read part of a huge image stack--.tiff

[Guanghua Du]

 
Dear ImageJ-colleagues
I have some image data(.tiff format) that are larger than 1.5 Gbyte, these image stacks cannot be read in ImageJ-32 bit, as there is no so much memory in the java virtual machine.
does anybody know some plugin which support to read only part of an image stack? so that I can read the huge file part by part for analysis?
 
Thanks!
 
 
Guanghua

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[Rasband, Wayne (NIH/NIMH) [E]]

On Jun 29, 2012, at 6:20 AM, Guanghua Du wrote:

> Dear ImageJ-colleagues
> I have some image data(.tiff format) that are larger than 1.5 Gbyte, these image stacks cannot be read in ImageJ-32 bit, as there is no so much memory in the java virtual machine.
> does anybody know some plugin which support to read only part of an image stack? so that I can read the huge file part by part for analysis?

Open the TIFF file as a virtual stack using File>Import>TIFF Virtual Stack and then use the Image>Duplicate command to convert parts of the virtual stack to in-memory stacks.

-wayne

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[ctrueden]

Hi Guangha,


> I have some image data(.tiff format) that are larger than 1.5 Gbyte, these
> image stacks cannot be read in ImageJ-32 bit, as there is no so much memory
> in the java virtual machine.
> does anybody know some plugin which support to read only part of an image
> stack? so that I can read the huge file part by part for analysis?


You can use the Bio-Formats Importer plugin (part of the Fiji distribution
of ImageJ; http://fiji.sc/) to open a subset of your data. Choose File >
Import > Bio-Formats, select your TIFF stack, then when the dialog appears,
check the "Specify range for each series" box. Click OK, and another dialog
will appear that gives control over which planes get opened. You can also
crop the image planes (i.e., reduce X and Y dimensions) by checking the
"Crop on import" box.

As Wayne says, another good option is virtual stacks. You can check the
"Use virtual stack" box for that.

-Curtis


On Fri, Jun 29, 2012 at 5:20 AM, Guanghua Du <[hidden email]> wrote:

>
> Dear ImageJ-colleagues
> I have some image data(.tiff format) that are larger than 1.5 Gbyte, these
> image stacks cannot be read in ImageJ-32 bit, as there is no so much memory
> in the java virtual machine.
> does anybody know some plugin which support to read only part of an image
> stack? so that I can read the huge file part by part for analysis?
>
> Thanks!
>
>
> Guanghua
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Guanghua Du]

Dear Wayne,
Thanks, the virtual stack works very well!
 
best
guanghua



----- Original Message -----
From: "Rasband, Wayne (NIH/NIMH) [E]" <[hidden email]>
To: <[hidden email]>
Subject: Re: read part of a huge image stack--.tiff
Date: 2012-06-29 20:50

On Jun 29, 2012, at 6:20 AM, Guanghua Du wrote:
> Dear ImageJ-colleagues
> I have some image data(.tiff format) that are larger than 1.5 Gbyte, these image stacks cannot be read in ImageJ-32 bit, as there is no so much memory in the java virtual machine.
> does anybody know some plugin which support to read only part of an image stack? so that I can read the huge file part by part for analysis?
Open the TIFF file as a virtual stack using File>Import>TIFF Virtual Stack and then use the Image>Duplicate command to convert parts of the virtual stack to in-memory stacks.
-wayne
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[Marijonas Tutkus]

Could you, please, remove my e-mail from the image-j interest group?


Marijonas Tutkus


On Jun 29, 2012, at 2:50 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

On Jun 29, 2012, at 6:20 AM, Guanghua Du wrote:

Dear ImageJ-colleagues
I have some image data(.tiff format) that are larger than 1.5 Gbyte, these image stacks cannot be read in ImageJ-32 bit, as there is no so much memory in the java virtual machine.
does anybody know some plugin which support to read only part of an image stack? so that I can read the huge file part by part for analysis?

Open the TIFF file as a virtual stack using File>Import>TIFF Virtual Stack and then use the Image>Duplicate command to convert parts of the virtual stack to in-memory stacks.

-wayne

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


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[Antoinette]

Tiff reading can involves wide options, such as tiff image and text encoding and decoding, tiff document matadata encoding and decoding, tiff windows, web and mobile viewers and readers creations as well as tiff document text extracting.