BigDataViewer Line ROIs for 3D CLEM




@fjug, @maarzt, @StephanPreibisch

I need a UI solution where the user can draw (linked) points and line ROIs into (two) 3-D data sets. The application will be to feed those coordinates into elastix to compute a 3D registration (I just found out that they also support point list based registrations). I guess the best would be to do this in the BigDataViewer because one can draw lines in arbitrary 3D orientation?!

Could someone provide me with some example java code of how to draw points and line ROIs into the BDV and read the coordinates?


Did you have a look at BigWarp? I guess @bogovicj and @hanslovsky can advise here.


wow…good I asked, looks like I don’t even have to write any code on my own…


Thanks @imagejan for catching this and giving the pointer.

@Christian_Tischer let me know if you have questions or issues.
If the main thing you need is point correspondences between volumes then Bigwarp may just be enough, but for visualizing annotations, its pretty bare-bones.



Thanks @imagejan

@Christian_Tischer besides the link to bigwarp, the BigCAT annotation controller could be useful for you.



+1 for BigWarp, we use it pretty extensively for our CLEM work, e.g. here:



Hi All,

@imagejan, @bogovicj

I tried using BigWarp, but when pressing the SpaceBar to enter the LandMark mode nothing happens (no message is displayed), and when I left-click on the image there is no Spot added either.
Pressing T does work in sense that it tries to transform => Somehow it does not seem to recognise me pressing the space bar… Did anyone experience similar issues?

…Adding to this: pressing SpaceBar in normal Fiji toggles on the scrolling tool. This works for me.



Just to be sure: You need to press and hold space (not just press).

If thats still broken… What os/java version?



Somehow does not work for me…
In the help it says that already pressing space alone should show a quick message that I am entering Landmark mode, should it? I also did press space and the left mouse button to add a point; nothing happened.

I am using:

MacBook Pro MacOs High Sierra
IJ 2.0.0-rc-65/1.51w
Java 1.8.0_66

Just checked: on a Windows10 PC it does work for me!
Maybe a Mac issue?


I just tried it on a similar machine and it seemed to work fine:

MacBook Pro Macos 10.13.2 (High sierra)
Java 1.8.0_66
Fresh Fiji (downloaded just now).

That makes debugging this extra tricky, unfortunately :frowning:
Anything else on your end you can think of? Do you have new/custom versions of any code in your Fiji install (maybe something that bigwarp depends on)?




Could not figure it out on my Mac, using others now…

We had two more questions:

  1. Is it possible to draw lines as landmarks? We have signal that is related to elongated structures and it is very tedious to paint points along the whole structure!

  2. Can one see the two images (transformed and fixed) as a color overlay as well? In order to judge how well the alignment currently is! I guess technically it should be possible to just open another BDV window showing them as an “overlay view”?


This is disappointing, but I can’t debug this effectively unless I can reproduce, sorry.

  1. No. The transformation model that Bigwarp uses deals with points only (afaik). You should not have to click every point on your structure though - if the model “interpolates” the transform well you should only need a few. Can elastix deal with lines?
  1. Yes. See the T and F shortcuts on the help page (F1) or here. The BigDataViewer page has a bit more detail on visualization (overlays).