@@ -0,0 +1,1922 @@
+package forBiic;%0A%0Aimport bdv.util.Bdv;%0Aimport bdv.util.BdvFunctions;%0Aimport ij.IJ;%0Aimport ij.ImagePlus;%0Aimport net.imglib2.FinalInterval;%0Aimport net.imglib2.img.Img;%0Aimport net.imglib2.img.display.imagej.ImageJFunctions;%0Aimport net.imglib2.type.numeric.real.FloatType;%0Aimport net.imglib2.util.Intervals;%0Aimport net.imglib2.view.IntervalView;%0Aimport net.imglib2.view.Views;%0A%0A/**%0A *%0A * Visualize current nicest brain and vnc templates for biic conference.%0A * %0A * Manually oriented the brain and vnc relative to one another, saved the settings here:%0A *%09/groups/saalfeld/public/fly-template/joint-brain-vnc-2.xml %0A *%0A * TODO - incorporate that transformation into this script%0A */%0Apublic class VisWithVNC%0A%7B%0A%0A%09public static void main( String%5B%5D args )%0A%09%7B%0A%09%09String brainTemplate = %22/groups/saalfeld/public/fly-template/template.tif%22;%0A%09%09String vncTemplate = %22/nrs/saalfeld/john/projects/flyChemStainAtlas/VNC_take6/all-flip-r1p5-affineCC/hiResRenders/VNC-template.tif%22;%0A%09%09%0A%09%09ImagePlus brainIp = IJ.openImage( brainTemplate );%0A%09%09ImagePlus vncIp = IJ.openImage( vncTemplate );%0A%09%09%0A%09%09Img%3C FloatType %3E brainimg = ImageJFunctions.convertFloat( brainIp );%0A%09%09Img%3C FloatType %3E vncimg = ImageJFunctions.convertFloat( vncIp );%0A%09%09%0A%09%09FinalInterval unionInterval = Intervals.union( brainimg, vncimg );%0A%0A//%09%09IntervalView%3C FloatType %3E both = Views.permute( %0A//%09%09%09%09Views.addDimension( %0A//%09%09%09%09%09%09Views.stack( brainimg, vncimg ), 0, 1), %0A//%09%09%09%094, 3);%0A%09%09%0A%09%09IntervalView%3C FloatType %3E brainpad = Views.interval( Views.extendZero( brainimg ), unionInterval );%0A%09%09IntervalView%3C FloatType %3E vncpad = Views.interval( Views.extendZero( vncimg ), unionInterval );%0A%0A%09%09IntervalView%3C FloatType %3E bothpad = Views.permute( %0A%09%09%09%09Views.addDimension( %0A%09%09%09%09%09%09Views.stack( brainpad, vncpad ), 0, 1), %0A%09%09%09%094, 3);%0A%09%09%0A%09%09Bdv bdv = BdvFunctions.show( bothpad, %22Brain and VNC%22 );%0A%09%09bdv.getBdvHandle().getSetupAssignments().getMinMaxGroups().get( 0 ).setRange( 0, 1000 );%0A%09%7D%0A%0A%7D%0A

Add script to create visualization for biic2017