confocal 3D image construction

[Santosh M]

Dear All

I have take images by using Z  stack in Olympus confocal microscope

All files are in OIB format

How can I construct 3D image by using image J.

Any suggestions are welcome.


शुभकामनायें/Best regards

Santosh

[rona baron]

Hi,

I use the OIF file format. convert the OIB file into OIF..

good luck
Rona

On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]> wrote:

> Dear All
>
> I have take images by using Z  stack in Olympus confocal microscope
>
> All files are in OIB format
>
> How can I construct 3D image by using image J.
>
> Any suggestions are welcome.
>
>
> शुभकामनायें/Best regards
>
> Santosh
>

[Santosh M]

Thank  you

But could please details of the image j plugin I have to install.

How can I convert Confocal OIB to OIF

regards

Santosh



On 25 March 2011 13:18, rona baron <[hidden email]> wrote:

> Hi,
>
> I use the OIF file format. convert the OIB file into OIF..
>
> good luck
> Rona
>
> On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]> wrote:
>
> > Dear All
> >
> > I have take images by using Z  stack in Olympus confocal microscope
> >
> > All files are in OIB format
> >
> > How can I construct 3D image by using image J.
> >
> > Any suggestions are welcome.
> >
> >
> > शुभकामनायें/Best regards
> >
> > Santosh
> >
>

--
शुभकामनायें/Best regards

Santosh

[Albert Cardona-2]

2011/3/25 Santosh M <[hidden email]>:
> Dear All
>
> I have take images by using Z  stack in Olympus confocal microscope
>
> All files are in OIB format
>
> How can I construct 3D image by using image J.
>
> Any suggestions are welcome.


Do you mean this:

  http://pacific.mpi-cbg.de/wiki/index.php/3D_Viewer

Albert

--
http://albert.rierol.net

[Glen MacDonald-2]

Dear Santosh,

First, you do not need to convert OIB to OIF.  The difference between the 2 formats is that the OIB is a single file while the OIF uses a text file to store metadata and a folder to store each image plane from each channel as a 16-bit tiff.  The text file 'filename.oif' must be kept with the folder 'filename.oif.files'.  The only advantage of the OIF is that if you don't have a means to read the OIB, the tiffs can always be imported from the OIF folder. Opening the OIF with software that can read the metadata requires selecting the filename.oif metadata file, not the folder.
ImageJ documentation is here:   http://imagej.nih.gov/ij/docs/
All plugins are installed by dragging into the /ImageJ/plugins directory and then restarting ImageJ.

Use this plugin to import import OIB, OIF and almost anything else, http://www.loci.wisc.edu/bio-formats/downloads and download the Loci-tools daily build.  Its documentation is builtin and appears as the cursor moves over the options.  Use the Custom color option to set your channels to correct color display if you want merged color.
You can use the 3D viewer plugin or  try the builtin Image>stacks>3D project... command.  Select maximum intensity and default settings to start (unless your file is really big then crop it first).   Again,go to the ImageJ documentation to see how the crop, duplicate and projection commands work.

Have fun,
Glen


Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]








On Mar 25, 2011, at 1:12 AM, Santosh M wrote:

> Thank  you
>
> But could please details of the image j plugin I have to install.
>
> How can I convert Confocal OIB to OIF
>
> regards
>
> Santosh
>
>
>
> On 25 March 2011 13:18, rona baron <[hidden email]> wrote:
>
>> Hi,
>>
>> I use the OIF file format. convert the OIB file into OIF..
>>
>> good luck
>> Rona
>>
>> On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]> wrote:
>>
>>> Dear All
>>>
>>> I have take images by using Z  stack in Olympus confocal microscope
>>>
>>> All files are in OIB format
>>>
>>> How can I construct 3D image by using image J.
>>>
>>> Any suggestions are welcome.
>>>
>>>
>>> शुभकामनायें/Best regards
>>>
>>> Santosh
>>>
>>
>
>
>
> --
> शुभकामनायें/Best regards
>
> Santosh

[rona baron]

Hi,

>How can I convert Confocal OIB to OIF

I guess that you are using the FLOUVIEW olympus software. To convert the
images right click on the OIB file and than a window will be opened with
some options.. one of them is "convert to OIF'





On Fri, Mar 25, 2011 at 10:12 AM, Santosh M <[hidden email]> wrote:

