These are chat archives for fiji/fiji

3rd
Dec 2015
Curtis Rueden
@ctrueden
Dec 03 2015 00:07
@omsai Are you sure you need to use Cell Counter, instead of ImageJ's built-in multi-point tool? It supports multiple marker types now, doesn't it?
Curtis Rueden
@ctrueden
Dec 03 2015 01:48
@omsai Try upgrading to the latest daily build, and double clicking the multi-point tool. It supports up to 100 counter types now.
Curtis Rueden
@ctrueden
Dec 03 2015 02:49
@omsai I really hope the updated multi-point tool works for your user, because updating the Cell Counter UI is a PITA. I spent ~30 minutes messing with it, but GridBagLayout is horrible. If we really have to fix it, I recommend redoing the UI with a different layout manager.
Pariksheet Nanda
@omsai
Dec 03 2015 03:11
Cheers, @ctrueden. I imagine the user would be happier with the multi-point tool, because having Cell Counter open did not allow switching to non-point ROIs (e.g. lines). To be honest I'm not all that familiar with Cell Counter (today was the first I heard of it). I'm playing with it now. Will try and stop by the user's lab tomorrow to understand their use case and workflow better. Thanks for the tip about the layout manager! Looks like BorderLayout might be more appropriate which I can look into if the user wants to continue with Cell Counter.
Curtis Rueden
@ctrueden
Dec 03 2015 15:33
@omsai Cool, let me know how it goes. For layout managers, I prefer MiGLayout. It generally works as you expect (as much as any layout manager does/can, anyway).
Pariksheet Nanda
@omsai
Dec 03 2015 16:43
@ctrueden nice! I was actually leaning towards MiGLayout from it's efficient API in the documentation, and see we have 3.7.4 bundled in FIJI. I'm going to meet the user in another 3 hours.
Nico Stuurman
@nicost
Dec 03 2015 19:56
@ctrueden Hope you can help! I am trying to build a bridge between Micro-Manager 2.0 and ClearVolume such that a ClearVolume renderer can be opened on a MM dataset. Making nice progress (http://valelab.ucsf.edu/~nstuurman/CV-MM-Desktop.png), but run into the strange problem that the code works fine when it is run under NetBeans, but not as a stand-alone. It seems to boil down to a class-loader issue and the exception occurs after bridj tries to register it’s own Callback type and after registering com.nativelibs4java.opencl.library.IOpenCLLibrary$clSetEventCallback_arg1_callback. Strangely, things are fine with the ClearVolume plugin under Fiji (which goes through the same sequence of calls). Is there a difference between class loading in Fiji and vanilla ImageJ1? Lots more details in the ClearVolume room here on gitter.
Ulrik Günther
@skalarproduktraum
Dec 03 2015 20:07
@ctrueden: with MM2 bolted on top of fiji, it actually works … some classloader issue?
Curtis Rueden
@ctrueden
Dec 03 2015 20:09
@nicost @skalarproduktraum There is a huge difference between ImageJ2 and ImageJ1 when it comes to class loading, yes.
Specifically: all ij.* classes are runtime patched in IJ2.
And that places serious restrictions on when/where/how you can reference them from your own stuff.
I'd need to see the exception to comment further.
Ulrik Günther
@skalarproduktraum
Dec 03 2015 20:11
would you mind coming over to the clearvolume room, we have already discussed it during the day and all the details are there :)
Curtis Rueden
@ctrueden
Dec 03 2015 20:11
@skalarproduktraum Yep, already joined just now.