Movie Corruption Issue

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Stephen Bunnell Stephen Bunnell
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Movie Corruption Issue

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

This is not technically a microscopy question, but I'm desperate:

I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
and .mov formats over many years of imaging.

Of late, I have noticed that _many_ of my older .mov files are seriously
corrupted on the Mac. It's not the data. Archived movies are the same. It's
the player- Quicktime. It no longer can play the old movies. However, 2-3
years ago, before this problem was widespread, we exported several .mov
files to .avi. These .avi movies (fortunately) play just fine. However,
attempt to export the corrupted .mov files now yield .avi files that look
just like the .mov files- that is to say, they look like garbage.

I have attempted to revert to older versions of quicktime- all the way to
v7.3. No luck. They're still corrupted.

The corruption is not a computer issue. The same movies are corrupted on
many others Macs with current system installations.

As you might expect, this makes for less than stellar presentations, when
half of your movies crash.

Oddly, some movies exported on the same day, using the same software, will
play, and others will not.

Has anyone else encountered this problem on the Mac? Any thoughts?

    --Steve



****************************************************************************
Stephen C. Bunnell, Ph.D.
Assistant Professor
Tufts University Medical School
Department of Pathology
Jaharis Bldg., Room 512
150 Harrison Ave.
Boston, MA 02111

Phone: (617) 636-2174
Fax:   (617) 636-2990
Email: [hidden email]

SHIPPING ADDRESS (for packages):
Tufts University Receiving
37 Tyler St.
Attn: Bunnell/Pathology/Jaharis 524
Boston, MA 02111
James Beals James Beals
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Re: Movie Corruption Issue

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Steve,
You may need to use QT pro.
Check the options under view.
Play all frames. It is an option with the pro version.
hope it helps
James Beals
[hidden email]
734.936-2051

205 Zina Pitcher Place
2038 MBNI
Molecular and Behavioral Neuroscience Institute
University of Michigan
Ann Arbor, Mi
48109





On Jan 18, 2008, at 2:43 PM, Stephen Bunnell wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> This is not technically a microscopy question, but I'm desperate:
>
> I use a mac. I have hundreds, if not thousands, of videos exported  
> into .mpg
> and .mov formats over many years of imaging.
>
> Of late, I have noticed that _many_ of my older .mov files are  
> seriously
> corrupted on the Mac. It's not the data. Archived movies are the  
> same. It's
> the player- Quicktime. It no longer can play the old movies.  
> However, 2-3
> years ago, before this problem was widespread, we exported  
> several .mov
> files to .avi. These .avi movies (fortunately) play just fine.  
> However,
> attempt to export the corrupted .mov files now yield .avi files  
> that look
> just like the .mov files- that is to say, they look like garbage.
>
> I have attempted to revert to older versions of quicktime- all the  
> way to
> v7.3. No luck. They're still corrupted.
>
> The corruption is not a computer issue. The same movies are  
> corrupted on
> many others Macs with current system installations.
>
> As you might expect, this makes for less than stellar  
> presentations, when
> half of your movies crash.
>
> Oddly, some movies exported on the same day, using the same  
> software, will
> play, and others will not.
>
> Has anyone else encountered this problem on the Mac? Any thoughts?
>
>     --Steve
>
>
>
> **********************************************************************
> ******
> Stephen C. Bunnell, Ph.D.
> Assistant Professor
> Tufts University Medical School
> Department of Pathology
> Jaharis Bldg., Room 512
> 150 Harrison Ave.
> Boston, MA 02111
>
> Phone: (617) 636-2174
> Fax:   (617) 636-2990
> Email: [hidden email]
>
> SHIPPING ADDRESS (for packages):
> Tufts University Receiving
> 37 Tyler St.
> Attn: Bunnell/Pathology/Jaharis 524
> Boston, MA 02111
Stephen C. Kempf Stephen C. Kempf
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Steve,

If no one comes up with a simple fix, you might try this.

Get Graphic Converter from,

http://www.lemkesoft.com/

Open movie with GC, then go to the file menu and select "Save a copy  
as". In the save window, select "pict", "Jpeg", or whatever as the  
format, make a new folder for the saved files, then click "Save". At  
this point you'll get a new window that will let you select "Export  
all available frames". Once you've selected this, click OK. All the  
frames will be saved as individual images in the format you selected.  
These can then be re-assembled as a movie with GC, Quicktime Pro, or  
some other such program.

Hope that helps,

Steve
  PS If GC won't open your Quicktime movies, there probably is a  
problem with them.

On Jan 18, 2008, at 1:43 PM, Stephen Bunnell wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> This is not technically a microscopy question, but I'm desperate:
>
> I use a mac. I have hundreds, if not thousands, of videos exported  
> into .mpg
> and .mov formats over many years of imaging.
>
> Of late, I have noticed that _many_ of my older .mov files are  
> seriously
> corrupted on the Mac. It's not the data. Archived movies are the  
> same. It's
> the player- Quicktime. It no longer can play the old movies.  
> However, 2-3
> years ago, before this problem was widespread, we exported  
> several .mov
> files to .avi. These .avi movies (fortunately) play just fine.  
> However,
> attempt to export the corrupted .mov files now yield .avi files  
> that look
> just like the .mov files- that is to say, they look like garbage.
>
> I have attempted to revert to older versions of quicktime- all the  
> way to
> v7.3. No luck. They're still corrupted.
>
> The corruption is not a computer issue. The same movies are  
> corrupted on
> many others Macs with current system installations.
>
> As you might expect, this makes for less than stellar  
> presentations, when
> half of your movies crash.
>
> Oddly, some movies exported on the same day, using the same  
> software, will
> play, and others will not.
>
> Has anyone else encountered this problem on the Mac? Any thoughts?
>
>     --Steve
>
>
>
> **********************************************************************
> ******
> Stephen C. Bunnell, Ph.D.
> Assistant Professor
> Tufts University Medical School
> Department of Pathology
> Jaharis Bldg., Room 512
> 150 Harrison Ave.
> Boston, MA 02111
>
> Phone: (617) 636-2174
> Fax:   (617) 636-2990
> Email: [hidden email]
>
> SHIPPING ADDRESS (for packages):
> Tufts University Receiving
> 37 Tyler St.
> Attn: Bunnell/Pathology/Jaharis 524
> Boston, MA 02111
Steve Paddock Steve Paddock
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Steve,

Larry Jordan is a wonderful resource for Quicktime related issues...

http://www.larryjordan.biz/

Steve
--
Steve Paddock, Ph.D.,
Howard Hughes Medical Institute,
Dept. Molecular Biology,
Univ. Wisconsin,
1525 Linden Drive,
Madison, WI 53706.

