Re: I need to copy and crop mutiple ROI from each image

Posted by Pariksheet Nanda on Oct 23, 2012; 11:15pm
URL: http://imagej.273.s1.nabble.com/I-need-to-copy-and-crop-mutiple-ROI-from-each-image-tp5000475p5000500.html

On Mon, Oct 22, 2012 at 11:08 AM, Jasvinder Ahuja
<[hidden email]> wrote:
> I want to make a plugin that copies the in focus section of these individual
> nuclei as ROI and saves it to a new location.
>

Can you explain in a little more detail why you want to do this?
What is the information you want to extract from your multi-channel Z series?

If you want a better view of in focus sections of the image, you could use:
    Image > Stacks > Z Project...
Although this command is in the Stacks menu, it will also work on your
Hyperstack.
Then, to see multiple channels at once you can use the contrast tools from:
   Image > Color > Channels Tool
...and use "Composite" and check the channels you want.
Lastly to limit the Lookup Table (LUT) to in-focus fluorescence you can use:
    Image > Adjust > Brightness/Contrast...
...and adjust the minimum threshold (first slider)


> I have no knowledge of JAVA.  Recently, I learnt VBA.
--snip--
> It would be great if I can do this in a batch mode.
>

I don't yet see that you have a need for programming in ImageJ.
If you wanted to, you should start with the Macro programming ability:
http://imagej.nih.gov/ij/developer/index.html
The top link "Macro Language" describes this in some detail.
The Macro Language is similar to JavaScript, but does not have many of
JavaScript's other features like objects and instead relies on
declaring functions outside of the macro for reusable code.


> Jasvinder
>

Pariksheet

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