Feature request: "Composite" view and writer

There was already a kind of support for showing the channels in the colors defined by the image file, right? Somehow I'm missing that one.

Moreover, I would like to view my images in a way that is called "Composite" in ImageJ: all channels overlaid on the same picture (and custom colors again, not RGB). That would be e.g. blue, red, white for the nucleus, antibody, and brightfield channel, respectively.

Consequently, the image writer should also support this mode.

Actually, this one feature made me write a very long ImageJ script... Thinking of that: maybe I could simulate that behaviour with an ImageJ Macro node that switches to the Compsite view and converts the image to RGB then?

Hi Lorenz,

in the TableCellViewer (attached to each and every node), you can find the "ColorTableBased" Renderer and the "RGB Renderer". The ColorTableBasedRenderer allows you to render your images in composite, the RGB Renderer can interpret arbitrary dimensions as channels, if the dimensionality is two or three (e.g. two or three channels). Are there problems with showing the ColorTable or now ColorTable Renderer is available? Then please send me a sample image and I can have a look whats going wrong.

Additionally we have a "Labeling to RGB Image" node, which you can use before the image writer to create a nice overlay image.

Does this help?


Christian

 

 

The TableCellViewer does not show the ColorTableBased renderer for me, only the RGB renderer. The image is the same big one I sent you a few days ago.

The background image option of the Labeling to RGB Image node is a cool thing, the Composite mode I am searching for should just overlay the image channels with their custom colors.

Concerning the ColorTables: see https://github.com/scifio/scifio-bf-compat/issues/8. As soon as we have a solution here you will see the color tables in the TableCellViewer.

Concerning the writing of composite images: You want to write each channel individually, in its propers color or do you want to write a (X,Y,Channel) image + colortable? What output do you want to have?
 

ColorTables: thanks!

Output: The output that I have in mind is merely a PNG image that helps to visualize the image to the "outside world", like Powerpoint ;) It should have a Scale Bar, though...

Being able to write a "full spec" ome-tiff with more than 4 channels and ColorTables is probably also a good idea in the long run, but that's another issue.