608 262 7898 (lab.)
608 242 7391 (home)
608 770 5467 (cell)
608 770 1301 (cell)
608 262 9343 (FAX)
http://www.molbio.wisc.edu/carroll
Hanspeter Niederstrasser-3 Hanspeter Niederstrasser-3
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Stephen Bunnell wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> This is not technically a microscopy question, but I'm desperate:
>
> I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
> and .mov formats over many years of imaging.
>
> Of late, I have noticed that _many_ of my older .mov files are seriously
> corrupted on the Mac. It's not the data. Archived movies are the same. It's
> the player- Quicktime. It no longer can play the old movies. However, 2-3
> years ago, before this problem was widespread, we exported several .mov
> files to .avi. These .avi movies (fortunately) play just fine. However,
> attempt to export the corrupted .mov files now yield .avi files that look
> just like the .mov files- that is to say, they look like garbage.
>
> I have attempted to revert to older versions of quicktime- all the way to
> v7.3. No luck. They're still corrupted.
>
> The corruption is not a computer issue. The same movies are corrupted on
> many others Macs with current system installations.
>
> As you might expect, this makes for less than stellar presentations, when
> half of your movies crash.
>
> Oddly, some movies exported on the same day, using the same software, will
> play, and others will not.
>
> Has anyone else encountered this problem on the Mac? Any thoughts?

I noticed this a couple months ago with some files made in older
versions of QuickTime (v7.2.something I think) and saved using certain
codecs, and now v7.3.something will garble it.  I would need to go back
to my files to see what codec and Quicktime version was at fault, but I
_think_ it might have been the Animation codec.  If you view a QuickTime
movie and press pretzel-I, it will tell you the codec that was used, and
you can see if there's a similarity between the 'good' movies and the
'bad' movies.

Do you have access to a Mac with an older version of QuickTime (v7.2 or
earlier) to test view the files with?  Reinstalling an older quicktime
over a new version might not clear the updated decoders, so a

Other than that, I agree with Stephen Kempf about Graphic Converter.
It's great software, if anything for very rapid batch conversions
between formats.  Also, you might want to try VLC player
<http://www.videolan.org/vlc/> for movies.

Hanspeter

--
Hanspeter Niederstrasser, Ph.D.      Dept. of Microbiology
hn2157 at columbia dot edu           701 W. 168th St.
Chang Lab                            New York, NY 10032
Columbia University
Haberman, Ann Haberman, Ann
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear Steve,

This often happens in current QuickTime versions when the movie file
size is large. The movies will seemingly stutter - start to play for
a few frames and then stop. Especially if they were originally
created with Apple animation. This will not happen with smaller
files. Is there a way that you can compress before you open them with
QuickTime?

best,
Ann

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>This is not technically a microscopy question, but I'm desperate:
>
>I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
>and .mov formats over many years of imaging.
>
>Of late, I have noticed that _many_ of my older .mov files are seriously
>corrupted on the Mac. It's not the data. Archived movies are the same. It's
>the player- Quicktime. It no longer can play the old movies. However, 2-3
>years ago, before this problem was widespread, we exported several .mov
>files to .avi. These .avi movies (fortunately) play just fine. However,
>attempt to export the corrupted .mov files now yield .avi files that look
>just like the .mov files- that is to say, they look like garbage.
>
>I have attempted to revert to older versions of quicktime- all the way to
>v7.3. No luck. They're still corrupted.
>
>The corruption is not a computer issue. The same movies are corrupted on
>many others Macs with current system installations.
>
>As you might expect, this makes for less than stellar presentations, when
>half of your movies crash.
>
>Oddly, some movies exported on the same day, using the same software, will
>play, and others will not.
>
>Has anyone else encountered this problem on the Mac? Any thoughts?
>
>     --Steve
>
>
>
>****************************************************************************
>Stephen C. Bunnell, Ph.D.
>Assistant Professor
>Tufts University Medical School
>Department of Pathology
>Jaharis Bldg., Room 512
>150 Harrison Ave.
>Boston, MA 02111
>
>Phone: (617) 636-2174
>Fax:   (617) 636-2990
>Email: [hidden email]
>
>SHIPPING ADDRESS (for packages):
>Tufts University Receiving
>37 Tyler St.
>Attn: Bunnell/Pathology/Jaharis 524
>Boston, MA 02111


--

Ann Haberman, PhD
Department of Laboratory Medicine
Yale University School of Medicine
1 Gilbert  St.
TAC S541
New Haven, CT 06510

203-785-7349
203-785-5415 (fax)
[hidden email]
Urs Utzinger Urs Utzinger
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Re: Movie Corruption Issue

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

It you want to consider a different format,

it seems as x264 (H264) and XviD are one of the best freely available
encoders for movie type data. You can use different containers MP4, AVI, MPG
using the same encoder.
You can check Wikipedia for codecs and  follow the many links.
I found MediaCoder very useful for re-encoding. This program seems to
partially work with WINE on OSX so it probably is not the best choice for OS
X. If you use double or triple pass very little contrast is lost due to
compression, however these codecs have primarily applications in encoding
movies and as jpeg will use compression resulting in data quality reduction.

Maybe others can comment on best "scientific" approach for video encoding.

You might also want to check on windows computers and most likely they use a
different decoder and it could be that your movies are played correctly.
Beside quick time, there is also "windows media player classic" which should
be able to play quick time movies.

Once you are sure data is not corrupted, you can consider re-encoding or
purchasing different media player software or getting a different codec.

It's unlikely your data is corrupted but that your player does not
render/decompress the video correctly.

Urs Utzinger
University of Arizona

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Ann Haberman
Sent: Friday, January 18, 2008 2:20 PM
To: [hidden email]
Subject: Re: Movie Corruption Issue

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear Steve,

This often happens in current QuickTime versions when the movie file
size is large. The movies will seemingly stutter - start to play for
a few frames and then stop. Especially if they were originally
created with Apple animation. This will not happen with smaller
files. Is there a way that you can compress before you open them with
QuickTime?

best,
Ann

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>This is not technically a microscopy question, but I'm desperate:
>
>I use a mac. I have hundreds, if not thousands, of videos exported into
.mpg

>and .mov formats over many years of imaging.
>
>Of late, I have noticed that _many_ of my older .mov files are seriously
>corrupted on the Mac. It's not the data. Archived movies are the same. It's
>the player- Quicktime. It no longer can play the old movies. However, 2-3
>years ago, before this problem was widespread, we exported several .mov
>files to .avi. These .avi movies (fortunately) play just fine. However,
>attempt to export the corrupted .mov files now yield .avi files that look
>just like the .mov files- that is to say, they look like garbage.
>
>I have attempted to revert to older versions of quicktime- all the way to
>v7.3. No luck. They're still corrupted.
>
>The corruption is not a computer issue. The same movies are corrupted on
>many others Macs with current system installations.
>
>As you might expect, this makes for less than stellar presentations, when
>half of your movies crash.
>
>Oddly, some movies exported on the same day, using the same software, will
>play, and others will not.
>
>Has anyone else encountered this problem on the Mac? Any thoughts?
>
>     --Steve
>
>
>
>***************************************************************************
*

>Stephen C. Bunnell, Ph.D.
>Assistant Professor
>Tufts University Medical School
>Department of Pathology
>Jaharis Bldg., Room 512
>150 Harrison Ave.
>Boston, MA 02111
>
>Phone: (617) 636-2174
>Fax:   (617) 636-2990
>Email: [hidden email]
>
>SHIPPING ADDRESS (for packages):
>Tufts University Receiving
>37 Tyler St.
>Attn: Bunnell/Pathology/Jaharis 524
>Boston, MA 02111


--

Ann Haberman, PhD
Department of Laboratory Medicine
Yale University School of Medicine
1 Gilbert  St.
TAC S541
New Haven, CT 06510

203-785-7349
203-785-5415 (fax)
[hidden email]
Bill Oliver-3 Bill Oliver-3
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

On Fri, 18 Jan 2008, Stephen Bunnell wrote:

>
> Has anyone else encountered this problem on the Mac? Any thoughts?
>

I've run into something similar, though in Windows.  I had a PowerPoint presentation that I created in 1999 and decided to display it recently.  It worked fine, except that none of the .mov files would display.  When I converted it to OpenOffice Presenter in Linux, it worked fine.


