Re: Set options for Overlay Brush Tool in a macro

Posted by PEARSON Matthew on Dec 07, 2016; 10:31am
URL: http://imagej.273.s1.nabble.com/Double-clicking-TIFF-opens-ImageJ-but-not-the-image-with-Java-8-tp5017568p5017708.html

Hi Michael,

It might be easier i explain the analysis a little to see what options are available.  Say i have a 3 channel image as shown below and i have split the channels.  I add a wait for user so the user can mark different points on each image using the overlay brush.  I then need to analyse the pixels under each overlay spot separately, specifically the auto-thresholded pixels under each spot.  Once the interactive step is complete each channel image's different overlays would be analysed somehow.. I'd prefer not to put them in a stack if possible.

Thanks,

Matt


[cid:[hidden email]]
--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU




On 7 Dec 2016, at 10:17, "Straatman, Kees (Dr.)" <[hidden email]<mailto:[hidden email]>>
 wrote:

According to a post from Wayne on Aug 6, 2013:

"Deselect" in the ROI Manager is the same as "select all" since all ROIs are processed if none are selected.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid
Sent: 07 December 2016 09:35
To: [hidden email]
Subject: Re: Set options for Overlay Brush Tool in a macro

Hi Matt,

concerning multiple selections in the ROI Manager:
You will see all of them if you enable the 'Show All' checkbox.
Nevertheless, the current selection will be just one ROI, or no ROI.
You need More>>Or (Combine) to select all ROIs of the ROIs at once, or more specifically, make one combined ROI from them.

Concerning the workflow, having several selections for different images, it depends a lot what you want to do.
If you can have a stack of your images, you can associate the ROIs with stack slices, which can also affect the 'show all' (More>>Options).
For single images, having the (combined?) ROI as overlay and saving the image as tiff or zip (which preserves overlays) might be helpful.

Michael
________________________________________________________________

On 2016-12-07 10:20, PEARSON Matthew wrote:
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#setForeground
Color

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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