100644
--- a/auto_examples/DICOMExample/crop3DDataAroundROI.ipynb
+++ b/auto_examples/DICOMExample/crop3DDataAroundROI.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/exampleImageResampling.ipynb b/auto_examples/DICOMExample/exampleImageResampling.ipynb
index 70c593f..da0b031 100644
--- a/auto_examples/DICOMExample/exampleImageResampling.ipynb
+++ b/auto_examples/DICOMExample/exampleImageResampling.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/generateDRRAndGTVMasks.ipynb b/auto_examples/DICOMExample/generateDRRAndGTVMasks.ipynb
index c52c244..7edc939 100644
--- a/auto_examples/DICOMExample/generateDRRAndGTVMasks.ipynb
+++ b/auto_examples/DICOMExample/generateDRRAndGTVMasks.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DICOMExample/run_generateRandomSamplesFromModel.ipynb b/auto_examples/DICOMExample/run_generateRandomSamplesFromModel.ipynb
index f20d67c..ea29647 100644
--- a/auto_examples/DICOMExample/run_generateRandomSamplesFromModel.ipynb
+++ b/auto_examples/DICOMExample/run_generateRandomSamplesFromModel.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseComputation/run_SimpleDoseCalculation.ipynb b/auto_examples/DoseComputation/run_SimpleDoseCalculation.ipynb
index 033e84c..30b32cf 100644
--- a/auto_examples/DoseComputation/run_SimpleDoseCalculation.ipynb
+++ b/auto_examples/DoseComputation/run_SimpleDoseCalculation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.ipynb b/auto_examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.ipynb
index 06ed26f..cfc1282 100644
--- a/auto_examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.ipynb
+++ b/auto_examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.ipynb b/auto_examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.ipynb
index e824fce..e0bf73b 100644
--- a/auto_examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.ipynb
+++ b/auto_examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.ipynb b/auto_examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.ipynb
index fa66b16..4f7fa98 100644
--- a/auto_examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.ipynb
+++ b/auto_examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseDeliverySimulation/PlanDeliverySimulation.ipynb b/auto_examples/DoseDeliverySimulation/PlanDeliverySimulation.ipynb
index d136d87..5dfe500 100644
--- a/auto_examples/DoseDeliverySimulation/PlanDeliverySimulation.ipynb
+++ b/auto_examples/DoseDeliverySimulation/PlanDeliverySimulation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/DoseDeliverySimulation/run_PBSDeliveryTimings.ipynb b/auto_examples/DoseDeliverySimulation/run_PBSDeliveryTimings.ipynb
index 5219fd5..1717775 100644
--- a/auto_examples/DoseDeliverySimulation/run_PBSDeliveryTimings.ipynb
+++ b/auto_examples/DoseDeliverySimulation/run_PBSDeliveryTimings.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_4DProtonOptimization.ipynb b/auto_examples/PlanOptimization/run_4DProtonOptimization.ipynb
index 0f765e8..63a58dc 100644
--- a/auto_examples/PlanOptimization/run_4DProtonOptimization.ipynb
+++ b/auto_examples/PlanOptimization/run_4DProtonOptimization.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_4DprotonEvaluation.ipynb b/auto_examples/PlanOptimization/run_4DprotonEvaluation.ipynb
index 252956d..2873813 100644
--- a/auto_examples/PlanOptimization/run_4DprotonEvaluation.ipynb
+++ b/auto_examples/PlanOptimization/run_4DprotonEvaluation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_SimpleOptimizationPhoton.ipynb b/auto_examples/PlanOptimization/run_SimpleOptimizationPhoton.ipynb
index f07cb2f..cef4e68 100644
--- a/auto_examples/PlanOptimization/run_SimpleOptimizationPhoton.ipynb
+++ b/auto_examples/PlanOptimization/run_SimpleOptimizationPhoton.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_SimpleOptimizationProton.ipynb b/auto_examples/PlanOptimization/run_SimpleOptimizationProton.ipynb
index de6acd3..a7ec3be 100644
--- a/auto_examples/PlanOptimization/run_SimpleOptimizationProton.ipynb
+++ b/auto_examples/PlanOptimization/run_SimpleOptimizationProton.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_beamletFreeOpti.ipynb b/auto_examples/PlanOptimization/run_beamletFreeOpti.ipynb
index 6468e4f..7daa13b 100644
--- a/auto_examples/PlanOptimization/run_beamletFreeOpti.ipynb
+++ b/auto_examples/PlanOptimization/run_beamletFreeOpti.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_boundConstraintsOpti.ipynb b/auto_examples/PlanOptimization/run_boundConstraintsOpti.ipynb
index 1fdcdb0..93cd9af 100644
--- a/auto_examples/PlanOptimization/run_boundConstraintsOpti.ipynb