A friend pointed out a Microsoft announcement about it.  According to Microsoft, it was necessary to convert the file to .avi.  I did it two ways -- first I used Quicktime Pro to convert the files to avi.  Later, someone told me all I had to do was *rename* the files, so I tried it and that worked, too.

It turns out that it isn't the *format* as much as the *compression scheme* and a codec change.  See:

http://support.microsoft.com/kb/q266983/


I suspect, then, that it may not be a OS issue, but an application issue, probably involving a codec mismatch.

billo
http://www.billoblog.com/billoblog
Michael Cammer Michael Cammer
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Re: Movie Corruption Issue

Search the CONFOCAL archive at
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I've also had a problem with AVI files on Vista.

On my HP desktop running Vista, AVI files from one of my digital cameras
and some older AVI files from work just don't play.  This means that none
of the Microsoft home video editing tools work with them.  I've tooled
around the Microsoft site a little and done some Google searches but
haven't figured out how to get the codecs into Vista.

On my daughters' Toshiba Vista laptop they all work just fine.  So if I
really really need a file, I chase them off YouTube and IMing and use
their laptop.

Good luck with Vista.

-mc

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> On Fri, 18 Jan 2008, Stephen Bunnell wrote:
>
>>
>> Has anyone else encountered this problem on the Mac? Any thoughts?
>>
>
> I've run into something similar, though in Windows.  I had a PowerPoint
> presentation that I created in 1999 and decided to display it recently.
> It worked fine, except that none of the .mov files would display.  When I
> converted it to OpenOffice Presenter in Linux, it worked fine.
>
>
> A friend pointed out a Microsoft announcement about it.  According to
> Microsoft, it was necessary to convert the file to .avi.  I did it two
> ways -- first I used Quicktime Pro to convert the files to avi.  Later,
> someone told me all I had to do was *rename* the files, so I tried it and
> that worked, too.
>
> It turns out that it isn't the *format* as much as the *compression
> scheme* and a codec change.  See:
>
> http://support.microsoft.com/kb/q266983/
>
>
> I suspect, then, that it may not be a OS issue, but an application issue,
> probably involving a codec mismatch.
>
> billo
> http://www.billoblog.com/billoblog
>


_________________________________________
Michael Cammer   http://www.aecom.yu.edu/aif/
Stephen Bunnell Stephen Bunnell
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Re: Movie Corruption Issue ( Part II )

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Thanks to everybody for all of their comments!

To clarify what is going on:

    None of my movies are corrupted. All of my movies play perfectly on an
old OS9.2 iMac running Quicktime 6.0.

    My installation of Quicktime 7.4, and previously QT 7.3, seem to lack a
codec required to view my older movies. I have not yet tried reverting to a
QT older than 7.3. I am worried that this will goober up my nice new Mac.
The suspect codec is likely to be Apple's 'Animation' codec, which is what I
used to export all of these movies prior to 2004.

    When I view the movies on 'fresh from the shop' Macs without outside
software, the movies are also not playing correctly. (OK. I snuck into an
Apple Store and checked the movies from a memory stick...) Therefore the
problem is not likely to be with any extraneous installed software or
codecs. It is most likely with the Apple standard Mac QT codecs.

    I have QT Pro- the same problem manifests under normal and pro versions.

    Graphic Converter is a joy. But it also appears to use the QT engine.
Therefore, every movie that is incorrectly read by the QT Player is also
'bad' in Graphic Converter. Same with VLC, which I also love, normally.

    I have emailed Larry Jordan, and will let you all know if he has any
words of genius. I hope so!
   
    Regarding file size: The files are only a few MB, so I rather hope this
isn't the problem. In any case, I can't compress them, since nothing can
read them, barring the old iMac with QT6.
   
    Regarding alternate formats: Back in the day, when these movies still
worked, I exported several to AVI. The quality was reduced a bit, but it was
acceptable. These movies still play. Clearly, other codecs are more robust.

    Nevertheless, these are the movies I have. I do not fancy retooling PPT
presentations with dozens of movies. Nor do I fancy having to move >2000
movies from my MBP to an iMac, batch converting to AVI, and then re-creating
every PPT presentations I've prepared since 2004! This is a huge backwards
compatibility issue for scientific data. I'd rather get the movies to play
with a repaired codec. Does anyone know how to raise such issues with Apple?

    -Steve
   
   
   


****************************************************************************
Stephen C. Bunnell, Ph.D.
Assistant Professor
Tufts University Medical School
Department of Pathology
Jaharis Bldg., Room 512
150 Harrison Ave.
Boston, MA 02111

Phone: (617) 636-2174
Fax:   (617) 636-2990
Email: [hidden email]


This is not technically a microscopy question, but I'm desperate:

I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
and .mov formats over many years of imaging.

Of late, I have noticed that _many_ of my older .mov files are seriously
corrupted on the Mac. It's not the data. Archived movies are the same. It's
the player- Quicktime. It no longer can play the old movies. However, 2-3
years ago, before this problem was widespread, we exported several .mov
files to .avi. These .avi movies (fortunately) play just fine. However,
attempt to export the corrupted .mov files now yield .avi files that look
just like the .mov files- that is to say, they look like garbage.

I have attempted to revert to older versions of quicktime- all the way to
v7.3. No luck. They're still corrupted.

The corruption is not a computer issue. The same movies are corrupted on
many others Macs with current system installations.

As you might expect, this makes for less than stellar presentations, when
half of your movies crash.

Oddly, some movies exported on the same day, using the same software, will
play, and others will not.

Has anyone else encountered this problem on the Mac? Any thoughts?

    --Steve
Urs Utzinger Urs Utzinger
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Re: Movie Corruption Issue

In reply to this post by Michael Cammer
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

There is a free vista codec pack one can obtain for versions of vista that
do not come with advanced codecs such as the Vista Business Edition. This
codec pack is based on open source libraries but I would not call it
consumer grade software (simply because of its hundreds of options and the
level of documentation).

To maintain scientific grade quality, often lossless compression is required
such as the QuickTime Animation Codec. So far I have not been successful in
figuring out what products would allow lossless encoding with other
algorithms such as MPEG-4.

The issue of not being able to play certain movie files is probably due to
companies desire to create revenue opportunities with movie playback
software (e.g. Windows Vista Business does not natively play DVD movies). It
seems when implementing those revenue opportunities, backwards compatibility
is compromised.
 
Urs Utzinger
University of Arizona


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Michael Cammer
Sent: Monday, January 21, 2008 8:07 PM
To: [hidden email]
Subject: Re: Movie Corruption Issue

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I've also had a problem with AVI files on Vista.

On my HP desktop running Vista, AVI files from one of my digital cameras
and some older AVI files from work just don't play.  This means that none
of the Microsoft home video editing tools work with them.  I've tooled
around the Microsoft site a little and done some Google searches but
haven't figured out how to get the codecs into Vista.

On my daughters' Toshiba Vista laptop they all work just fine.  So if I
really really need a file, I chase them off YouTube and IMing and use
their laptop.

