ImageJ

combining/montaging stacks?

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

3 messages Options

Cammer, Michael

combining/montaging stacks?

We have between 10 and 36 stacks of about 100 X 100 X 36 pixels each in XY that we want to combine together into one stack. Essentially, the result would be a montage of stacks.

Has anyone written a macro or plugin for this that they'd be willing to share? Otherwise I'll write a macro.

Please see http://www.flickr.com/photos/mcammer/11954287235/ for a case where we're want to montage as 6 X 4.

Thanks!

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

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

Olivier Burri

Re: combining/montaging stacks?

Dear Michael,

If I understand correctly, you have 10 to 36 stacks of images that are 100x100x36

What you want to do is:
1. Montage each of these small stacks
2. Make a stack of the montaged images

If this is correct, then a very simple macro would be

run("Make Montage...", 'OPTIONS HERE'); // You can check with the macro recorder what options you need. Just make sure that at the end of the montage, you give it an easy name
rename("Montage of Stack "+stackNumber);

Then you can use
run("Images to Stack", "name=[My New Stack of Montages] title=[Montage of Stack] use");
Which will only take the images that have "Montage of Stack" in the title.

Then you'll get a stack of all the montages. Seeing as all the images are the same size in XYZ, the montage should also be identical for each slice of your new stack..

Hope I got it.

Best

Oli

Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Cammer, Michael
> Sent: mardi 14 janvier 2014 23:35
> To: [hidden email]
> Subject: combining/montaging stacks?
>
> We have between 10 and 36 stacks of about 100 X 100 X 36 pixels each in XY
> that we want to combine together into one stack. Essentially, the result
> would be a montage of stacks.
>
> Has anyone written a macro or plugin for this that they'd be willing to share?
> Otherwise I'll write a macro.
>
> Please see http://www.flickr.com/photos/mcammer/11954287235/ for a
> case where we're want to montage as 6 X 4.
>
> Thanks!
>
> ==========================================================
> =================
> Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU
> Langone Medical Center
> Cell: 914-309-3270 Lab: 212-263-3208
> http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-
> lab/dustinlab/
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email and
> delete the original message. Please note, the recipient should check this
> email and any attachments for the presence of viruses. The organization
> accepts no liability for any damage caused by any virus transmitted by this
> email.
> =================================
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

Cammer, Michael

Re: combining/montaging stacks?

Hi.
I solved the problem. May not be elegant, but it works. If interested, result is here: http://cammer.net/notes/imagej/tilestacks/index.html
Thanks all who replied!

===========================================================================
Michael Cammer, Microscopy Core & Dustin Lab , Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 Lab: 212-263-3208
http://ocs.med.nyu.edu/microscopy & http://www.med.nyu.edu/skirball-lab/dustinlab/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Burri Olivier
Sent: Friday, January 17, 2014 8:28 AM
To: [hidden email]
Subject: Re: combining/montaging stacks?

Dear Michael,

If I understand correctly, you have 10 to 36 stacks of images that are 100x100x36

What you want to do is:
1. Montage each of these small stacks
2. Make a stack of the montaged images

If this is correct, then a very simple macro would be

run("Make Montage...", 'OPTIONS HERE'); // You can check with the macro recorder what options you need. Just make sure that at the end of the montage, you give it an easy name rename("Montage of Stack "+stackNumber);

Then you can use
run("Images to Stack", "name=[My New Stack of Montages] title=[Montage of Stack] use"); Which will only take the images that have "Montage of Stack" in the title.

Then you'll get a stack of all the montages. Seeing as all the images are the same size in XYZ, the montage should also be identical for each slice of your new stack..

Hope I got it.

Best

Oli

Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

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

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

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