+++ b/auto_examples/PlanOptimization/run_boundConstraintsOpti.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_evaluatePhotonRobustness.ipynb b/auto_examples/PlanOptimization/run_evaluatePhotonRobustness.ipynb
index fb7f880..0fb7a43 100644
--- a/auto_examples/PlanOptimization/run_evaluatePhotonRobustness.ipynb
+++ b/auto_examples/PlanOptimization/run_evaluatePhotonRobustness.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_evaluateProtonRobustness.ipynb b/auto_examples/PlanOptimization/run_evaluateProtonRobustness.ipynb
index 7cfd1f3..eafc278 100644
--- a/auto_examples/PlanOptimization/run_evaluateProtonRobustness.ipynb
+++ b/auto_examples/PlanOptimization/run_evaluateProtonRobustness.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_robustOptimizationProtons.ipynb b/auto_examples/PlanOptimization/run_robustOptimizationProtons.ipynb
index c866998..52942cd 100644
--- a/auto_examples/PlanOptimization/run_robustOptimizationProtons.ipynb
+++ b/auto_examples/PlanOptimization/run_robustOptimizationProtons.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/PlanOptimization/run_simpleOptimization_createDicomStudy.ipynb b/auto_examples/PlanOptimization/run_simpleOptimization_createDicomStudy.ipynb
index 4e50910..b04c499 100644
--- a/auto_examples/PlanOptimization/run_simpleOptimization_createDicomStudy.ipynb
+++ b/auto_examples/PlanOptimization/run_simpleOptimization_createDicomStudy.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
@@ -274,7 +274,7 @@
       },
       "outputs": [],
       "source": [
-        "fig, ax = plt.subplots(1, 3, figsize=(15, 5))\nax[0].axes.get_xaxis().set_visible(False)\nax[0].axes.get_yaxis().set_visible(False)\nax[0].imshow(img_ct, cmap='gray')\nax[0].imshow(img_mask, alpha=.2, cmap='binary')  # PTV\ndose = ax[0].imshow(img_dose, cmap='jet', alpha=.2)\nplt.colorbar(dose, ax=ax[0])\nax[1].plot(target_DVH.histogram[0], target_DVH.histogram[1], label=target_DVH.name)\nax[1].set_xlabel(\"Dose (Gy)\")\nax[1].set_ylabel(\"Volume (%)\")\nax[1].grid(True)\nax[1].legend()\n\nconvData = solver.getConvergenceData()\nax[2].plot(np.linspace(0, convData['time'], len(convData['func_0'])), convData['func_0'], 'bo-', lw=2,\n            label='Fidelity')\nax[2].set_xlabel('Time (s)')\nax[2].set_ylabel('Cost')\nax[2].set_yscale('symlog')\nax2 = ax[2].twiny()\nax2.set_xlabel('Iterations')\nax2.set_xlim(0, convData['nIter'])\nax[2].grid(True)\n\nplt.savefig(f'{output_path}/Dose_SimpleOptimization.png', format = 'png')\nplt.show()"
+        "fig, ax = plt.subplots(1, 3, figsize=(15, 5))\nax[0].axes.get_xaxis().set_visible(False)\nax[0].axes.get_yaxis().set_visible(False)\nax[0].imshow(img_ct, cmap='gray')\nax[0].imshow(img_mask, alpha=.2, cmap='binary')  # PTV\ndose = ax[0].imshow(img_dose, cmap='jet', alpha=.2)\nplt.colorbar(dose, ax=ax[0])\nax[1].plot(target_DVH.histogram[0], target_DVH.histogram[1], label=target_DVH.name)\nax[1].set_xlabel(\"Dose (Gy)\")\nax[1].set_ylabel(\"Volume (%)\")\nax[1].grid(True)\nax[1].legend()\n\nconvData = solver.getConvergenceData()\nax[2].plot(np.arange(0, convData['time'], convData['time'] / convData['nIter']), convData['func_0'], 'bo-', lw=2,\n            label='Fidelity')\nax[2].set_xlabel('Time (s)')\nax[2].set_ylabel('Cost')\nax[2].set_yscale('symlog')\nax2 = ax[2].twiny()\nax2.set_xlabel('Iterations')\nax2.set_xlim(0, convData['nIter'])\nax[2].grid(True)\n\nplt.savefig(f'{output_path}/Dose_SimpleOptimization.png', format = 'png')\nplt.show()"
       ]
     }
   ],
diff --git a/auto_examples/Segmentation/run_Segmentation.ipynb b/auto_examples/Segmentation/run_Segmentation.ipynb
index f5be4b7..c84f5d8 100644
--- a/auto_examples/Segmentation/run_Segmentation.ipynb
+++ b/auto_examples/Segmentation/run_Segmentation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/dynamicData/exampleInterFractionChanges.ipynb b/auto_examples/dynamicData/exampleInterFractionChanges.ipynb
index 39df236..2d02eaa 100644
--- a/auto_examples/dynamicData/exampleInterFractionChanges.ipynb
+++ b/auto_examples/dynamicData/exampleInterFractionChanges.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/dynamicData/run_exampleApplyBaselineShiftToModel.ipynb b/auto_examples/dynamicData/run_exampleApplyBaselineShiftToModel.ipynb
index ba73ad6..38a3d61 100644
--- a/auto_examples/dynamicData/run_exampleApplyBaselineShiftToModel.ipynb
+++ b/auto_examples/dynamicData/run_exampleApplyBaselineShiftToModel.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.ipynb b/auto_examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.ipynb
index 728cc1c..294b113 100644
--- a/auto_examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.ipynb
