In the meantime, I stumbled on a method using Stacks that I was just about to report on:
One question on this procedure: when I make the Composite stack, I see IDENTICAL images no matter what slice is selected.
Is this the expected behavior? Should there be any discernible difference between the slices when viewing as a “Composite”?
Are there controls to this view that would allow me to play with the relative intensities, or an alpha value to control transparency? I’d like the gray-scale image to be as prominent as possible, with only a tiny bit of perceptual space taken up by the mask. As is, the mask is a bit TOO prominent, at the expense of gray-scale resolution in the original image. Would the “selection object” approach allow for better control?
I have someone integrating this into our existing Java plug-in (which currently creates the initial binary mask). We had been editing the mask in isolation (with the original “off to the side”) - but decided that this was not optimal. For one thing, the images are 1536x1536 and are already scaled down for display; “side-by-side” wasn’t really working. When that version is complete, I’ll experiment with the “selection object” technique. One learns a large system like ImageJ one technique at a time.
"La lutte elle-même vers les sommets suffit à remplir un coeur d'homme; il faut imaginer Sisyphe heureux."
> On Feb 2, 2015, at 10:19 , Jerome Mutterer <
[hidden email]> wrote:
>
> Dear Kenneth,
>
> I understand you're trying to edit a mask over a grayscale image.
> You could try the following: convert your mask to a selection object,
> give this ROI a transparent red fill color and you're done.
> You can restore this selection on the grayscale image and edit it using the
> built in selection brush.
> Sincerely,
> Jerome
>
> run("AuPbSn 40 (56K)");
> id=getImageID;
> run("Duplicate...", " ");
> setOption("BlackBackground", false);
> run("Make Binary");
> run("Create Selection");
> roiManager("Add");
> selectWindow("AuPbSn40.jpg");
> roiManager("Select", 0);
> roiManager("Set Fill Color", "#33ff0000");
> setTool("brush");
>
>
>
>
>
> On 1 February 2015 at 23:11, Kenneth Sloan <
[hidden email]> wrote:
>>
>> 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."
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>
>
>
> --
> Jerome Mutterer
> CNRS - Institut de biologie moléculaire des plantes
> 12, rue du Général Zimmer
> 67084 Strasbourg Cedex
> T 0367155339
> www.ibmp.cnrs.fr
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html