FIJI Commands for BigDataViewer

Hi everybody,

Following this thread :

I’ve made a repository which aims at using BigDataViewer within Fiji by using SciJava commands:

The goal is to be able to manipulate BigDataViewer windows , display options as well as contained dataset, within FIJI. The repo contains plugins copied from the repo bigdataviewer_fiji, but it uses BdvHandle as a scijava Parameter and BdvFunctions helpers from bigdataviewer-vistools internally.

It’s currently very early and not functional in many ways (it cannot open an ImagePlus, see issue), but maybe there’s enough to start a discussion. Browsing a BigDataServer works, and for instance this BigDataServerPlugInSciJava command allows to append a dataset onto an already existing BigDataViewer frame.

What are your thoughts on this ? (@ctrueden, @tpietzsch, @imagejan )

As stated before, it’s partly functional, but maybe it’s worth discussing the general backbone already. For instance, how should such a set of commands match with DatasetService ? Or ImageDisplayService ? Should we bother with these service already ?

Hope that this could be useful.

Nicolas

6 Likes

Cool, @NicoKiaru. I’m sorry I haven’t time to dig in as much as I would like.

The original plan for ImageJ2 was for displays to be extensible, so that e.g. when opening an image that would be best displayed with BDV, the BDV would be automatically used. And when multiple equivalently optimal displays exist, the user would be prompted, analogously to how your phone asks which app to use to do a thing, and then remembers your choice, either locally or globally.

That plan did not come to fruition yet. But it’s worth mentioning so that we don’t necessarily proliferate too much code unnecessarily here. I don’t use BDV much personally, so I don’t feel like the best person to comment on the API. If it’s useful for your use cases, then it’s probably useful for others as well.

2 Likes