+++ b/auto_examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/dynamicData/run_exampleDeformationFromWeightMaps.ipynb b/auto_examples/dynamicData/run_exampleDeformationFromWeightMaps.ipynb
index 1868e81..f822f05 100644
--- a/auto_examples/dynamicData/run_exampleDeformationFromWeightMaps.ipynb
+++ b/auto_examples/dynamicData/run_exampleDeformationFromWeightMaps.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/dynamicData/run_exampleMidP.ipynb b/auto_examples/dynamicData/run_exampleMidP.ipynb
index 5a4a849..53043e8 100644
--- a/auto_examples/dynamicData/run_exampleMidP.ipynb
+++ b/auto_examples/dynamicData/run_exampleMidP.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/imageProcessing/run_exampleApplyBaselineShift.ipynb b/auto_examples/imageProcessing/run_exampleApplyBaselineShift.ipynb
index 0071943..474ec55 100644
--- a/auto_examples/imageProcessing/run_exampleApplyBaselineShift.ipynb
+++ b/auto_examples/imageProcessing/run_exampleApplyBaselineShift.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/imageProcessing/run_exampleDilateBinaryMask.ipynb b/auto_examples/imageProcessing/run_exampleDilateBinaryMask.ipynb
index b7a7884..be0154d 100644
--- a/auto_examples/imageProcessing/run_exampleDilateBinaryMask.ipynb
+++ b/auto_examples/imageProcessing/run_exampleDilateBinaryMask.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/imageProcessing/run_exampleTransform3D.ipynb b/auto_examples/imageProcessing/run_exampleTransform3D.ipynb
index 359c5ad..e42a837 100644
--- a/auto_examples/imageProcessing/run_exampleTransform3D.ipynb
+++ b/auto_examples/imageProcessing/run_exampleTransform3D.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/multiplePythonEnv/backAndForthChild.ipynb b/auto_examples/multiplePythonEnv/backAndForthChild.ipynb
index d57b4c4..ef7d4dc 100644
--- a/auto_examples/multiplePythonEnv/backAndForthChild.ipynb
+++ b/auto_examples/multiplePythonEnv/backAndForthChild.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/multiplePythonEnv/run_backAndForthParent.ipynb b/auto_examples/multiplePythonEnv/run_backAndForthParent.ipynb
index 766dee0..605f995 100644
--- a/auto_examples/multiplePythonEnv/run_backAndForthParent.ipynb
+++ b/auto_examples/multiplePythonEnv/run_backAndForthParent.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/multiplePythonEnv/run_sharedMemoryParent.ipynb b/auto_examples/multiplePythonEnv/run_sharedMemoryParent.ipynb
index 2500843..c194807 100644
--- a/auto_examples/multiplePythonEnv/run_sharedMemoryParent.ipynb
+++ b/auto_examples/multiplePythonEnv/run_sharedMemoryParent.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/multiplePythonEnv/sharedMemoryChild.ipynb b/auto_examples/multiplePythonEnv/sharedMemoryChild.ipynb
index 9ef3ae2..3dd498f 100644
--- a/auto_examples/multiplePythonEnv/sharedMemoryChild.ipynb
+++ b/auto_examples/multiplePythonEnv/sharedMemoryChild.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/registration/run_exampleMorphons.ipynb b/auto_examples/registration/run_exampleMorphons.ipynb
index ef4882b..57f70da 100644
--- a/auto_examples/registration/run_exampleMorphons.ipynb
+++ b/auto_examples/registration/run_exampleMorphons.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/auto_examples/registration/run_exampleRigid.ipynb b/auto_examples/registration/run_exampleRigid.ipynb
index a8a438a..1d6aa95 100644
--- a/auto_examples/registration/run_exampleRigid.ipynb
+++ b/auto_examples/registration/run_exampleRigid.ipynb
@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {
diff --git a/community/CommunityExample/SimpleDoseComputationAndOptOnCT.py b/community/CommunityExample/SimpleDoseComputationAndOptOnCT.py
index 3183b07..839b016 100644
--- a/community/CommunityExample/SimpleDoseComputationAndOptOnCT.py
+++ b/community/CommunityExample/SimpleDoseComputationAndOptOnCT.py
@@ -16,14 +16,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/community/Template/run_template.py b/community/Template/run_template.py
index c12fefc..6fa6c28 100644
--- a/community/Template/run_template.py
+++ b/community/Template/run_template.py
@@ -9,14 +9,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 #%%
 #imports
diff --git a/examples/DICOMExample/create3DSeqFromDicom.py b/examples/DICOMExample/create3DSeqFromDicom.py
index 36220a6..c2af800 100644
--- a/examples/DICOMExample/create3DSeqFromDicom.py
+++ b/examples/DICOMExample/create3DSeqFromDicom.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/create3DSeqFromImages.py b/examples/DICOMExample/create3DSeqFromImages.py
index 2ffc0be..8be935e 100644
--- a/examples/DICOMExample/create3DSeqFromImages.py
