Page history Edit this page How do I edit this website?
Original MediaWiki page

BigDataViewer Playground

The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the how to help guide!

As announced in the forum here and here, bigdataviewer playground aims at a better integration of BigDataViewer into Fiji by using the SciJava Framework.

Installation

Enable the bigdataviewer playground update site (https://biop.epfl.ch/Fiji-Bdv-Playground/).

What bigdataviewer-playground brings

  • Modularity for bigdataviewer! Bigdataviewer playground creates a way to access existing BDV instances when scripting or writing java code. Being able to combine scripts or code for display and processing is doable easily via scripting (Groovy, ImageJ macro, etc.)
  • Provide a set of macro recordable commands for bigdataviewer. Makes it possible to script basic actions on BigDataViewer with the ImageJ macro recorder.
  • Direct and lazy opening of multiresolution files, supported by bioformats. It is possible to open and visualize large files in bigdataviewer without resaving files. This is particularly convenient for large 2D images (à la QuPath).

How to open images in bigdataviewer-playground ?

Several options are available. Note that there’s a difference between opening and visualising an image. Images opened in bigdataviewer-playground are not visualized directly, but are sorted into a hierarchical tree displayed into an extra window. From this tree, images can be displayed using the right click contextual menu (see next section).

Open any bioformats supported files (tiff, vsi, czi, lif…)

Files (which can even be multi series) can be opened via the command [Plugins>BigDataViewer>Playground>BDVDataset>Open [BioFormats Bdv Bridge (Basic)]. Many files can be opened at the same time. To avoid going through all the hierarchy of Fiji’s menu, you can directly type bridge into Fiji’s search bar and click run.

Open a Bigdataviewer xml Dataset

A BigDataViewer dataset is an xml file which links to raw data and which contains additional metadata (positions, voxel size, channel descriptions etc.). These datasets can be generated by other BigDataViewer plugins such as BigStitcher, and bigdataviewer playground also provides a way to generate an xml bdv dataset.

Such datasets can be opened in bigdataviewer playground either via the command [Plugins>BigDataViewer>Playground>BDVDataset>Open XML BDV Datasets] (type open xml bdv into the search bar) or can be directly dragged and dropped into the bigdataviewer playground window (this window can be made visible with [Plugins>BigDataViewer>Playground>Show Bdv Playground Window]).

Import current ImageJ image

Similar to the command [Plugins>BigDataViewer>Open Current Image], it is possible to import the current ImageJ image as an image in the bigdataviewer playground hierarchical tree via the command [Plugins>BigDataViewer>Sources>Import>Get Sources From ImagePlus]

How to visualize images in bigdataviewer-playground ?

After one or several images have been opened in bigdataviewer playground, a window shows up which sorts the accessible images into a tree view:

image

The root node, always named Sources contains in brackets the number of accessible images contained in bigdataviewer-playground. This root node can be double clicked to be expanded and reveal its hierarchy:

image