bioformats import nd2-Files

[karo03]

Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ too).

One results in a hyperstack 1280x960x3x106, which is ok, the other results in a sequence of 104 images. The latter nd2 contains 105 images according "NIS Elements Viewer"! One image more or less might be acceptable, but how can I merge that set of images? Additionally the metadata of the latter show series alphabethical sorted.

Trying to do "Images to Stack" gives the message "There should be at least two images open", in fact 104 are open! Seemingly the opened images are 1-dim 3-color hyperstacks!

Perhaps there is some knowledge on the net to configure the bioformats importer to merge that heap of images?

Thanks in advance

Karsten


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

[karo03]

I have found a solution concerning the construction of one hyperstack instead of a bunch of images.

Bioformats plugin configuration : Nikon ND2: Switch off windowless
Bioformats importer : "Open all series" ON and "Concatenate series when compatible" ON

These settings read in both mentioned nd2 files.

Still there is a missing image, the last one.

Thanks for looking into my request.

Karsten

Anfang der weitergeleiteten Nachricht:

> Von: Karsten <[hidden email]>
> Betreff: bioformats import nd2-Files
> Datum: 11. Juli 2014 14:56:33 MESZ
> An: [hidden email]
>
>
> Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ too).
>
> One results in a hyperstack 1280x960x3x106, which is ok, the other results in a sequence of 104 images. The latter nd2 contains 105 images according "NIS Elements Viewer"! One image more or less might be acceptable, but how can I merge that set of images? Additionally the metadata of the latter show series alphabethical sorted.
>
> Trying to do "Images to Stack" gives the message "There should be at least two images open", in fact 104 are open! Seemingly the opened images are 1-dim 3-color hyperstacks!
>
> Perhaps there is some knowledge on the net to configure the bioformats importer to merge that heap of images?
>
> Thanks in advance
>
> Karsten
>

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

[ctrueden]

Hi Karsten,

> Bioformats importer : "Open all series" ON and "Concatenate series
> when compatible" ON

Glad you figured out the "Concatenate series when compatible" option. That
is indeed the easiest way to solve your specific issue.

> Still there is a missing image, the last one.

I have seen this bug before... but have not had time to reproduce. Have you
reported it to the Bio-Formats development team via the OME Users [1]
mailing list?

Does the problem also happen using the "showinf" Bio-Formats command line
tool [2] with the "-nopix" flag? I.e.: what does the metadata say? Is it
short one plane? Or is it correct?

Regards,
Curtis

[1] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
[2]
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/


On Fri, Jul 11, 2014 at 8:27 AM, Karsten <[hidden email]> wrote:

>
> I have found a solution concerning the construction of one hyperstack
> instead of a bunch of images.
>
> Bioformats plugin configuration : Nikon ND2: Switch off windowless
> Bioformats importer : "Open all series" ON and "Concatenate series when
> compatible" ON
>
> These settings read in both mentioned nd2 files.
>
> Still there is a missing image, the last one.
>
> Thanks for looking into my request.
>
> Karsten
>
> Anfang der weitergeleiteten Nachricht:
>
> > Von: Karsten <[hidden email]>
> > Betreff: bioformats import nd2-Files
> > Datum: 11. Juli 2014 14:56:33 MESZ
> > An: [hidden email]
> >
> >
> > Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ
> too).
> >
> > One results in a hyperstack 1280x960x3x106, which is ok, the other
> results in a sequence of 104 images. The latter nd2 contains 105 images
> according "NIS Elements Viewer"! One image more or less might be
> acceptable, but how can I merge that set of images? Additionally the
> metadata of the latter show series alphabethical sorted.
> >
> > Trying to do "Images to Stack" gives the message "There should be at
> least two images open", in fact 104 are open! Seemingly the opened images
> are 1-dim 3-color hyperstacks!
> >
> > Perhaps there is some knowledge on the net to configure the bioformats
> importer to merge that heap of images?
> >
> > Thanks in advance
> >
> > Karsten
> >
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[karo03]

Hi Curtis, thanks for responding.

showinf shows the same behaviour. Metadata are partially correct and partially not. At some places in the metadata the correct number of image(planes) appear at others, obviously more important, the reduced number. E.g. the list of scanning table coordinates show the existence of another image, the list of time stamps shows the reduced number!

I have send the meta data of the two files I have to the ome-users list.

