Thanks, Nicholas for your reply! I’m sorry, I should have explained more clearly. What I am after is the ability to get an RGB array from napari that is a composite of a four-channel image e.g. 405, 488, 561, 647. What would be ideal would be functionality something like:
img.shape # e.g. (4, 2048, 2048)
name=('405', '488', '561', '647'),
colormap=["cyan", "yellow", "magenta", "red"],
contrast_limits=[(0, 2000), (0, 4000), (0, 4000), (0, 4000)],
img_RGB = view.layers.RGB_image()
# access RGB composite image array, including added scale bar and using set contrast limits
img_RGB.shape # (2048, 2048, 3)
view.screenshot() gets close to what I would like. However, the returned RGB array is dependent on the size of the napari window.
Such functionality would be really helpful, as I could then add those images into matplotlib subplots etc. Here’s an example subplot that I would like to generate. At the moment it only shows a single channel, but I would like to add RGB composites.
BMP_day_3_test.pdf (8.4 MB)
Thanks so much for your help! If napari is not currently able to do this, could you possibly recommend any alternative libraries or functions for such a task?
I really appreciate all the awesome work you do with Napari! It is really helpful for my research!