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

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@pmascalchi pmascalchi released this 12 Aug 13:48
· 18 commits to master since this release
Aivia_15.0_Python_Recipes_v2
b17d505

Python virtual Environment For Aivia

(Scroll down to find the download link of the zip)

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
Assets 3
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