error on import of ND2 files

[Cole, Richard W (HEALTH)]

Dear imagers,

The file opens now, however, it does not open correctly.  The file is a T, XY, Z file but, Fiji opens only one of the XY positions.
 There are no errors on opening.  Any ideas?
File location: anonymous FTP site ftp://ftp.wadsworth.org/pub/rcole/ND2/

Cheers

Rich


Richard Cole
Research Scientist V
Director: Advanced Light Microscopy & Image Analysis Core
Wadsworth Center

Research Assistant Professor
Dept. of Biomedical Sciences
School of Public Health State University of New York

120 New Scotland Avenue, Albany N.Y. 12208
518-474-7048 Phone
518-408-1730 Fax
[core brand]
Website http://www.wadsworth.org/research/cores/alm
[twitter-128] twitter.com/microscopejock


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

[bnorthan]

Hi Rich

I downloaded your file and I think I was able to load it correctly.  I
simply went to "file->open" and it automatically started the bio-formats
plugin.  It gave me the option of opening 2 series, both were 11 frames, 10
timepoints, and seemed to open fine.

Does it automatically use bio-formats when you try to open??  If not try
going to  "File->import->bioformats", instead of just "file->open".

On Wed, Aug 9, 2017 at 12:54 PM, Cole, Richard W (HEALTH) <
[hidden email]> wrote:

> Dear imagers,
>
> The file opens now, however, it does not open correctly.  The file is a T,
> XY, Z file but, Fiji opens only one of the XY positions.
>  There are no errors on opening.  Any ideas?
> File location: anonymous FTP site ftp://ftp.wadsworth.org/pub/rcole/ND2/
>
> Cheers
>
> Rich
>
>
> Richard Cole
> Research Scientist V
> Director: Advanced Light Microscopy & Image Analysis Core
> Wadsworth Center
>
> Research Assistant Professor
> Dept. of Biomedical Sciences
> School of Public Health State University of New York
>
> 120 New Scotland Avenue, Albany N.Y. 12208
> 518-474-7048 Phone
> 518-408-1730 Fax
> [core brand]
> Website http://www.wadsworth.org/research/cores/alm
> [twitter-128] twitter.com/microscopejock
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[ctrueden]

Hi Rich,

In addition to Brian's comments: is it possible that you either:
A) Have the Nikon ND2 plugin installed [1]; or
B) Turned on windowless import for ND2 files [2]?

Regards,
Curtis

[1] https://imagej.net/plugins/nd2-reader.html
[2] Plugins > Bio-Formats > Bio-Formats Plugins Configuration, Formats tab,
Nikon ND2, ensure Windowless option is unchecked.


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


On Thu, Aug 10, 2017 at 9:31 AM, Brian Northan <[hidden email]> wrote:

> Hi Rich
>
> I downloaded your file and I think I was able to load it correctly.  I
> simply went to "file->open" and it automatically started the bio-formats
> plugin.  It gave me the option of opening 2 series, both were 11 frames, 10
> timepoints, and seemed to open fine.
>
> Does it automatically use bio-formats when you try to open??  If not try
> going to  "File->import->bioformats", instead of just "file->open".
>
> On Wed, Aug 9, 2017 at 12:54 PM, Cole, Richard W (HEALTH) <
> [hidden email]> wrote:
>
> > Dear imagers,
> >
> > The file opens now, however, it does not open correctly.  The file is a
> T,
> > XY, Z file but, Fiji opens only one of the XY positions.
> >  There are no errors on opening.  Any ideas?
> > File location: anonymous FTP site ftp://ftp.wadsworth.org/pub/rcole/ND2/
> >
> > Cheers
> >
> > Rich
> >
> >
> > Richard Cole
> > Research Scientist V
> > Director: Advanced Light Microscopy & Image Analysis Core
> > Wadsworth Center
> >
> > Research Assistant Professor
> > Dept. of Biomedical Sciences
> > School of Public Health State University of New York
> >
> > 120 New Scotland Avenue, Albany N.Y. 12208
> > 518-474-7048 Phone
> > 518-408-1730 Fax
> > [core brand]
> > Website http://www.wadsworth.org/research/cores/alm
> > [twitter-128] twitter.com/microscopejock
> >
> >
> > --
> > 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