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problem opening fluoview 1000 linescan files

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kjiremon

problem opening fluoview 1000 linescan files

Hi,
When I try to open linescan files (.oib) acquired in Olympus Fluoview 1000, ImageJ will open a file with pixel values for the first scanned line but no data for the other subsequent lines.
Do I need to do something special when importing these file types? I use the bio-formats importer for other types of fluoview obi files and it seems to work fine.

Thanks

Karl

Melissa Linkert-2

Re: problem opening fluoview 1000 linescan files

Hi Karl,

Which version of Bio-Formats are you using? The two most recent
stable versions (4.1 and 4.1.1) should display linescan files in the
same way that Olympus' software does, i.e. a single plane represents
the entire scan. You can see which version of Bio-Formats is
installed by selecting "Help > About Plugins > LOCI Plugins".

If you are using a version prior to 4.1, then I would recommend that
you update to the latest stable version. If you still see the problem
with 4.1.1, then it would be very helpful if you could send one of the
problematic files and a list of any options that you have checked in
the Bio-Formats import options window.

Regards,
-Melissa

On Wed, Jun 2, 2010 at 10:41 PM, kjiremon <[hidden email]> wrote:

> Hi,
> When I try to open linescan files (.oib) acquired in Olympus Fluoview 1000,
> ImageJ will open a file with pixel values for the first scanned line but no
> data for the other subsequent lines.
> Do I need to do something special when importing these file types? I use the
> bio-formats importer for other types of fluoview obi files and it seems to
> work fine.
>
> Thanks
>
> Karl
>
> --
> View this message in context: http://imagej.588099.n2.nabble.com/problem-opening-fluoview-1000-linescan-files-tp5133617p5133617.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

kjiremon

Re: problem opening fluoview 1000 linescan files

Thanks Melissa,
I was using Bio-formats 4.1, however, updating to the newest version did not fix my problem.
You mentioned that Bio-formats should present the linescan files the same way fluoview does, however, when I open them, ImageJ is presenting them like z-stacks.
I have tried every possible combination of import options and none seem to fix the issue.
I have attached a line scan file to see if you have the same issue (if it does not attach, please send me your email and I will send it to you directly- I am karl.iremonger@gmail.com)

Thanks again,
Karl

Image0009.oib

Melissa Linkert-2

Re: problem opening fluoview 1000 linescan files

Hi Karl,

Thank you for sending an example file. I was able to duplicate the
problem; the trunk build has been updated to fix the problem, so this
file should display correctly if you upgrade to the very latest build.

Regards,
-Melissa

On Mon, Jun 7, 2010 at 7:00 PM, kjiremon <[hidden email]> wrote:

> Thanks Melissa,
> I was using Bio-formats 4.1, however, updating to the newest version did not
> fix my problem.
> You mentioned that Bio-formats should present the linescan files the same
> way fluoview does, however, when I open them, ImageJ is presenting them like
> z-stacks.
> I have tried every possible combination of import options and none seem to
> fix the issue.
> I have attached a line scan file to see if you have the same issue (if it
> does not attach, please send me your email and I will send it to you
> directly- I am [hidden email])
>
> Thanks again,
> Karl
>
> http://imagej.588099.n2.nabble.com/file/n5151646/Image0009.oib Image0009.oib
> --
> View this message in context: http://imagej.588099.n2.nabble.com/problem-opening-fluoview-1000-linescan-files-tp5133617p5151646.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

Anda Cornea

Re: drag and drop for BioFormats

First, I want to express my gratitude to the BioFormats people, my life as a confocal (Leica and Zeiss) user is much better because of you.

Now, on one computer, it is slightly better than the others: bio-formats may be opened by dragging and dropping .lif files on the Image J icon. On the others I have to open the Bio-formats from the Plugins menu. I cannot find the difference. Drag and drop for .tif files works equally well on all computers (WindowsXP) in the lab.

Please help!

With thanks,

Anda

Anda Cornea, Ph.D.
Director of the Imaging Core
Oregon National Primate Research Center
Oregon Heath & Science University
503-690-5293

Melissa Linkert-2

Re: drag and drop for BioFormats

Hi Anda,

The first thing to do is make sure that the computer on which
drag-and-drop doesn't work has a version of ImageJ that is equal to or
greater than the version of ImageJ installed on the working computer.

If the problem still occurs when both computers have the same version
of ImageJ, then check both ImageJ plugins folders for a file named
'HandleExtraFileTypes.class'. If that file is present in the working
computer's plugins folder and missing from the non-working computer's
plugins folder, then simply adding the file to the non-working plugins
folder should solve the problem. If necessary, you can download the
file here: http://rsb.info.nih.gov/ij/plugins/file-handler.html.

If neither of the above solves the problem, then the last thing to
check is that both computers have the same version of Bio-Formats
installed. You can check which version is installed by selecting
"Help > About Plugins > LOCI Plugins".