Good luck with Vista.

-mc

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> On Fri, 18 Jan 2008, Stephen Bunnell wrote:
>
>>
>> Has anyone else encountered this problem on the Mac? Any thoughts?
>>
>
> I've run into something similar, though in Windows.  I had a PowerPoint
> presentation that I created in 1999 and decided to display it recently.
> It worked fine, except that none of the .mov files would display.  When I
> converted it to OpenOffice Presenter in Linux, it worked fine.
>
>
> A friend pointed out a Microsoft announcement about it.  According to
> Microsoft, it was necessary to convert the file to .avi.  I did it two
> ways -- first I used Quicktime Pro to convert the files to avi.  Later,
> someone told me all I had to do was *rename* the files, so I tried it and
> that worked, too.
>
> It turns out that it isn't the *format* as much as the *compression
> scheme* and a codec change.  See:
>
> http://support.microsoft.com/kb/q266983/
>
>
> I suspect, then, that it may not be a OS issue, but an application issue,
> probably involving a codec mismatch.
>
> billo
> http://www.billoblog.com/billoblog
>


_________________________________________
Michael Cammer   http://www.aecom.yu.edu/aif/
Hanspeter Niederstrasser-3 Hanspeter Niederstrasser-3
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Re: Movie Corruption Issue ( Part II )

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Stephen Bunnell wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Thanks to everybody for all of their comments!
>
> To clarify what is going on:
>
>     None of my movies are corrupted. All of my movies play perfectly on an
> old OS9.2 iMac running Quicktime 6.0.
>
>     My installation of Quicktime 7.4, and previously QT 7.3, seem to lack a
> codec required to view my older movies. I have not yet tried reverting to a
> QT older than 7.3. I am worried that this will goober up my nice new Mac.
> The suspect codec is likely to be Apple's 'Animation' codec, which is what I
> used to export all of these movies prior to 2004.

...

> with a repaired codec. Does anyone know how to raise such issues with Apple?

Steve,

You can file a bug directly with apple at
<http://bugreporter.apple.com/> and also ask in the Quicktime-users
mailing list: <http://lists.apple.com/mailman/listinfo/quicktime-users>.

Also, I would be wary of downgrading QT versions because a lot of the
system uses QT for backend stuff and it's unclear how things will react
to it.

If you can, try to find an OS X mac w/ Quicktime 7.2 with one of your
colleagues and test your videos there.  This will minimize the time
window to  when the codec was broken and help out the bug tracking
tremendously.

Hanspeter

--
Hanspeter Niederstrasser, Ph.D.      Dept. of Microbiology
hn2157 at columbia dot edu           701 W. 168th St.
Chang Lab                            New York, NY 10032
Columbia University
Bill Oliver-3 Bill Oliver-3
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Re: Movie Corruption Issue ( Part II )

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

On Tue, 22 Jan 2008, Hanspeter Niederstrasser wrote:

>
>> with a repaired codec. Does anyone know how to raise such issues with
>> Apple?

I have not found Apple to be very responsive.

However, there is one last thing you can try.  I'm more of a Linux guy than a Mac or Windoze person, and there is a player originally written for Linux but ported to the Mac called "mplayer."   It's primarily a command-line player (though it has a gui if you want to use it).  The nice thing about it is that it comes with a zillion codecs (that you have to download separately), and I have yet to find an unenrypted movie that it can't handle.  It comes with a function for translating between formats and codecs, and is generally the workhorse for this kind of in the Linux world.

Take a look at: http://www.mplayerhq.hu/design7/news.html

billo
George McNamara George McNamara
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Re: Movie Corruption Issue ... video codecs

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Dear Listserv,


I've been burned enough with compressed videos on different PC's that I now routinely use uncompressed AVI, made with MetaMorph or ImageJ. Big but safe.

Web sites where I've found video codec's are listed below. I am a fan of the K-Lite Mega Codec Pack. At bottom is a comparison table I made using MetaMorph to generate the movies (except for Quicktime, which Meta 6.x always crashed trying to make).

Download, install, use at your own risk!


Video Codec downloads

Siggraph Codec Central http://www.siggraph.org/education/materials/HyperGraph/video/codecs/Default.htm

FourCC codecs list (Four-Character Codes to identify video streams)      http://www.fourcc.org/codecs.php

Microsoft's FourCC for video compression   http://www.microsoft.com/whdc/archive/fourcc.mspx

Microsoft DirectX 9.0c end-user runtime      http://www.microsoft.com/downloads/details.aspx?FamilyID=0a9b6820-bfbb-4799-9908-d418cdeac197&displaylang=en

Microsoft Codec installation packages         http://www.microsoft.com/windows/windowsmedia/format/codecdownload.aspx

DivX codec                                                http://www.divx.com/divx/

Codec-Download (archive)                           http://www.codec-download.com/

K-Lite Mega Codec Pack                             http://www.codecguide.com/download_mega.htm

Ligos Indeo codec family                              http://www.ligos.com/indeo.htm

3ivx D4 4.5                                                  http://www.3ivx.com/

XviD codec                                                   http://www.xvidmovies.com/codec/

HuffYUV                                                      http://neuron2.net/www.math.berkeley.edu/benrg/huffyuv.html

Apple Quicktime                                          http://www.apple.com/quicktime/




filename                                        filesize            Score (sum)
VP61 Advanced Profile                  1,582,592        1
VP62 Heightened Sharpness          1,584,640        1
VP60 Simple Profile                       1,612,288        1
DivX MPEG-4 Fast-Motion             2,459,648        5
DivX MPEG-4 Low-Motion              4,312,064        4
Microsoft MPEG-4 V2                    6,698,496        2
Intel Indeo video R3.2                     20,154,880      6
Microsoft Windows Media Video 9  28,512,768      2
Cinepak                                        35,144,192      2
Intel Indeo Video 4.5                      38,092,800      2
Microsoft Video 1                          65,801,728      3
QuickTime                                     225,830,571     4
uncompressed                               363,842,048     2

average score (of 24 codecs)         50,512,800      3.16
standard deviation                         88,101,414      2.13
median                                          13,934,080      2
maximum possible score (high is bad)                  12


Videos made with MetaMorph 6.3.2.
Videos examined in Microsoft Windows Media Player 9.00.00.3250, zoom 200%, except for Quicktime movie viewed with Apple Quicktime Player 6.5.2.




At 03:54 PM 1/22/2008, you wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

On Tue, 22 Jan 2008, Hanspeter Niederstrasser wrote:


with a repaired codec. Does anyone know how to raise such issues with Apple?

I have not found Apple to be very responsive.

However, there is one last thing you can try.  I'm more of a Linux guy than a Mac or Windoze person, and there is a player originally written for Linux but ported to the Mac called "mplayer."   It's primarily a command-line player (though it has a gui if you want to use it).  The nice thing about it is that it comes with a zillion codecs (that you have to download separately), and I have yet to find an unenrypted movie that it can't handle.  It comes with a function for translating between formats and codecs, and is generally the workhorse for this kind of in the Linux world.

