Files not opening in Metamorph?

[krisford]

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Hi,

I took a live streaming in Metamorph and saved it in a TIFF video file.  I
tried to open it later in Metamorph and got the message unable to open.
The file was about 2 gigabytes and 5400 frames.  I'm using 64-Bit Windows
and have about 3 gigs of RAM.  Can anyone help?  It would be sincerely
appreciated.

Thanks,
Kris

[Christian Götze]

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*** Commercial response ***

Hi Kris,

what does "about 2 gigabytes" mean? Is it below 2 GB or above? Although
the TIFF standard uses 32 Bit pointers and thus defines TIFFs up to 4
GB, several of the TIFF libraries available use "signed pointers" and
therefore can't open stacks larger than 2 GB.

But of course the file could be simply corrupted and therefore can't be
read by Metamorph.

Perhaps you should try to open it with other software (ImageJ, Photoshop).

In our applications we use a special modded TIFF library to open large
TIFFs. You can download a trial at

http://www.arivis.com/en/arivis-Vision-4D

If your problems persist we could have a look on your data. Just write a
mail if interested.

Best,
Christian

Am 29.06.2011 21:06, schrieb krisford:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi,
>
> I took a live streaming in Metamorph and saved it in a TIFF video file.  I
> tried to open it later in Metamorph and got the message unable to open.
> The file was about 2 gigabytes and 5400 frames.  I'm using 64-Bit Windows
> and have about 3 gigs of RAM.  Can anyone help?  It would be sincerely
> appreciated.
>
> Thanks,
> Kris

--
Christian Götze

arivis - Multiple Image Tools GmbH
Kröpeliner Straße 54, D-18055 Rostock

Tel : [phone]
Fax : [phone]
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[krisford]

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Christian

The file is 2.076 GB in size.  Rougly 80% of the file opens in ImageJ, and
we are trying to adjust the file size limit to match the size of the file.
So we see 4000 of the roughly 5000 frames.  ImageJ isn't letting us go
beyond 1.6 GB, so we thought we'd go back and try Metamorph, but it
wouldn't open at all.  We will look at the download you sent, and see how
that goes.  If the problem persists I would definitely like to contact you
and send a sample .tif file.  Thanks for the assitance.

Kris


On Wed, 29 Jun 2011 21:35:02 +0200, Christian Götze
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> *** Commercial response ***
>
> Hi Kris,
>
> what does "about 2 gigabytes" mean? Is it below 2 GB or above? Although
> the TIFF standard uses 32 Bit pointers and thus defines TIFFs up to 4
> GB, several of the TIFF libraries available use "signed pointers" and
> therefore can't open stacks larger than 2 GB.
>
> But of course the file could be simply corrupted and therefore can't be
> read by Metamorph.
>
> Perhaps you should try to open it with other software (ImageJ,

Photoshop).

>
> In our applications we use a special modded TIFF library to open large
> TIFFs. You can download a trial at
>
> http://www.arivis.com/en/arivis-Vision-4D
>
> If your problems persist we could have a look on your data. Just write a
> mail if interested.
>
> Best,
> Christian
>
> Am 29.06.2011 21:06, schrieb krisford:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi,
>>
>> I took a live streaming in Metamorph and saved it in a TIFF video file.
>> I
>> tried to open it later in Metamorph and got the message unable to open.
>> The file was about 2 gigabytes and 5400 frames.  I'm using 64-Bit

Windows
>> and have about 3 gigs of RAM.  Can anyone help?  It would be sincerely
>> appreciated.
>>
>> Thanks,
>> Kris

[Cameron Nowell]

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To join, leave or search the confocal microscopy listserv, go to:
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Hi Kris,

Have you got stack buffering enabled in MetaMorph? A 2GB file on a system with 3GB of RAM is going to be pushing the limits a bit.

To enable stack buffering open MetaMorph, go to Edit--> Preferences and then go to the Stack buffering tab. You can then set the parameters as you need them so save RAM, the rest will be cached on the drive until needed.

Your other option would be to open as much as you can in ImageJ (or I recommend Fiji) and export each slice as a an individual tiff. Then you can rebuild it as a STK file in MetaMorph which will handle larger file sizes better. Then just repeat this for the other parts of the file (last 1000 frames or so) you couldn't open the first time.

Cheers

Cam


Cameron J. Nowell
Microscopy Manager
Centre for Advanced Microscopy
Ludwig Institute for Cancer Research Melbourne - Parkville Branch
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
Office: [phone]
Mobile: [phone]
Fax: [phone]
Facility Website




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of krisford
Sent: Thursday, 30 June 2011 6:39 AM
To: [hidden email]
Subject: Re: Files not opening in Metamorph?

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

Christian

The file is 2.076 GB in size.  Rougly 80% of the file opens in ImageJ, and
we are trying to adjust the file size limit to match the size of the file.
So we see 4000 of the roughly 5000 frames.  ImageJ isn't letting us go
beyond 1.6 GB, so we thought we'd go back and try Metamorph, but it
wouldn't open at all.  We will look at the download you sent, and see how
that goes.  If the problem persists I would definitely like to contact you
and send a sample .tif file.  Thanks for the assitance.

Kris


On Wed, 29 Jun 2011 21:35:02 +0200, Christian Götze
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> *** Commercial response ***
>
> Hi Kris,
>
> what does "about 2 gigabytes" mean? Is it below 2 GB or above? Although
> the TIFF standard uses 32 Bit pointers and thus defines TIFFs up to 4
> GB, several of the TIFF libraries available use "signed pointers" and
> therefore can't open stacks larger than 2 GB.
>
> But of course the file could be simply corrupted and therefore can't be
> read by Metamorph.
>
> Perhaps you should try to open it with other software (ImageJ,

Photoshop).

