Re: Overlay with Image5D

Posted by Joachim Walter on Jan 24, 2007; 9:54am
URL: http://imagej.273.s1.nabble.com/no-subject-tp3700530p3700534.html

Florian,

there are several ways to do that. If you have 2D images (not stacks),
maybe the simplest way is to open them in ImageJ, merge them to a stack
(Image->Stacks->Convert Images to Stack) and then use
"Plugins->Image5D->Stack to Image5D" to get them as separate channels in
an Image5D. In the dialog that pops up, you leave 3rd dimension as "z"
and 4th dimension as "ch", but change the 3rd dimension size to 1 and
the 4th dimension size to 2.
You get an Image5D with a scrollbar on the right to change the displayed
channel. When you select "ovl" from the  dropdown box (top right), you
get the overlay.

Joachim


Florian Blaschke schrieb:

> Hi Justin,
>
> thanks a lot for your help! Following your recommendation I used Image5D
> and I had no problems to colorize the pictures. However, I am struggling
> with the overlay. How do you open the two files as two different channels
> and how do you finally do the overlay.
> There was no reason to use FITC over DIC.
>
> Florian
>
>  
>> Hi,
>> I have DAPI/DIC images that I like to colorize and merge.  I was using
>> the color merge plugin, but I find that Image5D
>> http://rsb.info.nih.gov/ij/plugins/image5d.html is rather convenient
>> and it's easier to pick the colors you want.
>>
>> You need to open the two files as two different channels.  Then select
>> overlay in the drop down box (I think it actually says ovly or
>> something like that).  Then you simply select a channel and pick a
>> color.  The plugin does some other nice stuff as well.
>>
>> Is there any reason to use FITC over DIC?
>>
>> Justin
>>
>>    

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