> Thank  you
>
> But could please details of the image j plugin I have to install.
>
> How can I convert Confocal OIB to OIF
>
> regards
>
> Santosh
>
>
>
> On 25 March 2011 13:18, rona baron <[hidden email]> wrote:
>
> > Hi,
> >
> > I use the OIF file format. convert the OIB file into OIF..
> >
> > good luck
> > Rona
> >
> > On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]>
> wrote:
> >
> > > Dear All
> > >
> > > I have take images by using Z  stack in Olympus confocal microscope
> > >
> > > All files are in OIB format
> > >
> > > How can I construct 3D image by using image J.
> > >
> > > Any suggestions are welcome.
> > >
> > >
> > > शुभकामनायें/Best regards
> > >
> > > Santosh
> > >
> >
>
>
>
> --
>  शुभकामनायें/Best regards
>
> Santosh
>

[Santosh M]

Dear Glen and Rona,


Thank you Glen for your inputs. Its working fine.
To Rona: I am using FV10-ASW 2.0 Viewer to convert these files.

regards

Santosh

On 27 March 2011 01:20, rona baron <[hidden email]> wrote:

> Hi,
>
> >How can I convert Confocal OIB to OIF
>
> I guess that you are using the FLOUVIEW olympus software. To convert the
> images right click on the OIB file and than a window will be opened with
> some options.. one of them is "convert to OIF'
>
>
>
>
>
> On Fri, Mar 25, 2011 at 10:12 AM, Santosh M <[hidden email]> wrote:
>
> > Thank  you
> >
> > But could please details of the image j plugin I have to install.
> >
> > How can I convert Confocal OIB to OIF
> >
> > regards
> >
> > Santosh
> >
> >
> >
> > On 25 March 2011 13:18, rona baron <[hidden email]> wrote:
> >
> > > Hi,
> > >
> > > I use the OIF file format. convert the OIB file into OIF..
> > >
> > > good luck
> > > Rona
> > >
> > > On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]>
> > wrote:
> > >
> > > > Dear All
> > > >
> > > > I have take images by using Z  stack in Olympus confocal microscope
> > > >
> > > > All files are in OIB format
> > > >
> > > > How can I construct 3D image by using image J.
> > > >
> > > > Any suggestions are welcome.
> > > >
> > > >
> > > > शुभकामनायें/Best regards
> > > >
> > > > Santosh
> > > >
> > >
> >
> >
> >
> > --
> >  शुभकामनायें/Best regards
> >
> > Santosh
> >
>

--
शुभकामनायें/Best regards

Santosh

[Santosh M]

Dear All,

Can I run  3D image (OIB file--Confocal) in video player like VLC
Its run only in FLUOVIEW...Can I convert some file so that I can view
in vlc player or any other media player

Thanks and regards

Santosh M

On 29 March 2011 09:36, Santosh M <[hidden email]> wrote:

> Dear Glen and Rona,
>
>
> Thank you Glen for your inputs. Its working fine.
> To Rona: I am using FV10-ASW 2.0 Viewer to convert these files.
>
> regards
>
> Santosh
>
>
> On 27 March 2011 01:20, rona baron <[hidden email]> wrote:
>>
>> Hi,
>>
>> >How can I convert Confocal OIB to OIF
>>
>> I guess that you are using the FLOUVIEW olympus software. To convert the
>> images right click on the OIB file and than a window will be opened with
>> some options.. one of them is "convert to OIF'
>>
>>
>>
>>
>>
>> On Fri, Mar 25, 2011 at 10:12 AM, Santosh M <[hidden email]> wrote:
>>
>> > Thank  you
>> >
>> > But could please details of the image j plugin I have to install.
>> >
>> > How can I convert Confocal OIB to OIF
>> >
>> > regards
>> >
>> > Santosh
>> >
>> >
>> >
>> > On 25 March 2011 13:18, rona baron <[hidden email]> wrote:
>> >
>> > > Hi,
>> > >
>> > > I use the OIF file format. convert the OIB file into OIF..
>> > >
>> > > good luck
>> > > Rona
>> > >
>> > > On Fri, Mar 25, 2011 at 9:31 AM, Santosh M <[hidden email]>
>> > wrote:
>> > >
>> > > > Dear All
>> > > >
>> > > > I have take images by using Z  stack in Olympus confocal microscope
>> > > >
>> > > > All files are in OIB format
>> > > >
>> > > > How can I construct 3D image by using image J.
>> > > >
>> > > > Any suggestions are welcome.
>> > > >
>> > > >
>> > > > शुभकामनायें/Best regards
>> > > >
>> > > > Santosh
>> > > >
>> > >
>> >
>> >
>> >
>> > --
>> >  शुभकामनायें/Best regards
>> >
>> > Santosh
>> >
>
>
>
>
> --
> शुभकामनायें/Best regards
>
> Santosh

--
शुभकामनायें/Best regards

Santosh