Python recipes for Aivia (15.0.0, v2, Aug 12, 2025)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.12 - comes with Aivia 15.0

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" or "Recipes No Automated Tests" folders, and drag-and-drop it in Aivia to use it...

---

Updates

Due to the migration of python 3.9 to 3.12, some recipes might not work as expected.
Please let us know if anything is unusual, raising an issue within the Github website.

Some automated tests have now been implemented for the main recipes and can be found here:
https://github.com/AiviaCommunity/PythonForAivia/tree/master/PythonEnvForAivia/Tests
These are not shipped within the zip below...

New recipes:

• PythonEnvForAivia/Recipes_NoAutomatedTests/TransformImages/GenerateBatchResultSnapshots.py
• PythonEnvForAivia/Recipes_NoAutomatedTests/ProcessMeasurementTables/RenameExcelSheetTitlesAndColumns.py

Updated recipes (open script in text editor and check "changelog" at the bottom of the file):

• PythonEnvForAivia/Recipes_NoAutomatedTests/ProcessMeasurementTables/ProcessMultipleExcelTables_FromAivia.py
• PythonEnvForAivia/Recipes_NoAutomatedTests/ProcessImages/SkeletonizeWithNodesDetection_3D.py
• PythonEnvForAivia/Recipes_NoAutomatedTests/Others/Read_WorkFlowFile.py
• PythonEnvForAivia/Recipes_NoAutomatedTests/ConvertImagesForAivia/MultiWellPlateConverter_OperaPhenix.py
• PythonEnvForAivia/Recipes/ConvertImagesForAivia/AiviaExperimentCreator.py
• PythonEnvForAivia/Recipes/CollectImageMetrics/ImageComparisonMetrics.py

Other updates:

• Better compatibility with Aivia 15.0 / Python 3.12
• Some recipes were moved from one folder to another.

Removed recipes (old or not supported):

• PythonEnvForAivia/Recipes_NoAutomatedTests/ProcessMeasurementTables/CellAnalysis_RelationMeasurements.py
• PythonEnvForAivia/Recipes_NoAutomatedTests/Others/InspectLineIntersections.py

Python recipes for Aivia (15.0.0, May 14, 2025)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.12 - comes with Aivia 15.0

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates

Due to the migration of python 3.9 to 3.12, some recipes might not work as expected.
Please let us know if anything is unusual, raising an issue within the Github website.
Some recipes were removed from the zip below but are still available on Github here:
https://github.com/AiviaCommunity/PythonForAivia/tree/master/Recipes_NoAutomatedTests

Some automated tests have now been implemented for the main recipes and can be found here:
https://github.com/AiviaCommunity/PythonForAivia/tree/master/PythonEnvForAivia/Tests
These are not shipped within the zip below...

Python recipes for Aivia (14.1.0, Nov 12, 2024)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.9 - comes with Aivia

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates

Updated recipes:

• MultiWellPlateConverter_OperaPhenix.py
• Read_WorkFlowFile.py
• ExtractDeepLearningInfoInLogFile.py
• ProcessMultipleExcelTables_FromAivia.py

New recipes:

• Converter_Evos.py
• Arithmetics_SingleChannel.py
• Boundaries_From_3D_Labeled_Mask_1_00.py
• Dilate_2D_Labeled_Mask_1_00.py
• Objects_From_3D_Labeled_Mask_1_00.py
• Objects_From_3D_Seeds_and_Mask_1_00.py
• ReplicateFirstTimeFrame_1_00.py
• SkeletonizeWithNodesDetection_3D_1_00.py
• Watershed_1_00.py

Python recipes for Aivia (12.1.0, Sep 15, 2023)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.9 - comes with Aivia

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Update: FirstTimeSetup.py
  Shows an error message if chosen folder is not writable.
  Also adds the ability to compare requirements to existing for an update only if needed

Python recipes for Aivia (12.1.0, Sep 12, 2023)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.9 - comes with Aivia

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Updated scripts:
  ProcessMultipleExcelTables_FromAivia.py (Secondary relationship sets can be named differently if the main object is "Cells" / Handles NaN in summary tabs)

Python recipes for Aivia (12.1.0, Aug 11, 2023)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.9 - comes with Aivia

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Updated scripts:
  ProcessMultipleExcelTables_FromAivia.py (ability to provide relationship stats from Cell Analysis)

Python recipes for Aivia (12.1.0, July 03, 2023)

Python virtual Environment For Aivia

General Information

The FirstTimeSetup.py script will ensure a virtual environment is created to run the python recipes for Aivia with the appropriate packages.
No further install should be needed. Hence, the script is run once only.