+++ b/examples/DICOMExample/create3DSeqFromImages.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/createDynamic3DModelFromDicomFields.py b/examples/DICOMExample/createDynamic3DModelFromDicomFields.py
index eec5888..8a53493 100644
--- a/examples/DICOMExample/createDynamic3DModelFromDicomFields.py
+++ b/examples/DICOMExample/createDynamic3DModelFromDicomFields.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/createModelWithROIsFromDicomImages.py b/examples/DICOMExample/createModelWithROIsFromDicomImages.py
index a7cd8b0..acb5474 100644
--- a/examples/DICOMExample/createModelWithROIsFromDicomImages.py
+++ b/examples/DICOMExample/createModelWithROIsFromDicomImages.py
@@ -17,14 +17,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/crop3DDataAroundROI.py b/examples/DICOMExample/crop3DDataAroundROI.py
index 70de1d4..b7c89b1 100644
--- a/examples/DICOMExample/crop3DDataAroundROI.py
+++ b/examples/DICOMExample/crop3DDataAroundROI.py
@@ -16,14 +16,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/exampleImageResampling.py b/examples/DICOMExample/exampleImageResampling.py
index 98be1ac..cfa5385 100644
--- a/examples/DICOMExample/exampleImageResampling.py
+++ b/examples/DICOMExample/exampleImageResampling.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/generateDRRAndGTVMasks.py b/examples/DICOMExample/generateDRRAndGTVMasks.py
index a539d3a..250c522 100644
--- a/examples/DICOMExample/generateDRRAndGTVMasks.py
+++ b/examples/DICOMExample/generateDRRAndGTVMasks.py
@@ -16,14 +16,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DICOMExample/run_generateRandomSamplesFromModel.py b/examples/DICOMExample/run_generateRandomSamplesFromModel.py
index f1dfb32..1f9905e 100644
--- a/examples/DICOMExample/run_generateRandomSamplesFromModel.py
+++ b/examples/DICOMExample/run_generateRandomSamplesFromModel.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DoseComputation/run_SimpleDoseCalculation.py b/examples/DoseComputation/run_SimpleDoseCalculation.py
index 1b02481..068d8d3 100644
--- a/examples/DoseComputation/run_SimpleDoseCalculation.py
+++ b/examples/DoseComputation/run_SimpleDoseCalculation.py
@@ -11,15 +11,14 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
+
 #%%
 #imports
 
diff --git a/examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.py b/examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.py
index 4fb031f..d623616 100644
--- a/examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.py
+++ b/examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.py b/examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.py
index ea8a6ed..34b8ed4 100644
--- a/examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.py
+++ b/examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.py b/examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.py
index 43fb4fb..0ed27c0 100644
--- a/examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.py
+++ b/examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DoseDeliverySimulation/PlanDeliverySimulation.py b/examples/DoseDeliverySimulation/PlanDeliverySimulation.py
index 456489a..c29cd34 100644
--- a/examples/DoseDeliverySimulation/PlanDeliverySimulation.py
+++ b/examples/DoseDeliverySimulation/PlanDeliverySimulation.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py b/examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py
index 5383d38..f624a40 100644
--- a/examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py
+++ b/examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_4DProtonOptimization.py b/examples/PlanOptimization/run_4DProtonOptimization.py
index 618bbad..dd8bb18 100644
--- a/examples/PlanOptimization/run_4DProtonOptimization.py
+++ b/examples/PlanOptimization/run_4DProtonOptimization.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_4DprotonEvaluation.py b/examples/PlanOptimization/run_4DprotonEvaluation.py
index cb26845..3a4356b 100644
--- a/examples/PlanOptimization/run_4DprotonEvaluation.py
+++ b/examples/PlanOptimization/run_4DprotonEvaluation.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_SimpleOptimizationPhoton.py b/examples/PlanOptimization/run_SimpleOptimizationPhoton.py
index f2d2c68..4327ac1 100644
--- a/examples/PlanOptimization/run_SimpleOptimizationPhoton.py
+++ b/examples/PlanOptimization/run_SimpleOptimizationPhoton.py
@@ -10,15 +10,13 @@
 
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_SimpleOptimizationProton.py b/examples/PlanOptimization/run_SimpleOptimizationProton.py
index 9200f4c..3fceeda 100644
--- a/examples/PlanOptimization/run_SimpleOptimizationProton.py
