diff --git a/src/main/java/mpicbg/stitching/ImageCollectionElement.java b/src/main/java/mpicbg/stitching/ImageCollectionElement.java index 0b47ce7..9f4a5f2 100644 --- a/src/main/java/mpicbg/stitching/ImageCollectionElement.java +++ b/src/main/java/mpicbg/stitching/ImageCollectionElement.java @@ -109,6 +109,7 @@ public ImagePlus open( final boolean virtual ) ImporterOptions options = new ImporterOptions(); options.setId( file.getAbsolutePath() ); + options.setSeriesOn(getIndex(), true); options.setSplitChannels( false ); options.setSplitTimepoints( false ); options.setSplitFocalPlanes( false ); diff --git a/src/main/java/plugin/Stitching_Grid.java b/src/main/java/plugin/Stitching_Grid.java index 3515279..d1640d9 100644 --- a/src/main/java/plugin/Stitching_Grid.java +++ b/src/main/java/plugin/Stitching_Grid.java @@ -892,7 +892,7 @@ protected ArrayList< ImageCollectionElement > getLayoutFromMultiSeriesFile( fina // CTR HACK: In the case of a single series, we treat each time point // as a separate series for the purpose of stitching tiles. timeHack = numSeries == 1; - + for ( int series = 0; series < numSeries; ++series ) { Log.debug( "fetching data for series: " + series ); @@ -956,14 +956,14 @@ protected ArrayList< ImageCollectionElement > getLayoutFromMultiSeriesFile( fina if ( dim == 2 ) { - element = new ImageCollectionElement( new File( multiSeriesFile ), elements.size() ); + element = new ImageCollectionElement( new File( multiSeriesFile ), series ); element.setModel( new TranslationModel2D() ); element.setOffset( new float[]{ (float)locationX, (float)locationY } ); element.setDimensionality( 2 ); } else { - element = new ImageCollectionElement( new File( multiSeriesFile ), elements.size() ); + element = new ImageCollectionElement( new File( multiSeriesFile ), series ); element.setModel( new TranslationModel3D() ); element.setOffset( new float[]{ (float)locationX, (float)locationY, (float)locationZ } ); element.setDimensionality( 3 );