The recipes are then containing some code to:

• Check the existence of the virtual environment,
• Automatically activate the virtual environment to be able to run with the appropriate packages,
• Fallback on main Aivia environment which we do not recommend to modify (i.e. add new packages).

Requirements

• Python 3.9 - comes with Aivia

• Accept the risks that come from running Python Scripts you download from the internet. These scripts are provided to you to use at your own risk.

Installation

1. Download the latest PythonEnvForAivia zip available in the releases:
   https://github.com/AiviaCommunity/PythonForAivia/releases

2. Unzip the downloaded folder PythonEnvForAivia in a location where there are no admin access restrictions.
   The tree structure of the folder is as follow

  PythonEnvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───[category subfolders]
          └───... .py

Execution

1. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

2. Load any 2D image in Aivia

3. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

4. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Updated scripts:
  ProcessMultipleExcelTables_FromAivia.py
  SuperpixelPainter.py

• New scripts:
  AiviaExperimentCreator.py
  MultiWellPlateConverter_OperaPhenix.py
  Rotate2D.py
  Rotate3D_90deg.py
  StackReg_ImageAlignment.py
  DrawArrayOfShapes_2D.py
  DrawShapes_2D.py
  DrawShollCircles_2D_AiviaGui.py
  Read_WorkFlowFile.py

Python recipes for Aivia (11.0.1, Nov 28, 2022)

Python recipes validated with Aivia 11.0.1 and the new Virtual Environment (ensuring all recipes work fine).
Download the zip and follow the instructions.

Installation

1. Unzip the downloaded folder PythonVenvForAivia in a location where there are no admin access restrictions. The tree structure of the folder is as follow

  PythonVenvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───... .py
  └───Utilities
      └───... .py

2. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

3. Load any 2D image in Aivia

4. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

5. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Security fix with upgrades: Pillow==9.3.0, numpy==1.22.0
• Corrected script in Recipes > SuperpixelPainter.py
• Corrected script in Utilities > ProcessMultipleExcelTables_FromAivia.py

Python recipes for Aivia (11.0.1, Nov 2, 2022)

Python recipes validated with Aivia 11.0.1 and the new Virtual Environment (ensuring all recipes work fine).
Download the zip and follow the instructions.

Installation

1. Unzip the downloaded folder PythonVenvForAivia in a location where there are no admin access restrictions. The tree structure of the folder is as follow

  PythonVenvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───... .py
  └───Utilities
      └───... .py

2. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

3. Load any 2D image in Aivia

4. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

5. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• New script in Utilities > Heatmap_FromExcelTable.py
• Corrected script in Utilities > ProcessMultipleExcelTables_FromAivia.py

Python recipes for Aivia (11.0.1, Sept 30, 2022)

Python recipes validated with Aivia 11.0.1 and the new Virtual Environment (ensuring all recipes work fine).
Download the zip and follow the instructions.

Installation

1. Unzip the downloaded folder PythonVenvForAivia in a location where there are no admin access restrictions. The tree structure of the folder is as follow

  PythonVenvForAivia
  ├───FirstTimeSetup.py
  ├───requirements.txt
  ├───README.md
  └───Recipes
      └───... .py
  └───Utilities
      └───... .py

2. Load FirstTimeSetup.py in Aivia by "File>Open" or drag-and-drop

3. Load any 2D image in Aivia

4. Click on "Start" button and wait for "Process Completed" message at the bottom of the recipe console

   • Please make sure that you have the Internet connection and wait if bandwidth is slow.

5. Choose a recipe in the "Recipes" and "Utilities" folders, and drag-and-drop it in Aivia to use it...

---

Updates:

• Corrected scripts in Utilities > ProcessMultipleExcelTables_FromAivia.py, ExtractDeepLearningInfoInLogFile.py, ReadTiffTags.py