Re: image names in stack

[Anda Cornea]

Hello!

On a somewhat related topic: Is there a way to keep the original names of images that were built into a stack that is then exposed to various transformations (SIFT registration, Advanced Weka Segmentation, Measure, etc.).  In my hands, each transformation generates a stack where slices are labeled 1 to n.  It is time consuming and error prone to match measurement data to the original images at the end.

Thank you for your help,

Anda  


Anda Cornea, PhD
Director of the Imaging and Morphology Support Core
Oregon National Primate Research Center
Oregon Health & Science University
503-690-5293




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rasband, Wayne (NIH/NIMH) [E]
Sent: Saturday, February 16, 2013 6:44 AM
To: [hidden email]
Subject: Re: images to stack

On Feb 14, 2013, at 11:49 AM, Agustin Lobo wrote:

> Hi!
> Is there any way to add images by name to an stack? My images are not
> in the same directory, and prefer not to move/copy them.
> I can open them all and the use images to stack, but there are too
> many and opening them all represents a memory problem.
> I can easily have the names (with their paths) in a list, bit do not
> know how to add each image to the stack (and close) within a loop.

You can use the File>Import>Stack from List command, which opens a stack, or virtual stack, from a text file or URL containing a list of image file paths. The images can be in different folders but they must all be the same size and type.

This macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack:

   http://imagej.nih.gov/ij/macros/VirtualStackFromList.txt

And this one demonstrates how to how to open an image series from a remote server:

   http://imagej.nih.gov/ij/macros/OpenStackUsingURLs.txt

-wayne

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[Christian Goosmann-2]

Dear Anda,
I had the same problem and was helped by Christophe Leterrier and his extremely useful macro 'Transfer Labels' that I am not able to locate more precisely at the moment since I am not at my Fiji-ImageJ-machine.
Maybe you can track it down. The macro lets you transfer all Labels from one opened stack to another of the same slice number (e.g. a resulting stack after an operation).
Best regards
Christian
________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Anda Cornea [[hidden email]]
Sent: Thursday, February 21, 2013 7:26 PM
To: [hidden email]
Subject: Re: image names in stack

Hello!

On a somewhat related topic: Is there a way to keep the original names of images that were built into a stack that is then exposed to various transformations (SIFT registration, Advanced Weka Segmentation, Measure, etc.).  In my hands, each transformation generates a stack where slices are labeled 1 to n.  It is time consuming and error prone to match measurement data to the original images at the end.

Thank you for your help,

Anda


Anda Cornea, PhD
Director of the Imaging and Morphology Support Core
Oregon National Primate Research Center
Oregon Health & Science University
503-690-5293




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rasband, Wayne (NIH/NIMH) [E]
Sent: Saturday, February 16, 2013 6:44 AM
To: [hidden email]
Subject: Re: images to stack

On Feb 14, 2013, at 11:49 AM, Agustin Lobo wrote:

> Hi!
> Is there any way to add images by name to an stack? My images are not
> in the same directory, and prefer not to move/copy them.
> I can open them all and the use images to stack, but there are too
> many and opening them all represents a memory problem.
> I can easily have the names (with their paths) in a list, bit do not
> know how to add each image to the stack (and close) within a loop.

You can use the File>Import>Stack from List command, which opens a stack, or virtual stack, from a text file or URL containing a list of image file paths. The images can be in different folders but they must all be the same size and type.

This macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack:

   http://imagej.nih.gov/ij/macros/VirtualStackFromList.txt

And this one demonstrates how to how to open an image series from a remote server:

   http://imagej.nih.gov/ij/macros/OpenStackUsingURLs.txt

-wayne

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

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[ctrueden]

Hi Christian,

> Christophe Leterrier and his extremely useful macro 'Transfer Labels'
> that I am not able to locate more precisely at the moment

Google suggests this one?
http://www.cleterrier.net/Macros/Transfer_Labels.txt

Regards,
Curtis


On Fri, Feb 22, 2013 at 3:14 AM, Christian Goosmann <
[hidden email]> wrote:

> Dear Anda,
> I had the same problem and was helped by Christophe Leterrier and his
> extremely useful macro 'Transfer Labels' that I am not able to locate more
> precisely at the moment since I am not at my Fiji-ImageJ-machine.
> Maybe you can track it down. The macro lets you transfer all Labels from
> one opened stack to another of the same slice number (e.g. a resulting
> stack after an operation).
> Best regards
> Christian
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Anda
> Cornea [[hidden email]]
> Sent: Thursday, February 21, 2013 7:26 PM
> To: [hidden email]
> Subject: Re: image names in stack
>
> Hello!
>
> On a somewhat related topic: Is there a way to keep the original names of
> images that were built into a stack that is then exposed to various
> transformations (SIFT registration, Advanced Weka Segmentation, Measure,
> etc.).  In my hands, each transformation generates a stack where slices are
> labeled 1 to n.  It is time consuming and error prone to match measurement
> data to the original images at the end.
>
> Thank you for your help,
>
> Anda
>
>
> Anda Cornea, PhD
> Director of the Imaging and Morphology Support Core
> Oregon National Primate Research Center
> Oregon Health & Science University
> 503-690-5293
>
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Rasband, Wayne (NIH/NIMH) [E]
> Sent: Saturday, February 16, 2013 6:44 AM
> To: [hidden email]
> Subject: Re: images to stack
>
> On Feb 14, 2013, at 11:49 AM, Agustin Lobo wrote:
>
> > Hi!
> > Is there any way to add images by name to an stack? My images are not
> > in the same directory, and prefer not to move/copy them.
> > I can open them all and the use images to stack, but there are too
> > many and opening them all represents a memory problem.
> > I can easily have the names (with their paths) in a list, bit do not
> > know how to add each image to the stack (and close) within a loop.
>
> You can use the File>Import>Stack from List command, which opens a stack,
> or virtual stack, from a text file or URL containing a list of image file
> paths. The images can be in different folders but they must all be the same
> size and type.
>
> This macro demonstrates how to generate a list of images and then use that
> list to open the images as a virtual stack:
>
>    http://imagej.nih.gov/ij/macros/VirtualStackFromList.txt
>
> And this one demonstrates how to how to open an image series from a remote
> server:
>
>    http://imagej.nih.gov/ij/macros/OpenStackUsingURLs.txt
>
> -wayne
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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