Stack Problem on Vista/Bioimageformats

[Robert Baer]

I have been experiencing some strange behavior when opening .zvi phase z-stacks with ImageJ 1.43b on a Vista Machine.  The individual frames of the stack have scrambled squares that each represent a small fraction of the normal image, but with no particular order to the squares.  The squares repeat maybe 4 times and don't together  represent the entire image.  Scrolling through the stack causes the frames to progress through the z-plane focus, but each frame is made of scrambled squares.

Strangely, the (mis)behavior is not 100% consistent.  I can occasionaly get the stacks to open like normal stacks.   I have superstiously attributed this "normalcy" to running ImageJ update, opening as a hyperstack, rebooting the computer, but in the end, none of thes seem to produce a consistent fix.  

The version of ImageJ that is doing this was downloaded from MacBiophotonics site.  I have installed and reinstalled this to no avail.  Interesting, I have an older imageJ on the same machine that will open the same Image Stack completely normally even as the MacBiophotonics 1.43b version is stuggling.

Of course this could be a pure Vista or Video driver problem, but I am at a loss as to how to debug the problem.   Any suggestions or ideas why this is happening?

Thanks

Rob

---------------------
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicne
A. T. Still University of Health Sciences
800 W. Jefferson St.
Kirksville, MO 63501

[Robert Baer]

I tried Wayne's suggestion of updating LOCI using both today's daily build
and the 2008 stable build to no avail.

I have the following behavior that may provide the more knowledge with
insight.  If I load a .zvi  image stack into ImageJ with load into Image5D
selected instead of standard ImageJ selected I still get the scambled image
displayed. If I now switch from grayscale to ovl on the right the first
frame of the stack is displayed completely properly.  If I now move the
z-slider to a subsequent frame, I get a scrambled view of that frame.
Moving to color or grayscale and back to ovl make this subsequent frame
appear normally.  Finally, moving the slider back to frame1 produces a
scrambled view of Frame1.  After using the ovl trick to get a normal image,
performing other ImageJ operations such as Image->Adjust->Brightness and
contrast causes the frame to scramble.

Any additional insights.

Thanks,
Rob

----- Original Message -----
From: "Robert W. Baer, Ph.D." <[hidden email]>
To: <[hidden email]>
Sent: Wednesday, July 08, 2009 11:48 AM
Subject: Stack Problem on Vista/Bioimageformats


I have been experiencing some strange behavior when opening .zvi phase
z-stacks with ImageJ 1.43b on a Vista Machine.  The individual frames of the
stack have scrambled squares that each represent a small fraction of the
normal image, but with no particular order to the squares.  The squares
repeat maybe 4 times and don't together  represent the entire image.
Scrolling through the stack causes the frames to progress through the
z-plane focus, but each frame is made of scrambled squares.

Strangely, the (mis)behavior is not 100% consistent.  I can occasionaly get
the stacks to open like normal stacks.   I have superstiously attributed
this "normalcy" to running ImageJ update, opening as a hyperstack, rebooting
the computer, but in the end, none of thes seem to produce a consistent fix.

The version of ImageJ that is doing this was downloaded from MacBiophotonics
site.  I have installed and reinstalled this to no avail.  Interesting, I
have an older imageJ on the same machine that will open the same Image Stack
completely normally even as the MacBiophotonics 1.43b version is stuggling.

Of course this could be a pure Vista or Video driver problem, but I am at a
loss as to how to debug the problem.   Any suggestions or ideas why this is
happening?

Thanks

Rob

---------------------
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicne
A. T. Still University of Health Sciences
800 W. Jefferson St.
Kirksville, MO 63501

[ctrueden]

Hi Rob,

Does the behavior happen with only ZVI files, or with all images in ImageJ?
(Try File > Open Samples) If all images, I am inclined to agree that it
might be a bug with your video hardware. You can turn down the video's
hardware acceleration (
http://www.pixelmetrics.com/Tips/VidBlank/GlobalAcceleration.php) to see if
that helps.

