Posted by
Kenneth Sloan on
Feb 01, 2015; 10:11pm
URL: http://imagej.273.s1.nabble.com/editing-an-overlay-tp5011378p5011403.html
Help, please - I’m making very slow progress on this and could really use some assistance.
If looks like I want to use an Image Overlay and the Overlay Brush Tool - but I’m having difficulty with the details.
So far…I have managed to combine the binary mask with the gray scale image - and have discovered that applying the “Red” color map to the binary mask gives me roughly the effect I want.
But, I can’t figure out how to EDIT the mask in the composite image. Perhaps this is not possible (without writing the drawing tool myself?)
Would I be better off performing this task in PhotoShop?
Again - my goal is to combine a grayscale original with a (RED) binary mask overlay, and then edit (use a brush tool to paint or erase) just the mask. If I get that far, I’d eventually like to be able to extract the edited mask (probably easy to do by flattening the composite and then finding pixels with a different value in the R channel - but it must be easier than that; I simply can’t find it in the documentation).
My users are PhotoShop hackers - I’m trying to move them as far as possible into ImageJ - but right now, I’m stuck.
Even an authoritative statement that “it doesn’t exist - write it yourself” would be helpful.
Do I want to instead consider an RGB stack? Is it reasonable to, say - put the original grayscale image in the GREEN channel, the mask in the RED channel - and then view the composite? If I do that, can I EDIT the RED channel while viewing the composite?
Grasping at straws here…
--
Kenneth Sloan
[hidden email]
"La lutte elle-même vers les sommets suffit à remplir un coeur d'homme; il faut imaginer Sisyphe heureux."
> On Jan 29, 2015, at 16:41 , Kenneth Sloan <
[hidden email]> wrote:
>
> I have a plugin which creates a binary image from a grayscale image, and then does a few clean-up operations on the binary image. After that, a trained observer is given the task of editing the binary image. In it’s current, crude state, the observer has very little help from the original data - at best, the observer can see the two images side-by-side.
>
> This is no longer acceptable - I would like to display the binary version as a transparent mask overlaid on top of the original grayscale image (say, coloring the grayscale in shades of red where the binary mask is 1). But, I also want the observer to be able to edit the mask.
>
> It’s not clear to me precisely how to do this. I would appreciate pointers to appropriate places in the API, or sample snippets of (Java, please) plug-in code that I can use as building blocks.
>
> So:
> input: 2 images, one grayscale the other a binary mask
> (original input is just the grayscale - I already generate the binary mask)
>
> behavior: display the grayscale image with shades of red where the mask is 1 and gray otherwise
> EDIT the mask (draw and erase - or, draw with either 0 or 1)
> an alternate view : color the grayscale GREEN where the mask is 0 and RED where
> the mask is 1 - allow the observer to “draw” in GREEN or RED
> output: the modified binary mask.
>
> Environment: FIJI - latest major, stable release.
>
> It may well be that this is trivial with ordinary FIJI controls - if so, I’m just ignorant of these.
>
> It would be acceptable to output the grayscale image (tinted in shades of RED or GREEN - mutually exclusively) - If this is easier, I will happily convert that image to a binary mask. My problem is in editing the mask information on a display which shows the grayscale and the mask in perfect overlay registration.
>
> Mostly, I’m trying to avoid the pain of writing yet-another-drawing-program - hoping that I can use a built-in process to allow the observer to use standard drawing tools to modify the mask.
>
> --
> Kenneth Sloan
>
[hidden email]
> "La lutte elle-même vers les sommets suffit à remplir un coeur d'homme; il faut imaginer Sisyphe heureux."
>
>
>
> --
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http://imagej.nih.gov/ij/list.html--
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