Take a look at: http://www.mplayerhq.hu/design7/news.html

billo




 

George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office
http://home.earthlink.net/~pubspectra/
http://home.earthlink.net/~geomcnamara/
http://www.sylvester.org/health_pro/shared_resources/index.asp (see Analytical Imaging Core Facility)


George McNamara George McNamara
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Re: Movie Corruption Issue ... video codecs

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Joel and listserv,

From my scoring scheme. Sorry about the (lack of) formatting in the raw data scoring sheet below - I tried sending the original Excel file (only 37 kb) but the message bounced. I've slightly formatted it here. I assume "brand marks" would go away if I paid for the codec (brand marks = "free" trial version). I've also included comments at bottom. The uncompressed did look 'slightly pixelated" compared to the original stack in MetaMorph.

filename                                   filesize                 Score (sum) B&W Title Text readability  Video quality Color text readability Color text color Brand marks
VP61 Advanced Profile            1,582,592       1 0 1 0 0 0
VP62 Heightened Sharpness                1,584,640       1 0 1 0 0 0
VP60 Simple Profile                       1,612,288       1 0 1 0 0 0
XviD MPEG-4                                2,207,744       1 0 0 0 0 1
DivX MPEG-4 Fast-Motion                  2,459,648       5 1 2 0 1 1
3ivx D4 4.5.1 Pro Video Codec            3,172,352       2 0 2 0 0 0
DivX 6.0 codec                    4,224,512       3 0 1 0 1 1
DivX MPEG-4 Low-Motion           4,312,064       4 1 1 0 1 1
Microsoft MPEG-4 V2                       6,698,496       2 1 0 0 1 0
Microsoft MPEG-4 V1                       6,865,920       2 1 0 0 1 0
Microsoft Windows Media Video   6,865,920       3 1 1 0 1 0
VP31 Compressor                           7,894,528       8 1 3 2 2 0
Intel I.263 Video Driver 2.55.01                 13,934,080      5 0 2 2 1 0
PICVideo MJPEG Codec             16,908,288      9 1 3 2 1 2
Intel Indeo video R3.2                    20,154,880      6 1 2 2 1 0
Microsoft Windows Media Video 9         28,512,768      2 0 1 0 1 0
Cinepak                                    35,144,192      2 1 1 0 0 0
Ligos Indeo Video 5.11           37,864,448      4 1 1 1 1 0
Ligos Indeo XP Video 5.2                 37,864,448      1 0 0 0 1 0
Intel Indeo Video 4.5                     38,092,800      2 0 1 0 1 0
Microsoft Video 1                         65,801,728      3 1 2 0 0 0
Huffyuv v2.1.1 - CESSP Patch             147,447,808     2 0 2 0 0 0
blank (no name) Codec            181,941,248     4 1 2 0 0 1
QuickTime                                  225,830,571     4 0 4 0 0 0
uncompressed                      363,842,048     2 0 2 0 0 0

average score                              50,512,800      3.2 0.5 1.4 0.4 0.6 0.3
standard deviation                        88,101,414      2.1 0.5 1.0 0.8 0.6 0.5
median                             13,934,080      2.0 0.0 1.0 0.0 1.0 0.0
Scoring   (0=good, 1=acceptable, 2=bad) (0=good, 1=slightly pixelated, 2=strongly pixelated; 3=blurry; 4=jitters) (0=good, 1=acceptable, 2=bad) (0=good, 1=acceptable, 2=bad) (0=absent; 1=present some frames; 2=present all frames)


Codec Comment
--------- ---------------
VP61 Advanced Profile            title text slightly pixelated (blue grunge at bottom on a 320x239 dataset, ok with 320x240 pixel data).
VP62 Heightened Sharpness                title text slightly pixelated (blue grunge at bottom on a 320x239 dataset).
VP60 Simple Profile                       title text slightly pixelated
XviD MPEG-4 Brand                         marks overlay over some early frames (on top of scale bar). title text slightly pixelated
DivX MPEG-4 Fast-Motion                  Brand marks overlay over some early frames (on top of scale bar). title text slightly pixelated
3ivx D4 4.5.1 Pro Video Codec            Brand marks. title text slightly pixelated
DivX 6.0 codec                    Brand marks overlay over some early frames (on top of scale bar). Slightly pixelated.
DivX MPEG-4 Low-Motion           Brand marks overlay over some early frames (on top of scale bar). title text slightly pixelated
Microsoft MPEG-4 V2                       title text off-white; title text oddly pixelated
Microsoft MPEG-4 V1                       title text slightly pixelated
Microsoft Windows Media Video   title text slightly pixelated
VP31 Compressor Blurry text,             blurry images.
Intel I.263 Video Driver 2.55.01                 ghosting around cells and color letters. Colors (k, d) washed out.
PICVideo MJPEG Codec             Brand marks overlay over all frames. Slightly pixelated.
Intel Indeo video R3.2                    strongly pixelated
Microsoft Windows Media Video 9         title text slightly pixelated. Colors (k, d) partly washed out.
Cinepak title text off-white,            slightly blurry.
Ligos Indeo Video 5.11           title text off-white
Ligos Indeo XP Video 5.2                 title text slightly pixelated
Intel Indeo Video 4.5                     Colors (k, d) partly washed out.
Microsoft Video 1                         pixelated
Huffyuv v2.1.1 - CESSP Patch             Pixelated.
blank (no name) Codec            Pixelated.
QuickTime                                  jitters mar playback.
uncompressed                      slightly pixelated

average score
standard deviation
median


At 10:39 PM 1/22/2008, you wrote:
George,

As always, I am impressed by the comprehensiveness of your posts. 
However, I am a little puzzled by the "score" item in your list. 
What do those numbers represent?

Joel


-------------- Original message ---------------
Date sent:      Tue, 22 Jan 2008 22:12:55 -0500
Send reply to:  Confocal Microscopy List
<[hidden email]>
From:   George McNamara <[hidden email]>
Subject:         Re: Movie Corruption Issue ... video codecs
To:      [hidden email]


Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
bin/wa?S1=confocal

Dear Listserv,


I've been burned enough with compressed videos on different PC's that
I now routinely use uncompressed AVI, made with MetaMorph or ImageJ.
Big but safe.

Web sites where I've found video codec's are listed below. I am a fan
of the K-Lite Mega Codec Pack. At bottom is a comparison table I made
using MetaMorph to generate the movies (except for Quicktime, which
Meta 6.x always crashed trying to make).

Download, install, use at your own risk!