+++ b/examples/PlanOptimization/run_SimpleOptimizationProton.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_beamletFreeOpti.py b/examples/PlanOptimization/run_beamletFreeOpti.py
index 18b7ee0..5362257 100644
--- a/examples/PlanOptimization/run_beamletFreeOpti.py
+++ b/examples/PlanOptimization/run_beamletFreeOpti.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_boundConstraintsOpti.py b/examples/PlanOptimization/run_boundConstraintsOpti.py
index c5ca325..2eeadfd 100644
--- a/examples/PlanOptimization/run_boundConstraintsOpti.py
+++ b/examples/PlanOptimization/run_boundConstraintsOpti.py
@@ -12,15 +12,13 @@
 
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_evaluatePhotonRobustness.py b/examples/PlanOptimization/run_evaluatePhotonRobustness.py
index 4e0af3b..421ab65 100644
--- a/examples/PlanOptimization/run_evaluatePhotonRobustness.py
+++ b/examples/PlanOptimization/run_evaluatePhotonRobustness.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_evaluateProtonRobustness.py b/examples/PlanOptimization/run_evaluateProtonRobustness.py
index 0dc2069..7920d39 100644
--- a/examples/PlanOptimization/run_evaluateProtonRobustness.py
+++ b/examples/PlanOptimization/run_evaluateProtonRobustness.py
@@ -10,15 +10,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_robustOptimizationProtons.py b/examples/PlanOptimization/run_robustOptimizationProtons.py
index 0b051b3..8c83bdf 100644
--- a/examples/PlanOptimization/run_robustOptimizationProtons.py
+++ b/examples/PlanOptimization/run_robustOptimizationProtons.py
@@ -10,15 +10,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/PlanOptimization/run_simpleOptimization_createDicomStudy.py b/examples/PlanOptimization/run_simpleOptimization_createDicomStudy.py
index 9a47395..6e93f5f 100644
--- a/examples/PlanOptimization/run_simpleOptimization_createDicomStudy.py
+++ b/examples/PlanOptimization/run_simpleOptimization_createDicomStudy.py
@@ -11,15 +11,13 @@
 
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/Segmentation/run_Segmentation.py b/examples/Segmentation/run_Segmentation.py
index df8c987..a24d086 100644
--- a/examples/Segmentation/run_Segmentation.py
+++ b/examples/Segmentation/run_Segmentation.py
@@ -8,15 +8,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/dynamicData/exampleInterFractionChanges.py b/examples/dynamicData/exampleInterFractionChanges.py
index 8e02dd7..df22005 100644
--- a/examples/dynamicData/exampleInterFractionChanges.py
+++ b/examples/dynamicData/exampleInterFractionChanges.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#---------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/dynamicData/run_exampleApplyBaselineShiftToModel.py b/examples/dynamicData/run_exampleApplyBaselineShiftToModel.py
index 56a8008..acc23da 100644
--- a/examples/dynamicData/run_exampleApplyBaselineShiftToModel.py
+++ b/examples/dynamicData/run_exampleApplyBaselineShiftToModel.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py b/examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py
index 5c97305..0a639e2 100644
--- a/examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py
+++ b/examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/dynamicData/run_exampleDeformationFromWeightMaps.py b/examples/dynamicData/run_exampleDeformationFromWeightMaps.py
index 9353a03..6469ee3 100644
--- a/examples/dynamicData/run_exampleDeformationFromWeightMaps.py
+++ b/examples/dynamicData/run_exampleDeformationFromWeightMaps.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/dynamicData/run_exampleMidP.py b/examples/dynamicData/run_exampleMidP.py
index 39fbc30..a1f76d9 100644
--- a/examples/dynamicData/run_exampleMidP.py
+++ b/examples/dynamicData/run_exampleMidP.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/imageProcessing/run_exampleApplyBaselineShift.py b/examples/imageProcessing/run_exampleApplyBaselineShift.py
index 7cc992b..34eb315 100644
--- a/examples/imageProcessing/run_exampleApplyBaselineShift.py
+++ b/examples/imageProcessing/run_exampleApplyBaselineShift.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/imageProcessing/run_exampleDilateBinaryMask.py b/examples/imageProcessing/run_exampleDilateBinaryMask.py
index 0f9322b..f887b74 100644
--- a/examples/imageProcessing/run_exampleDilateBinaryMask.py
+++ b/examples/imageProcessing/run_exampleDilateBinaryMask.py
@@ -9,15 +9,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#---------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/imageProcessing/run_exampleTransform3D.py b/examples/imageProcessing/run_exampleTransform3D.py
index fa96c27..72d6efd 100644
--- a/examples/imageProcessing/run_exampleTransform3D.py
+++ b/examples/imageProcessing/run_exampleTransform3D.py
