http://imagej.273.s1.nabble.com/Double-clicking-TIFF-opens-ImageJ-but-not-the-image-with-Java-8-tp5017568p5017709.html
The selection in the image is independent of this. You can have one of
selection. The current selection in the image determines the scope of
> 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>>
>>
>>
>> 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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http://imagej.nih.gov/ij/list.html>>
>>
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>>
>>
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>> Scotland, with registration number SC005336.
>>
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