Finally, there is an alternate method of dragging and dropping files,
assuming that you always want Bio-Formats to open your files. If you
select "Plugins > LOCI Plugins > LOCI Plugins Shortcut Window", you
should see a new window pop up; if you drag and drop files onto this
window, they should open using Bio-Formats.

Regards,
-Melissa

On Tue, Jun 8, 2010 at 1:51 PM, Anda Cornea <[hidden email]> wrote:

> First, I want to express my gratitude to the BioFormats people, my life as a confocal (Leica and Zeiss) user is much better because of you.
>
> Now, on one computer, it is slightly better than the others: bio-formats may be opened by dragging and dropping .lif files on the Image J icon. On the others I have to open the Bio-formats from the Plugins menu. I cannot find the difference. Drag and drop for .tif files works equally well on all computers (WindowsXP) in the lab.
>
> Please help!
>
> With thanks,
>
> Anda
>
> Anda Cornea, Ph.D.
> Director of the Imaging Core
> Oregon National Primate Research Center
> Oregon Heath & Science University
> 503-690-5293
>

Anda Cornea

Re: drag and drop for BioFormats

Melissa,

The ImageJ drag and drop working version was 1.42q. I installed it instead of 1.43n and indeed, it works. Life is good again.

Thank you so much again!
Anda

Anda Cornea, Ph.D.
Director of the Imaging Core
Oregon National Primate Research Center
Oregon Heath & Science University
503-690-5293

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Melissa Linkert
Sent: Tuesday, June 08, 2010 12:19 PM
To: [hidden email]
Subject: Re: drag and drop for BioFormats

Hi Anda,

The first thing to do is make sure that the computer on which
drag-and-drop doesn't work has a version of ImageJ that is equal to or
greater than the version of ImageJ installed on the working computer.

If the problem still occurs when both computers have the same version
of ImageJ, then check both ImageJ plugins folders for a file named
'HandleExtraFileTypes.class'. If that file is present in the working
computer's plugins folder and missing from the non-working computer's
plugins folder, then simply adding the file to the non-working plugins
folder should solve the problem. If necessary, you can download the
file here: http://rsb.info.nih.gov/ij/plugins/file-handler.html.

If neither of the above solves the problem, then the last thing to
check is that both computers have the same version of Bio-Formats
installed. You can check which version is installed by selecting
"Help > About Plugins > LOCI Plugins".

Finally, there is an alternate method of dragging and dropping files,
assuming that you always want Bio-Formats to open your files. If you
select "Plugins > LOCI Plugins > LOCI Plugins Shortcut Window", you
should see a new window pop up; if you drag and drop files onto this
window, they should open using Bio-Formats.

Regards,
-Melissa

On Tue, Jun 8, 2010 at 1:51 PM, Anda Cornea <[hidden email]> wrote:

Laura Lucia Prieto Godino

Re: drag and drop for BioFormats

Hi,
I actually have the same problem. I used to have installed an earlier
version in which i could drop my lif files into imgae j directly, but
when I installed the new version for mac 1.44a, it does not work
anymore. I have checked my plug in files and I do have the
'HandleExtraFileTypes.class' file. the version I have of the Bio-
formats it is said that it is 2007. Do you know how can I make it work
again?

thank you so much for your help!
lucia

Lucia Prieto Godino
PhD student.
Department of Zoology,
Downing street
University of Cambridge.
UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia

On 8 Jun 2010, at 20:38, Anda Cornea wrote:

> Melissa,
>
> The ImageJ drag and drop working version was 1.42q. I installed it
> instead of 1.43n and indeed, it works. Life is good again.
>
>
> Thank you so much again!
> Anda
>
>
> Anda Cornea, Ph.D.
> Director of the Imaging Core
> Oregon National Primate Research Center
> Oregon Heath & Science University
> 503-690-5293
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
> Of Melissa Linkert
> Sent: Tuesday, June 08, 2010 12:19 PM
> To: [hidden email]
> Subject: Re: drag and drop for BioFormats
>
> Hi Anda,
>
> The first thing to do is make sure that the computer on which
> drag-and-drop doesn't work has a version of ImageJ that is equal to or
> greater than the version of ImageJ installed on the working computer.
>
> If the problem still occurs when both computers have the same version
> of ImageJ, then check both ImageJ plugins folders for a file named
> 'HandleExtraFileTypes.class'. If that file is present in the working
> computer's plugins folder and missing from the non-working computer's
> plugins folder, then simply adding the file to the non-working plugins
> folder should solve the problem. If necessary, you can download the
> file here: http://rsb.info.nih.gov/ij/plugins/file-handler.html.
>
> If neither of the above solves the problem, then the last thing to
> check is that both computers have the same version of Bio-Formats
> installed. You can check which version is installed by selecting
> "Help > About Plugins > LOCI Plugins".
>
> Finally, there is an alternate method of dragging and dropping files,
> assuming that you always want Bio-Formats to open your files. If you
> select "Plugins > LOCI Plugins > LOCI Plugins Shortcut Window", you
> should see a new window pop up; if you drag and drop files onto this
> window, they should open using Bio-Formats.
>
> Regards,
> -Melissa
>
> On Tue, Jun 8, 2010 at 1:51 PM, Anda Cornea <[hidden email]> wrote:
>> First, I want to express my gratitude to the BioFormats people, my
>> life as a confocal (Leica and Zeiss) user is much better because of
>> you.
>>
>> Now, on one computer, it is slightly better than the others: bio-
>> formats may be opened by dragging and dropping .lif files on the
>> Image J icon. On the others I have to open the Bio-formats from
>> the Plugins menu. I cannot find the difference. Drag and drop
>> for .tif files works equally well on all computers (WindowsXP) in
>> the lab.
>>
>> Please help!
>>
>> With thanks,
>>
>> Anda
>>
>> Anda Cornea, Ph.D.
>> Director of the Imaging Core
>> Oregon National Primate Research Center
>> Oregon Heath & Science University
>> 503-690-5293
>>