Another thing to try: if you double-click on loci_tools.jar, it should
launch an ImageViewer application. Choose File > Open from the menu, and
open your ZVI. Does it look scrambled there? If so, it is probably a bug in
Bio-Formats, in which case we would like to obtain a sample nonworking
dataset from you, so that we can fix the problem. If you are willing to send
us a file but need somewhere to upload, let us know and we will pass along
our FTP server information.

-Curtis

On Wed, Jul 8, 2009 at 5:46 PM, Robert W. Baer, Ph.D. <[hidden email]>wrote:

> I tried Wayne's suggestion of updating LOCI using both today's daily build
> and the 2008 stable build to no avail.
>
> I have the following behavior that may provide the more knowledge with
> insight.  If I load a .zvi  image stack into ImageJ with load into Image5D
> selected instead of standard ImageJ selected I still get the scambled image
> displayed. If I now switch from grayscale to ovl on the right the first
> frame of the stack is displayed completely properly.  If I now move the
> z-slider to a subsequent frame, I get a scrambled view of that frame. Moving
> to color or grayscale and back to ovl make this subsequent frame appear
> normally.  Finally, moving the slider back to frame1 produces a scrambled
> view of Frame1.  After using the ovl trick to get a normal image, performing
> other ImageJ operations such as Image->Adjust->Brightness and contrast
> causes the frame to scramble.
>
> Any additional insights.
>
> Thanks,
> Rob
>
> ----- Original Message ----- From: "Robert W. Baer, Ph.D." <[hidden email]
> >
> To: <[hidden email]>
> Sent: Wednesday, July 08, 2009 11:48 AM
> Subject: Stack Problem on Vista/Bioimageformats
>
>
> I have been experiencing some strange behavior when opening .zvi phase
> z-stacks with ImageJ 1.43b on a Vista Machine.  The individual frames of the
> stack have scrambled squares that each represent a small fraction of the
> normal image, but with no particular order to the squares.  The squares
> repeat maybe 4 times and don't together  represent the entire image.
> Scrolling through the stack causes the frames to progress through the
> z-plane focus, but each frame is made of scrambled squares.
>
> Strangely, the (mis)behavior is not 100% consistent.  I can occasionaly get
> the stacks to open like normal stacks.   I have superstiously attributed
> this "normalcy" to running ImageJ update, opening as a hyperstack, rebooting
> the computer, but in the end, none of thes seem to produce a consistent fix.
>
> The version of ImageJ that is doing this was downloaded from
> MacBiophotonics site.  I have installed and reinstalled this to no avail.
>  Interesting, I have an older imageJ on the same machine that will open the
> same Image Stack completely normally even as the MacBiophotonics 1.43b
> version is stuggling.
>
> Of course this could be a pure Vista or Video driver problem, but I am at a
> loss as to how to debug the problem.   Any suggestions or ideas why this is
> happening?
>
> Thanks
>
> Rob
>
> ---------------------
> Robert W. Baer, Ph.D.
> Professor of Physiology
> Kirksville College of Osteopathic Medicne
> A. T. Still University of Health Sciences
> 800 W. Jefferson St.
> Kirksville, MO 63501
>

[Robert Baer]

Thanks Curtis.  At Wayne's suggestion, I traced the problem to Java
malfunction  and the Jave distributed with MBF.  Here is the resolution
summary I sent Wayne.

I have  an NVidia GEForce 6150SE video adaptor.  The driver is 7.15.11.7516
datated 5-2-2008 and according to an "update check" is current.  This leaves
Java.

Summary:
The MBF ImageJ was running version 1.43c with Java 1.6.0_10-rc (32-bit)
(from the JRE file in ImageJ directory) and produces scrambled slices on the
z-stack.  This Java is presumably part of the MBF Windows installation
package.

The older ImageJ is 1.40g with Java 1.6.0_05 again installed in the JRE
directory of ImageJ.  The plugin folder was a copy from the MBF folder
above.  It opens .zvi z-stacks fine.

The 32-bit windows Vista Machine had a native JAVA installation of 1.6.0.11.
Upon removing the JRE files from the MBF ImageJ folder, MBF ImageJ reverted,
as expedted, to using the Java 1.6.0_11 (32-bit) installed on the system.
The .zvi stack files are now apparently opening correctly with properly
rendered slices.

