http://imagej.273.s1.nabble.com/Double-clicking-TIFF-opens-ImageJ-but-not-the-image-with-Java-8-tp5017568p5017706.html
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> Hi Michael and Herbie,
>
> Thanks for the suggestions i will play with changing the overlay
> brush colours etc.
>
> I now have a somewhat related query concerning overlays. What i'm
> looking for is a tool that allows discrete spots to be selected on an
> image and really the overlay brush or standard paintbrush are ideal
> for me. However, these are not really tools for creating
> selections. I have used the "selection brush" in the past but you
> have to hold the shift key to mark discrete areas and then it is
> still one selection until i split it. I know i can use
> Image>Overlay>To ROI Manager to create selections from overlays but
> then when i try to threshold based on one of these selections it
> doesn't show the thresholded pixels on the image for some reason,
> also sometimes when i click on a selection made from an overlay it
> then doesn't show it on the image either but this seems intermittent.
> Once i do "To ROI Manager" can the overlays be considered selections
> as standard selections would be? I don't really understand the above
> behaviour however.
>
> Again, related to this analysis i'd like to add different selections
> to a couple of open images and keep track of which image they were
> drawn on as they will be selecting different structures in each image
> and i need to analyse them. I'd normally add all selections to the
> ROI Manager for processing but this doesn't work so well if you want
> to process more than one image with different selections, what would
> be the best way to go about this? I could process one image after
> the other so that the ROI manger only contains selections from one of
> the images at any one time but this isn't ideal in my case.
>
> Sorry michael for replying to another thread i forgot to compose a
> new mail.
>
> Thanks for the help,
>
> Matt
>
>
>
> -- Matt Pearson Microscopy Facility MRC Human Genetics Unit Institute
> of Genetics and Molecular Medicine (IGMM) University of Edinburgh
> Crewe Road EH4 2XU
>
>
>
>
> On 6 Dec 2016, at 21:03, Michael Schmid
> <
[hidden email]<mailto:
[hidden email]>> wrote:
>
> On 2016-12-06 11:57, PEARSON Matthew wrote:
>
> Could someone please remind me how i can set the options such as
> colour, size and transparency for the overlay brush tool within a
> macro.
>
> Hi Matt,
>
> the foreground and background colors used by the Overlay Brush Tool
> are those of the color picker; you can set them with the macro calls
> setForegroundColor and setBackgroundColor
>
https://imagej.nih.gov/ij/developer/macro/functions.html#setForegroundColor>
> The width is in the Preferences. In principle you could use
> oBrushWidth=5; call("ij.Prefs.set", "obrush.width",
> toString(oBrushWidth));
>
> Unfortunately, this has an effect only if the Overlay Brush has not
> been used in the current session yet. Otherwise it will effect the
> Overlay brush width after ImageJ is closed and opened. I see nothing
> better.
>
> Transparency: With the current ImageJ code, I see no way to set this
> from a macro.
>
> What you can also try is activating a given overlay and modifying it
> after it has been drawn, see
>
https://imagej.nih.gov/ij/developer/macro/functions.html#Overlay>
>
> [ As a side note, if it's a new topic, please don't reply to a
> previous thread but write a new mail to
[hidden email].
> Otherwise the mail threads will be messed up ]
>
>
> hth,
>
> Michael
>
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