Posted by
PEARSON Matthew on
Dec 07, 2016; 9:20am
URL: http://imagej.273.s1.nabble.com/Double-clicking-TIFF-opens-ImageJ-but-not-the-image-with-Java-8-tp5017568p5017705.html
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#setForegroundColorThe 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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