----- Original Message -----
From: "Curtis Rueden" <[hidden email]>
To: <[hidden email]>
Sent: Thursday, July 09, 2009 5:45 PM
Subject: Re: more info - Vista/Bioimageformats

> Hi Rob,
>
> Does the behavior happen with only ZVI files, or with all images in
> ImageJ?
> (Try File > Open Samples) If all images, I am inclined to agree that it
> might be a bug with your video hardware. You can turn down the video's
> hardware acceleration (
> http://www.pixelmetrics.com/Tips/VidBlank/GlobalAcceleration.php) to see
> if
> that helps.
>
> Another thing to try: if you double-click on loci_tools.jar, it should
> launch an ImageViewer application. Choose File > Open from the menu, and
> open your ZVI. Does it look scrambled there? If so, it is probably a bug
> in
> Bio-Formats, in which case we would like to obtain a sample nonworking
> dataset from you, so that we can fix the problem. If you are willing to
> send
> us a file but need somewhere to upload, let us know and we will pass along
> our FTP server information.
>
> -Curtis
>
> On Wed, Jul 8, 2009 at 5:46 PM, Robert W. Baer, Ph.D.
> <[hidden email]>wrote:
>
>> I tried Wayne's suggestion of updating LOCI using both today's daily
>> build
>> and the 2008 stable build to no avail.
>>
>> I have the following behavior that may provide the more knowledge with
>> insight.  If I load a .zvi  image stack into ImageJ with load into
>> Image5D
>> selected instead of standard ImageJ selected I still get the scambled
>> image
>> displayed. If I now switch from grayscale to ovl on the right the first
>> frame of the stack is displayed completely properly.  If I now move the
>> z-slider to a subsequent frame, I get a scrambled view of that frame.
>> Moving
>> to color or grayscale and back to ovl make this subsequent frame appear
>> normally.  Finally, moving the slider back to frame1 produces a scrambled
>> view of Frame1.  After using the ovl trick to get a normal image,
>> performing
>> other ImageJ operations such as Image->Adjust->Brightness and contrast
>> causes the frame to scramble.
>>
>> Any additional insights.
>>
>> Thanks,
>> Rob
>>
>> ----- Original Message ----- From: "Robert W. Baer, Ph.D."
>> <[hidden email]
>> >
>> To: <[hidden email]>
>> Sent: Wednesday, July 08, 2009 11:48 AM
>> Subject: Stack Problem on Vista/Bioimageformats
>>
>>
>> I have been experiencing some strange behavior when opening .zvi phase
>> z-stacks with ImageJ 1.43b on a Vista Machine.  The individual frames of
>> the
>> stack have scrambled squares that each represent a small fraction of the
>> normal image, but with no particular order to the squares.  The squares
>> repeat maybe 4 times and don't together  represent the entire image.
>> Scrolling through the stack causes the frames to progress through the
>> z-plane focus, but each frame is made of scrambled squares.
>>
>> Strangely, the (mis)behavior is not 100% consistent.  I can occasionaly
>> get
>> the stacks to open like normal stacks.   I have superstiously attributed
>> this "normalcy" to running ImageJ update, opening as a hyperstack,
>> rebooting
>> the computer, but in the end, none of thes seem to produce a consistent
>> fix.
>>
>> The version of ImageJ that is doing this was downloaded from
>> MacBiophotonics site.  I have installed and reinstalled this to no avail.
>>  Interesting, I have an older imageJ on the same machine that will open
>> the
>> same Image Stack completely normally even as the MacBiophotonics 1.43b
>> version is stuggling.
>>
>> Of course this could be a pure Vista or Video driver problem, but I am at
>> a
>> loss as to how to debug the problem.   Any suggestions or ideas why this
>> is
>> happening?
>>
>> Thanks
>>
>> Rob
>>
>> ---------------------
>> Robert W. Baer, Ph.D.
>> Professor of Physiology
>> Kirksville College of Osteopathic Medicne
>> A. T. Still University of Health Sciences
>> 800 W. Jefferson St.
>> Kirksville, MO 63501
>>
>