W. Chan

Re: drag and drop for BioFormats

Hi Laura

You might have the version of the plugin that does not call Bio-Formats.
If you have the source (HandleExtraFileTypes.java), you can see if
Bio-Format Importer is ever used. The latest version of the plugin should
correct for that. You can check the history for what this plugin supports
or misses on the imagej website. Cheers.

http://rsb.info.nih.gov/ij/plugins/file-handler.html

On Tue, 8 Jun 2010, Laura Lucia Prieto Godino wrote:

> Hi,
> I actually have the same problem. I used to have installed an earlier version
> in which i could drop my lif files into imgae j directly, but when I installed
> the new version for mac 1.44a, it does not work anymore. I have checked my
> plug in files and I do have the 'HandleExtraFileTypes.class' file. the version
> I have of the Bio-formats it is said that it is 2007. Do you know how can I
> make it work again?
>
> thank you so much for your help!
> lucia
>
> Lucia Prieto Godino
> PhD student.
> Department of Zoology,
> Downing street
> University of Cambridge.
> UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia
>
> On 8 Jun 2010, at 20:38, Anda Cornea wrote:
>
> > Melissa,
> >
> > The ImageJ drag and drop working version was 1.42q. I installed it instead
> > of 1.43n and indeed, it works. Life is good again.
> >
> >
> > Thank you so much again!
> > Anda
> >
> >
> > Anda Cornea, Ph.D.
> > Director of the Imaging Core
> > Oregon National Primate Research Center
> > Oregon Heath & Science University
> > 503-690-5293
> >
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Melissa Linkert
> > Sent: Tuesday, June 08, 2010 12:19 PM
> > To: [hidden email]
> > Subject: Re: drag and drop for BioFormats
> >
> > Hi Anda,
> >
> > The first thing to do is make sure that the computer on which
> > drag-and-drop doesn't work has a version of ImageJ that is equal to or
> > greater than the version of ImageJ installed on the working computer.
> >
> > If the problem still occurs when both computers have the same version
> > of ImageJ, then check both ImageJ plugins folders for a file named
> > 'HandleExtraFileTypes.class'. If that file is present in the working
> > computer's plugins folder and missing from the non-working computer's
> > plugins folder, then simply adding the file to the non-working plugins
> > folder should solve the problem. If necessary, you can download the
> > file here: http://rsb.info.nih.gov/ij/plugins/file-handler.html.
> >
> > If neither of the above solves the problem, then the last thing to
> > check is that both computers have the same version of Bio-Formats
> > installed. You can check which version is installed by selecting
> > "Help > About Plugins > LOCI Plugins".
> >
> > Finally, there is an alternate method of dragging and dropping files,
> > assuming that you always want Bio-Formats to open your files. If you
> > select "Plugins > LOCI Plugins > LOCI Plugins Shortcut Window", you
> > should see a new window pop up; if you drag and drop files onto this
> > window, they should open using Bio-Formats.
> >
> > Regards,
> > -Melissa
> >
> > On Tue, Jun 8, 2010 at 1:51 PM, Anda Cornea <[hidden email]> wrote:
> > > First, I want to express my gratitude to the BioFormats people, my life as
> > > a confocal (Leica and Zeiss) user is much better because of you.
> > >
> > > Now, on one computer, it is slightly better than the others: bio-formats
> > > may be opened by dragging and dropping .lif files on the Image J icon. On
> > > the others I have to open the Bio-formats from the Plugins menu. I cannot
> > > find the difference. Drag and drop for .tif files works equally well on
> > > all computers (WindowsXP) in the lab.
> > >
> > > Please help!
> > >
> > > With thanks,
> > >
> > > Anda
> > >
> > > Anda Cornea, Ph.D.
> > > Director of the Imaging Core
> > > Oregon National Primate Research Center
> > > Oregon Heath & Science University
> > > 503-690-5293

--
Pang (Wai Pang Chan, [hidden email], PAB A087, 206-685-1519)
The Biology Imaging Facility (http://depts.washington.edu/if/)