@@ -10,14 +10,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/multiplePythonEnv/backAndForthChild.py b/examples/multiplePythonEnv/backAndForthChild.py
index a41576c..9fd1d4d 100644
--- a/examples/multiplePythonEnv/backAndForthChild.py
+++ b/examples/multiplePythonEnv/backAndForthChild.py
@@ -8,15 +8,14 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
+
 #%%
 import numpy as np
 import sys
diff --git a/examples/multiplePythonEnv/run_backAndForthParent.py b/examples/multiplePythonEnv/run_backAndForthParent.py
index 6102441..67e2408 100644
--- a/examples/multiplePythonEnv/run_backAndForthParent.py
+++ b/examples/multiplePythonEnv/run_backAndForthParent.py
@@ -25,14 +25,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/multiplePythonEnv/run_sharedMemoryParent.py b/examples/multiplePythonEnv/run_sharedMemoryParent.py
index 85fb57b..537b7b2 100644
--- a/examples/multiplePythonEnv/run_sharedMemoryParent.py
+++ b/examples/multiplePythonEnv/run_sharedMemoryParent.py
@@ -17,14 +17,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/multiplePythonEnv/sharedMemoryChild.py b/examples/multiplePythonEnv/sharedMemoryChild.py
index c732cdb..3db883e 100644
--- a/examples/multiplePythonEnv/sharedMemoryChild.py
+++ b/examples/multiplePythonEnv/sharedMemoryChild.py
@@ -8,14 +8,12 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/registration/run_exampleMorphons.py b/examples/registration/run_exampleMorphons.py
index b8b10b3..2498647 100644
--- a/examples/registration/run_exampleMorphons.py
+++ b/examples/registration/run_exampleMorphons.py
@@ -8,15 +8,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/examples/registration/run_exampleRigid.py b/examples/registration/run_exampleRigid.py
index 906899e..b7b4aaf 100644
--- a/examples/registration/run_exampleRigid.py
+++ b/examples/registration/run_exampleRigid.py
@@ -8,15 +8,13 @@
 '''
 #%% 
 # Setting up the environment in google collab
-#--------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+#--------------------------------------------
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
     get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')
     get_ipython().system('pip install ./opentps')
     get_ipython().system('pip install scipy==1.10.1')
-    get_ipython().system('pip install cupy-cuda12x')
     import opentps
 
 #%%
diff --git a/sg_execution_times.rst b/sg_execution_times.rst
index ebaa86a..9d05a1d 100644
--- a/sg_execution_times.rst
+++ b/sg_execution_times.rst
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:33.871** total execution time for 44 files **from all galleries**:
+**02:16.013** total execution time for 44 files **from all galleries**:
 
 .. container::
 
@@ -32,55 +32,94 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
+   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleDeformableBreathigDataAugmentation.py` (``examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py``)
+     - 00:30.837
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleDeformationFromWeightMaps.py` (``examples/dynamicData/run_exampleDeformationFromWeightMaps.py``)
+     - 00:26.141
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleApplyBaselineShiftToModel.py` (``examples/dynamicData/run_exampleApplyBaselineShiftToModel.py``)
+     - 00:12.782
+     - 0.0
    * - :ref:`sphx_glr_auto_examples_DICOMExample_run_generateRandomSamplesFromModel.py` (``examples/DICOMExample/run_generateRandomSamplesFromModel.py``)
-     - 00:11.194
+     - 00:11.683
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleTransform3D.py` (``examples/imageProcessing/run_exampleTransform3D.py``)
+     - 00:10.336
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleMidP.py` (``examples/dynamicData/run_exampleMidP.py``)
+     - 00:09.531
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_Segmentation_run_Segmentation.py` (``examples/Segmentation/run_Segmentation.py``)
+     - 00:06.616
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleApplyBaselineShift.py` (``examples/imageProcessing/run_exampleApplyBaselineShift.py``)
+     - 00:03.697
      - 0.0
    * - :ref:`sphx_glr_auto_examples_DoseComputation_run_UseOfRangeShifterForProtonPlan.py` (``examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.py``)
-     - 00:02.770
+     - 00:03.043
      - 0.0
    * - :ref:`sphx_glr_auto_examples_DoseComputation_run_SimpleDoseCalculation.py` (``examples/DoseComputation/run_SimpleDoseCalculation.py``)
-     - 00:02.749
+     - 00:02.449
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_simpleOptimization_createDicomStudy.py` (``examples/PlanOptimization/run_simpleOptimization_createDicomStudy.py``)