>
> In our applications we use a special modded TIFF library to open large
> TIFFs. You can download a trial at
>
> http://www.arivis.com/en/arivis-Vision-4D
>
> If your problems persist we could have a look on your data. Just write a
> mail if interested.
>
> Best,
> Christian
>
> Am 29.06.2011 21:06, schrieb krisford:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi,
>>
>> I took a live streaming in Metamorph and saved it in a TIFF video file.
>> I
>> tried to open it later in Metamorph and got the message unable to open.
>> The file was about 2 gigabytes and 5400 frames.  I'm using 64-Bit

Windows
>> and have about 3 gigs of RAM.  Can anyone help?  It would be sincerely
>> appreciated.
>>
>> Thanks,
>> Kris


This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waive any rights if you have received this communication in error.
The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd.

[krisford]

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Cameron,

Thanks for the reply. I will be trying both ideas at my first opportunity.
Your help is greatly appreciated, thanks again.

Kris  

On Thu, 30 Jun 2011 08:43:14 +1000, Cameron Nowell
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Kris,
>
> Have you got stack buffering enabled in MetaMorph? A 2GB file on a system
> with 3GB of RAM is going to be pushing the limits a bit.
>
> To enable stack buffering open MetaMorph, go to Edit--> Preferences and
> then go to the Stack buffering tab. You can then set the parameters as

you
> need them so save RAM, the rest will be cached on the drive until needed.
>
> Your other option would be to open as much as you can in ImageJ (or I
> recommend Fiji) and export each slice as a an individual tiff. Then you
can

> rebuild it as a STK file in MetaMorph which will handle larger file sizes
> better. Then just repeat this for the other parts of the file (last 1000
> frames or so) you couldn't open the first time.
>
> Cheers
>
> Cam
>
>
> Cameron J. Nowell
> Microscopy Manager
> Centre for Advanced Microscopy
> Ludwig Institute for Cancer Research Melbourne - Parkville Branch
> PO Box 2008
> Royal Melbourne Hospital
> Victoria, 3050
> AUSTRALIA
> Office: [phone]
> Mobile: [phone]
> Fax: [phone]
> Facility Website
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]

On

> Behalf Of krisford
> Sent: Thursday, 30 June 2011 6:39 AM
> To: [hidden email]
> Subject: Re: Files not opening in Metamorph?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Christian
>
> The file is 2.076 GB in size.  Rougly 80% of the file opens in ImageJ,

and
> we are trying to adjust the file size limit to match the size of the
file.
> So we see 4000 of the roughly 5000 frames.  ImageJ isn't letting us go
> beyond 1.6 GB, so we thought we'd go back and try Metamorph, but it
> wouldn't open at all.  We will look at the download you sent, and see how
> that goes.  If the problem persists I would definitely like to contact
you

> and send a sample .tif file.  Thanks for the assitance.
>
> Kris
>
>
> On Wed, 29 Jun 2011 21:35:02 +0200, Christian Götze
> <[hidden email]> wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> *** Commercial response ***
>>
>> Hi Kris,
>>
>> what does "about 2 gigabytes" mean? Is it below 2 GB or above? Although
>> the TIFF standard uses 32 Bit pointers and thus defines TIFFs up to 4
>> GB, several of the TIFF libraries available use "signed pointers" and
>> therefore can't open stacks larger than 2 GB.
>>
>> But of course the file could be simply corrupted and therefore can't be
>> read by Metamorph.
>>
>> Perhaps you should try to open it with other software (ImageJ,
> Photoshop).
>>
>> In our applications we use a special modded TIFF library to open large
>> TIFFs. You can download a trial at
>>
>> http://www.arivis.com/en/arivis-Vision-4D
>>
>> If your problems persist we could have a look on your data. Just write a

>> mail if interested.
>>
>> Best,
>> Christian
>>
>> Am 29.06.2011 21:06, schrieb krisford:
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Hi,
>>>
>>> I took a live streaming in Metamorph and saved it in a TIFF video file.

>>> I
>>> tried to open it later in Metamorph and got the message unable to open.
>>> The file was about 2 gigabytes and 5400 frames.  I'm using 64-Bit
> Windows
>>> and have about 3 gigs of RAM.  Can anyone help?  It would be sincerely
>>> appreciated.
>>>
>>> Thanks,
>>> Kris
>
>
> This communication is intended only for the named recipient and may

contain
> information that is confidential, legally privileged or subject to
> copyright; the Ludwig Institute for Cancer Research Ltd does not waive
any
> rights if you have received this communication in error.
> The views expressed in this communication are those of the sender and do
> not necessarily reflect the views of the Ludwig Institute for Cancer
> Research Ltd.

[Steffen Dietzel]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

On 29.06.2011 22:39, krisford wrote:
>
> The file is 2.076 GB in size.  Rougly 80% of the file opens in ImageJ, and
> we are trying to adjust the file size limit to match the size of the file.
> So we see 4000 of the roughly 5000 frames.  ImageJ isn't letting us go
> beyond 1.6 GB,

Kris, do you use the 32-bit Version of ImageJ? If so, you are limited in
file size (usable RAM) to about that, so maybe this is the problem and
not the file itself. On a 64-bit operating system with ImageJ 64 bit
this is not a limitation, I had much bigger files on Linux-64 or Win7-64

Steffen

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

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