How to get StarDist working with Vision4D
The StarDist python package is required to get it to work with Vision4D and must be added to an existing python 3.x enviroment. We tested & strongly recommend the Anaconda 3.x python package for the scope of this application.
Once the StarDist package has been correctly set up, Vision4D must also be configured accordingly by changing the scripting preferences.
Setting up Vision4D preferences
With Vision4D open, go to Extras> Preferences.
In the preferences window, select the Scripting tab on the left and select "Anaconda environment".
You will then need to browse your computer for the Anaconda installation folder and select the Stardist environment previously created.
By default, the new enviroments are stored under the \envs folder located in the Anaconda installation folder e.g. C:\Anaconda3\envs\stardist
Having selected the correct environemtn folder we can then run “Install arivis package” and "Test Environment" for compatibility:
arivis also provides a free python script to run the StarDist algorithm inside of V4D.
The script allows the user to select the active channel, as well as the time points and Z planes (full-range or sub-selection thereof), from which to segment objects. A new channel will be created to store the labeled objects found by StarDist.