Modify to use the rendered view as opposed to the original image

Hi,

Thank you so much for this extension!

I'm looking for some pointers to figure out how to change the bufferedImage in line 149 below, so this is compatible with multi-channel images that aren't RGB to begin with or single channel tif (like ome.tif, etc):

qupath-extension-sam/src/main/java/org/elephant/sam/SAMExtension.java

Line 149 in 66e4c4e

    
           bufferedImage = qupath.getImageData().getServer().readRegion(downsample, x1, y1, x2 - x1, y2 - y1);

Is there a way to use the RenderedImageServer in QuPath directly? I tried:
bufferedImage = qupath.getViewer().getImageDisplay().getImageData().getServer().readRegion(downsample, x1, y1, x2 - x1, y2 - y1);
but that did not seem to work.

Best,
Ady

Hi @adyprat , thank you for your question.

It can be done as shown here. It's already implemented in v0.2.0.

qupath-extension-sam/src/main/java/org/elephant/sam/SAMExtension.java

Lines 151 to 155 in 221fafc

    
           final ImageServer<BufferedImage> renderedServer = new RenderedImageServer 
        
           		.Builder(qupath.getViewer().getImageData()) 
        
           		.store(qupath.getViewer().getImageRegionStore()) 
        
           		.renderer(qupath.getViewer().getImageDisplay()) 
        
           		.build();

Please try the latest version and if it works, please close this issue, thanks!

	final ImageServer<BufferedImage> renderedServer = new RenderedImageServer
	.Builder(qupath.getViewer().getImageData())
	.store(qupath.getViewer().getImageRegionStore())
	.renderer(qupath.getViewer().getImageDisplay())
	.build();