Video Codec downloads

Siggraph Codec Central
http://www.siggraph.org/education/materials/HyperGraph/video/codecs/De
fault.htm

FourCC codecs list (Four-Character Codes to identify video
streams) http://www.fourcc.org/codecs.php

Microsoft's FourCC for video compression
http://www.microsoft.com/whdc/archive/fourcc.mspx

Microsoft DirectX 9.0c end-user runtime
http://www.microsoft.com/downloads/details.aspx?FamilyID=0a9b6820-
bfbb-4799-9908-d418cdeac197&displaylang=en

Microsoft Codec installation packages
http://www.microsoft.com/windows/windowsmedia/format/codecdownload.asp
x

DivX codec
http://www.divx.com/divx/

Codec-Download (archive) http://www.codec-
download.com/

K-Lite Mega Codec Pack 
http://www.codecguide.com/download_mega.htm

Ligos Indeo codec family
http://www.ligos.com/indeo.htm

3ivx D4
4.5http://www.3ivx.co
m/

XviD codec
http://www.xvidmovies.com/codec/

HuffYUV
http://neuron2.net/www.math.berkeley.edu/benrg/huffyuv.html

Apple Quicktime
http://www.apple.com/quicktime/




filenamefilesizeScor
e (sum)
VP61 Advanced Profile1,582,592 1
VP62 Heightened Sharpness1,584,640 1
VP60 Simple Profile1,612,288 1
DivX MPEG-4 Fast-Motion2,459,648 5
DivX MPEG-4 Low-Motion4,312,064 4
Microsoft MPEG-4 V26,698,496 2
Intel Indeo video R3.220,154,880 6
Microsoft Windows Media Video 928,512,768 2
Cinepak35,144,192 2
Intel Indeo Video 4.538,092,800 2
Microsoft Video 165,801,728 3
QuickTime225,830,571 4
uncompressed363,842,048 2

average score (of 24 codecs)50,512,800 3.16
standard deviation88,101,414 2.13
median13,934,080 2
maximum possible score (high is bad) 12


Videos made with MetaMorph 6.3.2.
Videos examined in Microsoft Windows Media Player 9.00.00.3250, zoom
200%, except for Quicktime movie viewed with Apple Quicktime Player
6.5.2.




At 03:54 PM 1/22/2008, you wrote:
    Search the CONFOCAL archive at
    http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
   
    On Tue, 22 Jan 2008, Hanspeter Niederstrasser wrote:


    with a repaired codec. Does anyone know how to raise such issues with
    Apple?
   
    I have not found Apple to be very responsive.
   
    However, there is one last thing you can try. I'm more of a Linux
    guy than a Mac or Windoze person, and there is a player originally
    written for Linux but ported to the Mac called "mplayer." It's
    primarily a command-line player (though it has a gui if you want to
    use it). The nice thing about it is that it comes with a zillion
    codecs (that you have to download separately), and I have yet to find
    an unenrypted movie that it can't handle. It comes with a function
    for translating between formats and codecs, and is generally the
    workhorse for this kind of in the Linux world.
   
    Take a look at: http://www.mplayerhq.hu/design7/news.html
   
    billo





George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office
http://home.earthlink.net/~pubspectra/
http://home.earthlink.net/~geomcnamara/
http://www.sylvester.org/health_pro/shared_resources/index.asp (see
Analytical Imaging Core Facility)




Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs




 

George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office
http://home.earthlink.net/~pubspectra/
http://home.earthlink.net/~geomcnamara/
http://www.sylvester.org/health_pro/shared_resources/index.asp (see Analytical Imaging Core Facility)


Stephen Bunnell Stephen Bunnell
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Re: Movie Corruption Issue

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

In follow up to my own post on the failure of old movies exported using the
'Apple Animation' codec:

The defect is in Apple's new versions of Quicktime. Both Quicktime 7.3 and
7.4 fail to play these movies. After reinstalling my entire OS, with
Quicktime 7.1.3 and OSX version 10.4.11, all of these movies now play
perfectly. I've not tested Quicktime 7.2.

As to a solution... I've heard nothing at all from Apple. I'm not going to
upgrade Quicktime again for at least a year. My advice is to be very wary up
performing any Quicktime upgrades before a presentation! The new versions
(7.3 and 7.4 for the Mac) appear to have _many_ bugs, judging from the
online discussions.

Every other Mac-based player I tried failed in exactly the same way, despite
many good suggestions from the list. Ultimately, I will need a Mac fix for
Quicktime, or else I will have to re-export thousands of movies...

     -Thanks for all your advice.




On 1/18/08 2:43 PM, "Stephen C. Bunnell" <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> This is not technically a microscopy question, but I'm desperate:
>
> I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
> and .mov formats over many years of imaging.
>
> Of late, I have noticed that _many_ of my older .mov files are seriously
> corrupted on the Mac. It's not the data. Archived movies are the same. It's
> the player- Quicktime. It no longer can play the old movies. However, 2-3
> years ago, before this problem was widespread, we exported several .mov
> files to .avi. These .avi movies (fortunately) play just fine. However,
> attempt to export the corrupted .mov files now yield .avi files that look
> just like the .mov files- that is to say, they look like garbage.
>
> I have attempted to revert to older versions of quicktime- all the way to
> v7.3. No luck. They're still corrupted.
>
> The corruption is not a computer issue. The same movies are corrupted on
> many others Macs with current system installations.
>
> As you might expect, this makes for less than stellar presentations, when
> half of your movies crash.
>
> Oddly, some movies exported on the same day, using the same software, will
> play, and others will not.
>
> Has anyone else encountered this problem on the Mac? Any thoughts?
>
>     --Steve
>
>
>
> ****************************************************************************
> Stephen C. Bunnell, Ph.D.
> Assistant Professor
> Tufts University Medical School
> Department of Pathology
> Jaharis Bldg., Room 512
> 150 Harrison Ave.
> Boston, MA 02111
>
> Phone: (617) 636-2174
> Fax:   (617) 636-2990
> Email: [hidden email]
>
> SHIPPING ADDRESS (for packages):
> Tufts University Receiving
> 37 Tyler St.
> Attn: Bunnell/Pathology/Jaharis 524
> Boston, MA 02111

****************************************************************************
Stephen C. Bunnell, Ph.D.
Assistant Professor
Tufts University Medical School
Department of Pathology
Jaharis Bldg., Room 512
150 Harrison Ave.
Boston, MA 02111

Phone: (617) 636-2174
Fax:   (617) 636-2990
Email: [hidden email]

SHIPPING ADDRESS (for packages):
Tufts University Receiving
37 Tyler St.
Attn: Bunnell/Pathology/Jaharis 524
Boston, MA 02111
Mathieu Marchand-2 Mathieu Marchand-2
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Re: Movie Corruption Issue

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

To comment the previous post,

Everybody should be aware that using any other version than the latest
available Quicktime is a major security risk, on both Mac and Windows.

The last 7.3, 7.3.1 and 7.4 updates of Quicktime corrected some CRITICAL flaws:
http://secunia.com/advisories/28502/
http://secunia.com/advisories/28092/
http://secunia.com/advisories/27755/
http://secunia.com/advisories/27523/
and these are the flaws for only the past 3 months

These flaws are rated "extremely critical" and could give an attacker
remote access on your system just by visiting a malicious website with
your favorite browser.
Since Quicktime 7.2 and later does not support Windows 2000 any more,
I recommend to uninstall Quicktime on computers running Windows 2000.

Support for old codecs like "animation" for quicktime or "cinepak" for
vista is broken or problematic and people should stop using them, and
plan to convert old movies to more recent codec. "Codec Packs" can
sometimes solve your problem, but they usually have major stability /
legality / security risks attached to them. They can introduce new
problems, too (for example: the Perian codec pack for MacOS brakes the
play out of 'ARAW' coded avi files including avi files generated by
ImageJ).

Picking a codec is a complex issue and there is no easy choice.  It is
something worth discussing with a specialist to make the best decision
for your situation.

--
Mathieu Marchand
--
Bio-Imaging Resource Center, The Rockefeller University
1230 York Avenue, box 209, New York, NY 10021
http://www.rockefeller.edu/bioimaging .
+1-212-327-7487 (7489 for fax)
http://www.pfid.org/html/ppms_agree/?fr .