-     - 00:02.321
+     - 00:02.031
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_4DProtonOptimization.py` (``examples/PlanOptimization/run_4DProtonOptimization.py``)
-     - 00:02.199
+     - 00:02.029
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_SimpleOptimizationProton.py` (``examples/PlanOptimization/run_SimpleOptimizationProton.py``)
-     - 00:02.082
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_boundConstraintsOpti.py` (``examples/PlanOptimization/run_boundConstraintsOpti.py``)
-     - 00:02.079
+   * - :ref:`sphx_glr_auto_examples_registration_run_exampleMorphons.py` (``examples/registration/run_exampleMorphons.py``)
+     - 00:01.944
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_robustOptimizationProtons.py` (``examples/PlanOptimization/run_robustOptimizationProtons.py``)
-     - 00:02.076
+     - 00:01.903
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_beamletFreeOpti.py` (``examples/PlanOptimization/run_beamletFreeOpti.py``)
-     - 00:01.482
+   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_boundConstraintsOpti.py` (``examples/PlanOptimization/run_boundConstraintsOpti.py``)
+     - 00:01.881
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_SimpleOptimizationProton.py` (``examples/PlanOptimization/run_SimpleOptimizationProton.py``)
+     - 00:01.859
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_4DprotonEvaluation.py` (``examples/PlanOptimization/run_4DprotonEvaluation.py``)
-     - 00:01.425
+     - 00:01.217
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_beamletFreeOpti.py` (``examples/PlanOptimization/run_beamletFreeOpti.py``)
+     - 00:01.183
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_evaluateProtonRobustness.py` (``examples/PlanOptimization/run_evaluateProtonRobustness.py``)
-     - 00:01.318
+     - 00:01.057
      - 0.0
    * - :ref:`sphx_glr_auto_examples_DoseComputation_run_protonPlanCreationAndDoseCalculation.py` (``examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.py``)
-     - 00:00.808
+     - 00:00.821
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_registration_run_exampleRigid.py` (``examples/registration/run_exampleRigid.py``)
+     - 00:00.658
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_evaluatePhotonRobustness.py` (``examples/PlanOptimization/run_evaluatePhotonRobustness.py``)
-     - 00:00.543
+     - 00:00.539
      - 0.0
    * - :ref:`sphx_glr_auto_examples_PlanOptimization_run_SimpleOptimizationPhoton.py` (``examples/PlanOptimization/run_SimpleOptimizationPhoton.py``)
-     - 00:00.534
+     - 00:00.536
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_run_backAndForthParent.py` (``examples/multiplePythonEnv/run_backAndForthParent.py``)
+     - 00:00.464
      - 0.0
    * - :ref:`sphx_glr_auto_examples_DoseComputation_run_photonPlanCreationAndDoseCalculation.py` (``examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.py``)
-     - 00:00.288
+     - 00:00.292
      - 0.0
-   * - :ref:`sphx_glr_auto_community_CommunityExample_SimpleDoseComputationAndOptOnCT.py` (``community/CommunityExample/SimpleDoseComputationAndOptOnCT.py``)
-     - 00:00.000
+   * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_run_sharedMemoryParent.py` (``examples/multiplePythonEnv/run_sharedMemoryParent.py``)
+     - 00:00.247
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleDilateBinaryMask.py` (``examples/imageProcessing/run_exampleDilateBinaryMask.py``)
+     - 00:00.214
      - 0.0
    * - :ref:`sphx_glr_auto_community_Template_run_template.py` (``community/Template/run_template.py``)
+     - 00:00.019
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_DoseDeliverySimulation_run_PBSDeliveryTimings.py` (``examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py``)
+     - 00:00.005
+     - 0.0
+   * - :ref:`sphx_glr_auto_community_CommunityExample_SimpleDoseComputationAndOptOnCT.py` (``community/CommunityExample/SimpleDoseComputationAndOptOnCT.py``)
      - 00:00.000
      - 0.0
    * - :ref:`sphx_glr_auto_examples_DICOMExample_create3DSeqFromDicom.py` (``examples/DICOMExample/create3DSeqFromDicom.py``)
@@ -107,27 +146,9 @@ Computation times
