I’m trying to do the elastic alignment on my images through the TrakEM2 but it doesn’t work. Here is what I did:
.1 The images were rigid aligned and cropped, and that part works fine. .2 The aligned images were loaded into TrakEM2. Each layer contains 4 patches from different channels. Then I used 'task = AlignLayersTask.alignLayersTask(layerset.getLayers().get(0))' to do the elastic alignment. Actually, to figure out whether the error is because something goes wrong in my script, I also tried to load the images to TrakEM2, right click on the canvas, and use the "align" tool manually, it gives me the same log message and doesn't work either. .3 A GUI window comes out and asks me for proper parameters. I selected "elastic alignment" and parameters which had already been tested by "Test block ..." plugin in Fiji. The elastic alignment runs. and in the log window, it reports no candidates passed the filter. The output images look same as the inputs.
I also tried to do the elastic alignment without TrakEM2 (using Fiji-plugin-registration-elastic alignment) and it works fine. Hundreds of blocks are detected and pass the filter. So I totally have no idea why TrakEM2 can’t do the alignment. Does anybody know why? Or where can I find documentation explaining how to use the “align” tool in TrakEM2 in details? I read the User Manual of TrakEM2 (https://www.ini.uzh.ch/~acardona/trakem2_manual.html#registration) and it seems like it’s just as easy as “click it and select parameters”…