Regards
Karsten


Am 14.07.2014 um 18:09 schrieb Curtis Rueden <[hidden email]>:

> Hi Karsten,
>
>> Bioformats importer : "Open all series" ON and "Concatenate series
>> when compatible" ON
>
> Glad you figured out the "Concatenate series when compatible" option. That
> is indeed the easiest way to solve your specific issue.
>
>> Still there is a missing image, the last one.
>
> I have seen this bug before... but have not had time to reproduce. Have you
> reported it to the Bio-Formats development team via the OME Users [1]
> mailing list?
>
> Does the problem also happen using the "showinf" Bio-Formats command line
> tool [2] with the "-nopix" flag? I.e.: what does the metadata say? Is it
> short one plane? Or is it correct?
>
> Regards,
> Curtis
>
> [1] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
> [2]
> https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/
>
>
> On Fri, Jul 11, 2014 at 8:27 AM, Karsten <[hidden email]> wrote:
>
>>
>> I have found a solution concerning the construction of one hyperstack
>> instead of a bunch of images.
>>
>> Bioformats plugin configuration : Nikon ND2: Switch off windowless
>> Bioformats importer : "Open all series" ON and "Concatenate series when
>> compatible" ON
>>
>> These settings read in both mentioned nd2 files.
>>
>> Still there is a missing image, the last one.
>>
>> Thanks for looking into my request.
>>
>> Karsten
>>
>> Anfang der weitergeleiteten Nachricht:
>>
>>> Von: Karsten <[hidden email]>
>>> Betreff: bioformats import nd2-Files
>>> Datum: 11. Juli 2014 14:56:33 MESZ
>>> An: [hidden email]
>>>
>>>
>>> Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ
>> too).
>>>
>>> One results in a hyperstack 1280x960x3x106, which is ok, the other
>> results in a sequence of 104 images. The latter nd2 contains 105 images
>> according "NIS Elements Viewer"! One image more or less might be
>> acceptable, but how can I merge that set of images? Additionally the
>> metadata of the latter show series alphabethical sorted.
>>>
>>> Trying to do "Images to Stack" gives the message "There should be at
>> least two images open", in fact 104 are open! Seemingly the opened images
>> are 1-dim 3-color hyperstacks!
>>>
>>> Perhaps there is some knowledge on the net to configure the bioformats
>> importer to merge that heap of images?
>>>
>>> Thanks in advance
>>>
>>> Karsten
>>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Karsten,

> I have send the meta data of the two files I have to the ome-users
> list.

Thanks a lot!

For the archives: that thread can be found at:
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-July/004580.html

Regards,
Curtis


On Mon, Jul 14, 2014 at 3:43 PM, Karsten <[hidden email]> wrote:

> Hi Curtis, thanks for responding.
>
> showinf shows the same behaviour. Metadata are partially correct and
> partially not. At some places in the metadata the correct number of
> image(planes) appear at others, obviously more important, the reduced
> number. E.g. the list of scanning table coordinates show the existence of
> another image, the list of time stamps shows the reduced number!
>
> I have send the meta data of the two files I have to the ome-users list.
>
> Regards
> Karsten
>
>
> Am 14.07.2014 um 18:09 schrieb Curtis Rueden <[hidden email]>:
>
> > Hi Karsten,
> >
> >> Bioformats importer : "Open all series" ON and "Concatenate series
> >> when compatible" ON
> >
> > Glad you figured out the "Concatenate series when compatible" option.
> That
> > is indeed the easiest way to solve your specific issue.
> >
> >> Still there is a missing image, the last one.
> >
> > I have seen this bug before... but have not had time to reproduce. Have
> you
> > reported it to the Bio-Formats development team via the OME Users [1]
> > mailing list?
> >
> > Does the problem also happen using the "showinf" Bio-Formats command line
> > tool [2] with the "-nopix" flag? I.e.: what does the metadata say? Is it
> > short one plane? Or is it correct?
> >
> > Regards,
> > Curtis
> >
> > [1] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
> > [2]
> >
> https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/
> >
> >
> > On Fri, Jul 11, 2014 at 8:27 AM, Karsten <[hidden email]> wrote:
> >
> >>
> >> I have found a solution concerning the construction of one hyperstack
> >> instead of a bunch of images.
> >>
> >> Bioformats plugin configuration : Nikon ND2: Switch off windowless
> >> Bioformats importer : "Open all series" ON and "Concatenate series when
> >> compatible" ON
> >>
> >> These settings read in both mentioned nd2 files.
> >>
> >> Still there is a missing image, the last one.
> >>
> >> Thanks for looking into my request.
> >>
> >> Karsten
> >>
> >> Anfang der weitergeleiteten Nachricht:
> >>
> >>> Von: Karsten <[hidden email]>
> >>> Betreff: bioformats import nd2-Files
> >>> Datum: 11. Juli 2014 14:56:33 MESZ
> >>> An: [hidden email]
> >>>
> >>>
> >>> Hi I am just trying to read Nikon nd2 Files with Fiji (and pure ImageJ
> >> too).
> >>>
> >>> One results in a hyperstack 1280x960x3x106, which is ok, the other
> >> results in a sequence of 104 images. The latter nd2 contains 105 images
> >> according "NIS Elements Viewer"! One image more or less might be
> >> acceptable, but how can I merge that set of images? Additionally the
> >> metadata of the latter show series alphabethical sorted.
> >>>
> >>> Trying to do "Images to Stack" gives the message "There should be at
> >> least two images open", in fact 104 are open! Seemingly the opened
> images
> >> are 1-dim 3-color hyperstacks!
> >>>
> >>> Perhaps there is some knowledge on the net to configure the bioformats
> >> importer to merge that heap of images?
> >>>
> >>> Thanks in advance
> >>>
> >>> Karsten
> >>>
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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