Re: Create stack without showing each image on screen?

[anon]

> Hi, thanks for making this program, it's the best..Is it possible to
> create an image stack without having to open all the images in separate
> windows? Or at least not having to show them on the screen, but just load
> them into memory? This would be useful when a large number of images is
> needed.
>
> It would be something like the following, I guess, except instead of
> openImage it would be something else. I looked at the macro language
> reference guide but it wasn't obvious what command it would be. File.open
> seems to be only for text files.
>
> Opener opener = new Opener();
> ImagePlus imp1 = opener.openImage("c-003-01.bmp");
> ImagePlus imp2 = opener.openImage("c-003-08.bmp");
> ImageStack stack = new ImageStack(imp1.getWidth(), imp1.getHeight(), 2);
> stack.addSlice("first slice",imp1.getProcessor().getPixels());
> stack.addSlice("second slice",imp2.getProcessor().getPixels());
> (from
> https://list.nih.gov/cgi-bin/wa.exe?A2=ind1201&L=IMAGEJ&P=R3364&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
> )
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[anon]

On Mon, Jun 4, 2012 at 6:52 PM, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]> wrote:

Hi Sylvia,
 
The easy way to open a series of image as a stack is to use the File>Import>Image Sequence command. Is there some reason why you cannot use this command? Use the command recorder to generate macro or Java code that uses this command.
 
Best regards,
 
-wayne
 

---------------

Thanks for the response, this worked.

What threw me off was the fact that when I put Images - Stack - Images to Stack, it said "you need to have at least 2 images open." But that was because it was already a stack, which I didn't realize.
However, the 3d rendering displays as grayscale, while this doesn't happen when the stack is created from individual images. The individual images are not grayscale. I didn't change any of the default options on the 3d dialog. I guess this is better than nothing, though.

Also, I don't really need to save the image sequence but just thought I'd mention that if I try to do File - Save As - Image Sequence, only tiff format will actually save a file. If I select jpg or png, no file is actually saved even though the window says "images.jpg" or "images.png." I was only doing this to see if it would help the grayscale, but it doesn't seem to.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[anon]

> On Tue, Jun 5, 2012 at 2:00 PM, Rasband, Wayne (NIH/NIMH) [E] <

> [hidden email]> wrote:
>
> Send me two or three of the images and I will try to figure out why the
> File>Import>Image Sequence and File>Save As>Image Sequence command are not
> working as expected.
>
> Best regards,
>
> -wayne
>
>
> Import>Image Sequence is working fine. I just tested Save As>Image
> Sequence on another computer (XP, the other one was 7 but I guess the
> platform shouldn't matter since it's java) and tiff outputs one file
> containing the stack, png outputs a file for each image, and jpg outputs
> one file of the current image. But maybe that's what it is supposed to do?
>
> The other thing I commented on is that the 3d picture is grayscale, even
> though the 2d images are not. I'll attach the 3d image in a separate
> message to avoid message size limitations. Thanks for your attention.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[anon]

Here's the 3d image as mentioned previously.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html