.oib to DICOM?

[edenm]

Hi all,

I need to convert a .oib (off of an Olympus Fluoview) z-stack into a DICOM file for analysis. If that is not possible, I need it in another file format besides .oib so that a collaborator of mine (who usually works with DICOM but is not familiar with .oib) can analyze the pixel data. He didn't specify a particular file format, so I imagine there are a number of formats that might work for what he needs?

Thanks in advance for your help!

[ctrueden]

Hi Eden,

> I need to convert a .oib (off of an Olympus Fluoview) z-stack into a
> DICOM file for analysis.

You can read OIB files using the Bio-Formats Importer plugin:
    http://imagej.net/Bio-Formats

You can save to DICOM using the Tudor DICOM tools. See:
    http://imagej.net/DICOM#How_to_save_DICOM_files_from_ImageJ.3F

The easiest way to get Bio-Formats is to use the Fiji distribution of
ImageJ:
    http://fiji.sc/

But you will need to install the Tudor DICOM tools manually.

Alternately, you could save to one of the supported open formats such as
TIFF.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Apr 11, 2016 at 4:32 PM, edenm <[hidden email]> wrote:

> Hi all,
>
> I need to convert a .oib (off of an Olympus Fluoview) z-stack into a DICOM
> file for analysis. If that is not possible, I need it in another file
> format
> besides .oib so that a collaborator of mine (who usually works with DICOM
> but is not familiar with .oib) can analyze the pixel data. He didn't
> specify
> a particular file format, so I imagine there are a number of formats that
> might work for what he needs?
>
> Thanks in advance for your help!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/oib-to-DICOM-tp5016100.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[edenm]

Thanks!  I use Fiji and have had no problems reading the .oib files. I found that Tudor DICOM plugin previously, but I have not been able to figure out how to actually save my file as a DICOM using it. (Save as -> Save DICOM, does nothing). Perhaps the plugin did not install correctly? I have not been able to find any other literature on the Tudor plugin about how to save as a DICOM.

If you don't mind, could you give more specific instructions on how to save as a DICOM using the Tudor plugin?

Thanks!

E

[Kenneth Sloan-2]

When I tried to install the Tudor DICOM tools, I got a flurry of “duplicate name” errors.
I would also appreciate *specific* instructions on how to install, and how to avoid name conflicts.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Apr 14, 2016, at 11:00 , edenm <[hidden email]> wrote:
>
> Thanks!  I use Fiji and have had no problems reading the .oib files. I found
> that Tudor DICOM plugin previously, but I have not been able to figure out
> how to actually save my file as a DICOM using it. (Save as -> Save DICOM,
> does nothing). Perhaps the plugin did not install correctly? I have not been
> able to find any other literature on the Tudor plugin about how to save as a
> DICOM.
>
> If you don't mind, could you give more specific instructions on how to save
> as a DICOM using the Tudor plugin?
>
> Thanks!
>
> E
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/oib-to-DICOM-tp5016100p5016138.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Eden & Kenneth,

> could you give more specific instructions on how to save as a DICOM
> using the Tudor plugin?

Since saving as DICOM—and hence, setting up the Tudor DICOM Tools—is a
perennial question in the ImageJ community, I am CCing the authors of that
plugin suite, inviting them to set up an ImageJ update site that provides
this work to users in a more accessible and convenient way.

Andreas, Christian, Johannes: I think a Tudor/LIST update site would be
really helpful for users. As things stand, installing the Tudor DICOM Tools
into ImageJ2 is very challenging due to all the dependency issues. So I
warmly offer my assistance in creating such an update site: if you need any
advice on it, post on the ImageJ Forum (http://forum.imagej.net/) and we
will be happy to help overcome any roadblocks!

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Apr 15, 2016 at 12:19 AM, Kenneth Sloan <[hidden email]>
wrote:

> When I tried to install the Tudor DICOM tools, I got a flurry of
> “duplicate name” errors.
> I would also appreciate *specific* instructions on how to install, and how
> to avoid name conflicts.
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
> > On Apr 14, 2016, at 11:00 , edenm <[hidden email]> wrote:
> >
> > Thanks!  I use Fiji and have had no problems reading the .oib files. I
> found
> > that Tudor DICOM plugin previously, but I have not been able to figure
> out
> > how to actually save my file as a DICOM using it. (Save as -> Save DICOM,
> > does nothing). Perhaps the plugin did not install correctly? I have not
> been
> > able to find any other literature on the Tudor plugin about how to save
> as a
> > DICOM.
> >
> > If you don't mind, could you give more specific instructions on how to
> save
> > as a DICOM using the Tudor plugin?
> >
> > Thanks!
> >
> > E
> >
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/oib-to-DICOM-tp5016100p5016138.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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