On Jan 25, 2008 12:30 PM, Stephen Bunnell <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> In follow up to my own post on the failure of old movies exported using the
> 'Apple Animation' codec:
>
> The defect is in Apple's new versions of Quicktime. Both Quicktime 7.3 and
> 7.4 fail to play these movies. After reinstalling my entire OS, with
> Quicktime 7.1.3 and OSX version 10.4.11, all of these movies now play
> perfectly. I've not tested Quicktime 7.2.
>
> As to a solution... I've heard nothing at all from Apple. I'm not going to
> upgrade Quicktime again for at least a year. My advice is to be very wary up
> performing any Quicktime upgrades before a presentation! The new versions
> (7.3 and 7.4 for the Mac) appear to have _many_ bugs, judging from the
> online discussions.
>
> Every other Mac-based player I tried failed in exactly the same way, despite
> many good suggestions from the list. Ultimately, I will need a Mac fix for
> Quicktime, or else I will have to re-export thousands of movies...
>
>      -Thanks for all your advice.
>
>
>
>
>
> On 1/18/08 2:43 PM, "Stephen C. Bunnell" <[hidden email]> wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > This is not technically a microscopy question, but I'm desperate:
> >
> > I use a mac. I have hundreds, if not thousands, of videos exported into .mpg
> > and .mov formats over many years of imaging.
> >
> > Of late, I have noticed that _many_ of my older .mov files are seriously
> > corrupted on the Mac. It's not the data. Archived movies are the same. It's
> > the player- Quicktime. It no longer can play the old movies. However, 2-3
> > years ago, before this problem was widespread, we exported several .mov
> > files to .avi. These .avi movies (fortunately) play just fine. However,
> > attempt to export the corrupted .mov files now yield .avi files that look
> > just like the .mov files- that is to say, they look like garbage.
> >
> > I have attempted to revert to older versions of quicktime- all the way to
> > v7.3. No luck. They're still corrupted.
> >
> > The corruption is not a computer issue. The same movies are corrupted on
> > many others Macs with current system installations.
> >
> > As you might expect, this makes for less than stellar presentations, when
> > half of your movies crash.
> >
> > Oddly, some movies exported on the same day, using the same software, will
> > play, and others will not.
> >
> > Has anyone else encountered this problem on the Mac? Any thoughts?
> >
> >     --Steve
> >
> >
> >
> > ****************************************************************************
> > Stephen C. Bunnell, Ph.D.
> > Assistant Professor
> > Tufts University Medical School
> > Department of Pathology
> > Jaharis Bldg., Room 512
> > 150 Harrison Ave.
> > Boston, MA 02111
> >
> > Phone: (617) 636-2174
> > Fax:   (617) 636-2990
> > Email: [hidden email]
> >
> > SHIPPING ADDRESS (for packages):
> > Tufts University Receiving
> > 37 Tyler St.
> > Attn: Bunnell/Pathology/Jaharis 524
> > Boston, MA 02111
>
> ****************************************************************************
> Stephen C. Bunnell, Ph.D.
> Assistant Professor
> Tufts University Medical School
> Department of Pathology
> Jaharis Bldg., Room 512
> 150 Harrison Ave.
> Boston, MA 02111
>
> Phone: (617) 636-2174
> Fax:   (617) 636-2990
> Email: [hidden email]
>
> SHIPPING ADDRESS (for packages):
> Tufts University Receiving
> 37 Tyler St.
> Attn: Bunnell/Pathology/Jaharis 524
> Boston, MA 02111
>
Stephen Bunnell Stephen Bunnell
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Re: Movie Corruption Issue & Codecs

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I agree that my short-term solution poses a security risk, but the inability
to play my archived movies had effectively deleted my work product from
1999-2004. This was not recoverable without reinstalling an earlier version
of the OS in order to downgrade Quicktime. Obviously, this is not the best
strategy.

Apple explicitly advertises legacy support for _all_ previous Quicktime
codecs. This is an extremely appealing feature when legacy access to old
scientific data is at issue. However, this is currently false. If Apple
intends to discontinue/disable old codecs, they should make this apparent in
the upgrade notes, so that users may convert their movies _before_ their
ability to convert them is deleted.

I cannot imagine any sane individual who would enjoy the prospect of
retroactively re-encoding 5 years worth of compiled imaging data solely to
maintain legacy access.

So, I seek advice: Are there industry-standard lossless codecs that are
expected to be supported for 10-20 years? What are the best options for
long-term storage of imaging data? What resources are available that discuss
the costs and benefits of various formats vis a vis scientific data?

    Best regards,

    Steve Bunnell

 



On 1/25/08 1:16 PM, "Mathieu Marchand" <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> To comment the previous post,
>
> Everybody should be aware that using any other version than the latest
> available Quicktime is a major security risk, on both Mac and Windows.
>
> The last 7.3, 7.3.1 and 7.4 updates of Quicktime corrected some CRITICAL
> flaws:
> http://secunia.com/advisories/28502/
> http://secunia.com/advisories/28092/
> http://secunia.com/advisories/27755/
> http://secunia.com/advisories/27523/
> and these are the flaws for only the past 3 months
>
> These flaws are rated "extremely critical" and could give an attacker
> remote access on your system just by visiting a malicious website with
> your favorite browser.
> Since Quicktime 7.2 and later does not support Windows 2000 any more,
> I recommend to uninstall Quicktime on computers running Windows 2000.
>
> Support for old codecs like "animation" for quicktime or "cinepak" for
> vista is broken or problematic and people should stop using them, and
> plan to convert old movies to more recent codec. "Codec Packs" can
> sometimes solve your problem, but they usually have major stability /
> legality / security risks attached to them. They can introduce new
> problems, too (for example: the Perian codec pack for MacOS brakes the
> play out of 'ARAW' coded avi files including avi files generated by
> ImageJ).
>
> Picking a codec is a complex issue and there is no easy choice.  It is
> something worth discussing with a specialist to make the best decision
> for your situation.

****************************************************************************
Stephen C. Bunnell, Ph.D.
Assistant Professor
Tufts University Medical School
Department of Pathology
Jaharis Bldg., Room 512
150 Harrison Ave.
Boston, MA 02111

Phone: (617) 636-2174
Fax:   (617) 636-2990
Email: [hidden email]

SHIPPING ADDRESS (for packages):
Tufts University Receiving
37 Tyler St.
Attn: Bunnell/Pathology/Jaharis 524
Boston, MA 02111
Greg Martin-8 Greg Martin-8
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Re: Movie Corruption Issue & Codecs

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hey Folks --
 
    Steve, I know this doesn't help you with your problem, but I guess the advice I'd throw out for long term storage would be to always keep the original data -- I'm assuming that the images were not collected directly as a movie file.  If you have a series of tiffs you can always re-make the movie with a current codec.  Sure they take up space, but so what -- I learned and took to heart the mantra "film is cheap and time isn't" and now I teach that digital storage space is cheap, and time still isn't.
 
Be peace!  Greg.
 