    * - :ref:`sphx_glr_auto_examples_DoseDeliverySimulation_PlanDeliverySimulation.py` (``examples/DoseDeliverySimulation/PlanDeliverySimulation.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_DoseDeliverySimulation_run_PBSDeliveryTimings.py` (``examples/DoseDeliverySimulation/run_PBSDeliveryTimings.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_Segmentation_run_Segmentation.py` (``examples/Segmentation/run_Segmentation.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_auto_examples_dynamicData_exampleInterFractionChanges.py` (``examples/dynamicData/exampleInterFractionChanges.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleApplyBaselineShiftToModel.py` (``examples/dynamicData/run_exampleApplyBaselineShiftToModel.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleDeformableBreathigDataAugmentation.py` (``examples/dynamicData/run_exampleDeformableBreathigDataAugmentation.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleDeformationFromWeightMaps.py` (``examples/dynamicData/run_exampleDeformationFromWeightMaps.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_dynamicData_run_exampleMidP.py` (``examples/dynamicData/run_exampleMidP.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_auto_examples_imageProcessing_cupyVSsitkTransforms.py` (``examples/imageProcessing/cupyVSsitkTransforms.py``)
      - 00:00.000
      - 0.0
@@ -137,30 +158,9 @@ Computation times
    * - :ref:`sphx_glr_auto_examples_imageProcessing_exampleTransform3DCupy.py` (``examples/imageProcessing/exampleTransform3DCupy.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleApplyBaselineShift.py` (``examples/imageProcessing/run_exampleApplyBaselineShift.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleDilateBinaryMask.py` (``examples/imageProcessing/run_exampleDilateBinaryMask.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_imageProcessing_run_exampleTransform3D.py` (``examples/imageProcessing/run_exampleTransform3D.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_backAndForthChild.py` (``examples/multiplePythonEnv/backAndForthChild.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_run_backAndForthParent.py` (``examples/multiplePythonEnv/run_backAndForthParent.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_run_sharedMemoryParent.py` (``examples/multiplePythonEnv/run_sharedMemoryParent.py``)
-     - 00:00.000
-     - 0.0
    * - :ref:`sphx_glr_auto_examples_multiplePythonEnv_sharedMemoryChild.py` (``examples/multiplePythonEnv/sharedMemoryChild.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_auto_examples_registration_run_exampleMorphons.py` (``examples/registration/run_exampleMorphons.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_auto_examples_registration_run_exampleRigid.py` (``examples/registration/run_exampleRigid.py``)
-     - 00:00.000
-     - 0.0

From afd6f1961c3fd23243285aa68dda5b0fc3c3febb Mon Sep 17 00:00:00 2001
From: Romane Carryn <romane.carryn@student.uclouvain.be>
Date: Tue, 26 Aug 2025 15:43:57 +0200
Subject: [PATCH 2/2] Gpu setup

---
 examples/imageProcessing/cupyVSsitkTransforms.py   | 2 +-
 examples/imageProcessing/exampleDRRwithTigre.py    | 2 +-
 examples/imageProcessing/exampleTransform3DCupy.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/examples/imageProcessing/cupyVSsitkTransforms.py b/examples/imageProcessing/cupyVSsitkTransforms.py
index 304a3bd..c2e44a5 100644
--- a/examples/imageProcessing/cupyVSsitkTransforms.py
+++ b/examples/imageProcessing/cupyVSsitkTransforms.py
@@ -10,7 +10,7 @@
 #%% 
 # Setting up the environment in google collab
 #---------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+# You will first need to change the execution parameters in your Colab environment (bottom left) from CPU to GPU so that you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
diff --git a/examples/imageProcessing/exampleDRRwithTigre.py b/examples/imageProcessing/exampleDRRwithTigre.py
index 23b8f77..5c1c881 100644
--- a/examples/imageProcessing/exampleDRRwithTigre.py
+++ b/examples/imageProcessing/exampleDRRwithTigre.py
@@ -10,7 +10,7 @@
 #%% 
 # setting up the environment in google colab
 #-------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+# You will first need to change the execution parameters in your Colab environment (bottom left) from CPU to GPU so that you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython
diff --git a/examples/imageProcessing/exampleTransform3DCupy.py b/examples/imageProcessing/exampleTransform3DCupy.py
index ac1cc23..fb2a733 100644
--- a/examples/imageProcessing/exampleTransform3DCupy.py
+++ b/examples/imageProcessing/exampleTransform3DCupy.py
@@ -10,7 +10,7 @@
 #%% 
 # Setting up the environment in google collab
 #--------------------------------------------
-# First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.
+# You will first need to change the execution parameters in your Colab environment (bottom left) from CPU to GPU so that you can run the example.
 import sys
 if "google.colab" in sys.modules:
     from IPython import get_ipython