BDV playground / toolbox / actions

In this repository, we collect useful additions for the BigDataViewer in Fiji. These functionalities are accessible by enabling the PTBIOP Fiji update site, accessible via Help>Update>Manage Update Sites.

User documentation is located can be found at https://imagej.github.io/plugins/bdv/playground/bdv-playground

Coding guides

We tried to follow these general guidelines:

• Specific (atomic) functionality lives in a class implementing Runnable
  • More mandatory parameters for the functionality are handed over as additional constructor parameters.
  • Optional parameters are set with setter methods.
  • The run() method executes the concrete action.
  • Results are retrieved using getter methods. The getter methods may internally run the run() method if necessary.

Pseudo-code example:

  Class Action {
    Action(BdvHandle)
    setParameter(Parameter)
    run()
    getResult()
  }

• Furthermore, Demo code in the test sources directory should demonstrate the individual functionality, and how to be called programmatically.

• Higher level functions, which may execute several actions sequentially, are implemented as SciJava Commands. This enables additional user access.

List of actions

• Read a source from disc
• Add a source to a BDV
• Log the current mouse position
• Log the current viewer transform
• Change the current viewer transform
• Take a screenshot

List of SciJava Commands

Wishlist of actions

Here we document actions we would like to have. If you know similar functionality in other repositories, feel free to contribute it here or send us a link where we can adopt code! Thanks :-)

• Log intensity in current source at mouse position