Greg Martin
Keck Microscopy Facility
University of Washington
Box 357290
Seattle, WA 98195-7290
206-685-8784 (office)
425-344-2632 (cell)
www.depts.washington.edu/keck
----- Original Message -----
From: "Stephen Bunnell" <[hidden email]>
Sent: Friday, January 25, 2008 1:32 PM
Subject: Re: Movie Corruption Issue & Codecs

> Search the CONFOCAL archive at
>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>

> I agree that my short-term solution poses a security risk, but the inability
> to play my archived movies had effectively deleted my work product from
> 1999-2004. This was not recoverable without reinstalling an earlier version
> of the OS in order to downgrade Quicktime. Obviously, this is not the best
> strategy.
>
> Apple explicitly advertises legacy support for _all_ previous Quicktime
> codecs. This is an extremely appealing feature when legacy access to old
> scientific data is at issue. However, this is currently false. If Apple
> intends to discontinue/disable old codecs, they should make this apparent in
> the upgrade notes, so that users may convert their movies _before_ their
> ability to convert them is deleted.
>
> I cannot imagine any sane individual who would enjoy the prospect of
> retroactively re-encoding 5 years worth of compiled imaging data solely to
> maintain legacy access.
>
> So, I seek advice: Are there industry-standard lossless codecs that are
> expected to be supported for 10-20 years? What are the best options for
> long-term storage of imaging data? What resources are available that discuss
> the costs and benefits of various formats vis a vis scientific data?
>
>    Best regards,
>
>    Steve Bunnell
>

>
>
>
> On 1/25/08 1:16 PM, "Mathieu Marchand" <
[hidden email]> wrote:
>
>> Search the CONFOCAL archive at
>>
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> To comment the previous post,
>>
>> Everybody should be aware that using any other version than the latest
>> available Quicktime is a major security risk, on both Mac and Windows.
>>
>> The last 7.3, 7.3.1 and 7.4 updates of Quicktime corrected some CRITICAL
>> flaws:
>>
http://secunia.com/advisories/28502/
>> http://secunia.com/advisories/28092/
>> http://secunia.com/advisories/27755/
>> http://secunia.com/advisories/27523/
>> and these are the flaws for only the past 3 months

>>
>> These flaws are rated "extremely critical" and could give an attacker
>> remote access on your system just by visiting a malicious website with
>> your favorite browser.
>> Since Quicktime 7.2 and later does not support Windows 2000 any more,
>> I recommend to uninstall Quicktime on computers running Windows 2000.
>>
>> Support for old codecs like "animation" for quicktime or "cinepak" for
>> vista is broken or problematic and people should stop using them, and
>> plan to convert old movies to more recent codec. "Codec Packs" can
>> sometimes solve your problem, but they usually have major stability /
>> legality / security risks attached to them. They can introduce new
>> problems, too (for example: the Perian codec pack for MacOS brakes the
>> play out of 'ARAW' coded avi files including avi files generated by
>> ImageJ).
>>
>> Picking a codec is a complex issue and there is no easy choice.  It is
>> something worth discussing with a specialist to make the best decision
>> for your situation.
>
> ****************************************************************************
> Stephen C. Bunnell, Ph.D.
> Assistant Professor
> Tufts University Medical School
> Department of Pathology
> Jaharis Bldg., Room 512
> 150 Harrison Ave.
> Boston, MA 02111
>
> Phone: (617) 636-2174
> Fax:   (617) 636-2990
> Email:
[hidden email]
>
> SHIPPING ADDRESS (for packages):
> Tufts University Receiving
> 37 Tyler St.
> Attn: Bunnell/Pathology/Jaharis 524
> Boston, MA 02111
>
Urs Utzinger Urs Utzinger
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Re: Movie Corruption Issue & Codecs

In reply to this post by Stephen Bunnell
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I suggest well documented standards such as MPEG4 and JPEG2000.

Open source encoders such as Xvid or x264 where you have access to the
software code might be useful, however once the movie is encoded any player
adhering to the standard can decode it. The encoders differ in their ability
to compress and maintain quality but store data into a standard format.

Open source decoders are available for both MPEG4 and JPEG2000. It is likely
that in 20 years you will still find example source code.

Lossless encoding is often not entirely lossless and testing if a particular
configuration really did not change a single bit is time consuming.

Making a ZIP archive of the original data seems to be the way to go.

You might also want to check virtual machines such as VMWare where you can
build a virtual computer (appliance) that has all your image processing
software installed and at later time you can run it on another computer and
redo your analysis. The advantage would be that you can archive your virtual
computer and revive it in the future when there is no support for it anymore
(assuming a program playing your virtual machine still exists). There are
programs that create a virtual machine from a real hardware installed
operating system.

Urs Utzinger
University of Arizona


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Stephen Bunnell
Sent: Friday, January 25, 2008 2:32 PM
To: [hidden email]
Subject: Re: Movie Corruption Issue & Codecs

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I agree that my short-term solution poses a security risk, but the inability
to play my archived movies had effectively deleted my work product from
1999-2004. This was not recoverable without reinstalling an earlier version
of the OS in order to downgrade Quicktime. Obviously, this is not the best
strategy.

Apple explicitly advertises legacy support for _all_ previous Quicktime
codecs. This is an extremely appealing feature when legacy access to old
scientific data is at issue. However, this is currently false. If Apple
intends to discontinue/disable old codecs, they should make this apparent in
the upgrade notes, so that users may convert their movies _before_ their
ability to convert them is deleted.

I cannot imagine any sane individual who would enjoy the prospect of
retroactively re-encoding 5 years worth of compiled imaging data solely to
maintain legacy access.

So, I seek advice: Are there industry-standard lossless codecs that are
expected to be supported for 10-20 years? What are the best options for
long-term storage of imaging data? What resources are available that discuss
the costs and benefits of various formats vis a vis scientific data?

    Best regards,

    Steve Bunnell

 



On 1/25/08 1:16 PM, "Mathieu Marchand" <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> To comment the previous post,
>
> Everybody should be aware that using any other version than the latest
> available Quicktime is a major security risk, on both Mac and Windows.
>
> The last 7.3, 7.3.1 and 7.4 updates of Quicktime corrected some CRITICAL
> flaws:
> http://secunia.com/advisories/28502/
> http://secunia.com/advisories/28092/
> http://secunia.com/advisories/27755/
> http://secunia.com/advisories/27523/
> and these are the flaws for only the past 3 months
>
> These flaws are rated "extremely critical" and could give an attacker
> remote access on your system just by visiting a malicious website with
> your favorite browser.
> Since Quicktime 7.2 and later does not support Windows 2000 any more,
> I recommend to uninstall Quicktime on computers running Windows 2000.
>
> Support for old codecs like "animation" for quicktime or "cinepak" for
> vista is broken or problematic and people should stop using them, and
> plan to convert old movies to more recent codec. "Codec Packs" can
> sometimes solve your problem, but they usually have major stability /
> legality / security risks attached to them. They can introduce new
> problems, too (for example: the Perian codec pack for MacOS brakes the
> play out of 'ARAW' coded avi files including avi files generated by
> ImageJ).
>
> Picking a codec is a complex issue and there is no easy choice.  It is
> something worth discussing with a specialist to make the best decision
> for your situation.

****************************************************************************
Stephen C. Bunnell, Ph.D.
Assistant Professor
Tufts University Medical School
Department of Pathology
Jaharis Bldg., Room 512
150 Harrison Ave.
Boston, MA 02111

Phone: (617) 636-2174
Fax:   (617) 636-2990
Email: [hidden email]

SHIPPING ADDRESS (for packages):
Tufts University Receiving
37 Tyler St.
Attn: Bunnell/Pathology/Jaharis 524
Boston, MA 02111
12