Is there a way to use Big Warp on images that have been exported as the BigDataViewer hdf5/xml file format? I can open the files well in BigDataViewer, but cannot perform Big Warp on the images (it looks for open images and doesn’t find any since they aren’t ImageJ proper windows).
The reason I am trying to do this is that I am encountering the following error when trying to warp tif files that are opened through imageJ proper:
(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_66 [64-bit]; Mac OS X 10.13.6; 68210MB of 88889MB (76%) java.lang.ArrayIndexOutOfBoundsException: 3 at bigwarp.BigWarpInit.namesFromImagePluses(BigWarpInit.java:513) at bigwarp.BigWarpInit.createBigWarpDataFromImages(BigWarpInit.java:406) at bdv.ij.BigWarpImagePlusPlugIn.run(BigWarpImagePlusPlugIn.java:82) at ij.IJ.runUserPlugIn(IJ.java:229) at ij.IJ.runPlugIn(IJ.java:193) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:745)
When I try this with just one of the channels from each image I don’t have any trouble with Big Warp so this seems to be a size issue. Thanks for any advice!