Posted by
Dubuis, Eric D on
Dec 13, 2012; 1:53pm
URL: http://imagej.273.s1.nabble.com/I-need-to-copy-and-crop-mutiple-ROI-from-each-image-tp5000475p5001143.html
To the question: How to save my ROI as image ?
If what you want is just an illustration of the ROI used, you can always copy system them while they are superimposed to your image (Alt Gr + Print Screen).
Alternatively, transform your tiff image to RGB, display your ROI on screen then in ROI manager window use the command Flatten (F), This will merge your ROI to the RGB image which you can later save as Tiff. I advise to have a thicker line to mark the edge of thr ROI si it is visible on the merged picture
If all you want to get is your ROI on a transparent background, open your image, im the menu select:
Image -> Stacks -> Add Slice
Give the new slice a black background and display your ROI (again, thick line for the edges). Use Flatten (F) command and answer "No" when the software ask if you want to flatten all images. You will get your ROI on a black background. Save that image (either as jpg, bmp or other).
Use an imaging software (photoshop or the gimp for example) and open the image. Using color select (or magic wand like method) select and remove all black from the picture so as to see your ROI without background. Save the image as png.
Later when inserting it into power point or in web pages, you will have your ROI on transparent background which you will be able to superimpose to whatever you want.
Cheers
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Pariksheet Nanda
Sent: 13 December 2012 13:36
To:
[hidden email]
Subject: Re: I need to copy and crop mutiple ROI from each image
On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
>
> 1) I cannot save the ROI as an image (.tiff file) On average I have
> 5-10 ROI per image.
Add your ROIs to the ROI manager. There are two ways to save the ROI
information:
- save to .roi file from the manager
http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager- if you just save the .tiff image it should include the ROI drawn on the
image as well, so you will see the ROI the next time you open it in ImageJ.
> I want to save each ROI as an image in a format easy for ImageJ
> to handle.
>
Using the .roi file explained above will accomplish this.
2) Also I am having problems opening deconvolved image files from
> deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> no clue, on how to go about it.
>
I don't see support for that file with the LOI Bioformats plugin[1] so
another approach could be to import the raw DeltaVision data into ImageJ
and run deconvolution in ImageJ instead, or have DeltaVision export to a
format ImageJ understands.
Jasvinder
>
Pariksheet
[1]
http://loci.wisc.edu/bio-formats/formats--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html