error with bioformat

[Cole, Richard W (HEALTH)]

Dear group,



All of a sudden when we drag & drop LIF files into FIJI it takes a LONG time and only opens one image w/o any of the usual dialog boxes.  Anyone else having these issues



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

P.O. Box 509 Albany N.Y. 12201-0509
518-474-7048 Phone
518-473-2895 Fax
[core brand]
Website www.wadsworth.org/cores/alm/index.htm<http://www.wadsworth.org/cores/alm/index.htm>


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[Theresa Swayne]

Hi Richard,

I had the same experience. I think it is because Fiji switched to use SCIFIO by default to open images, and SCIFIO doesn't seem to work with LIF yet.

Fiji now has 2 ways to open proprietary image formats: SCIFIO and Bio-Formats.  SCIFIO is better for some images, Bio-Formats is better for others. If you have problems with one setting, use the other.

To change the default setting to Bio-Formats: Edit > Options> ImageJ2 and UNcheck "Use SCIFIO when opening images."

To use Bio-Formats for one image but leave SCIFIO as the default: Plugins > Bio-Formats > Bio-Formats Importer and select the file you want. Bio-Formats will be used this time, and the default is not changed.

Hope this helps.
Theresa

On Jul 9, 2014, at 3:54 PM, "Cole, Richard (HEALTH)" <[hidden email]> wrote:

>
>
> Dear group,
>
>
>
> All of a sudden when we drag & drop LIF files into FIJI it takes a LONG time and only opens one image w/o any of the usual dialog boxes.  Anyone else having these issues
>
>
>
> 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
>
> P.O. Box 509 Albany N.Y. 12201-0509
> 518-474-7048 Phone
> 518-473-2895 Fax
> [core brand]
> Website www.wadsworth.org/cores/alm/index.htm<http://www.wadsworth.org/cores/alm/index.htm>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <image004.jpg><image001.gif>

------------------------------------
Theresa Swayne, Ph.D.
Associate Research Scientist
Manager, Confocal and Specialized Microscopy Shared Resource
Herbert Irving Comprehensive Cancer Center, Columbia University
1130 Saint Nicholas Ave, 222A
New York, NY 10032

212-851-4613

[hidden email]
http://hiccc.columbia.edu/research/sharedresources/confocal


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[dscho]

Hi Richard,

On Wed, 9 Jul 2014, Cole, Richard (HEALTH) wrote:

> All of a sudden when we drag & drop LIF files into FIJI it takes a LONG
> time and only opens one image w/o any of the usual dialog boxes.

Please provide a (small) sample image which you expect to open more than
one image.

As Teresa pointed out, we switched to SCIFIO (you can switch that off in
Edit>Options>ImageJ2) which is a very powerful concept replacing previous
attempts to provide extensible scientific image file reading/writing.

At the moment, we are working hard to address problems reported by users
(such as yours) where image opening did not work as expected. We will be
starting to address performance concerns soon.

Ciao,
Johannes

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[ctrueden]

Hi Richard & everyone,

> All of a sudden when we drag & drop LIF files into FIJI it takes a LONG
> time and only opens one image w/o any of the usual dialog boxes.

A couple of things in addition to Johannes's comments:

1) SCIFIO has a Bio-Formats plugin, which is what handles the proprietary
formats including LIF. Hence, performance should be comparable to the
Bio-Formats Importer plugin—if not, it's a bug.

2) SCIFIO does internally support opening multiple images, but at the UI
level the ImageJ integration only displays the first. We plan to resolve
this limitation soon.

Regards,
Curtis


On Thu, Jul 10, 2014 at 11:25 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Richard,
>
> On Wed, 9 Jul 2014, Cole, Richard (HEALTH) wrote:
>
> > All of a sudden when we drag & drop LIF files into FIJI it takes a LONG
> > time and only opens one image w/o any of the usual dialog boxes.
>
> Please provide a (small) sample image which you expect to open more than
> one image.
>
> As Teresa pointed out, we switched to SCIFIO (you can switch that off in
> Edit>Options>ImageJ2) which is a very powerful concept replacing previous
> attempts to provide extensible scientific image file reading/writing.
>
> At the moment, we are working hard to address problems reported by users
> (such as yours) where image opening did not work as expected. We will be
> starting to address performance concerns soon.
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Jordan Cocchiaro]

I have been having a problem similar to the one Richard describes.  I tried following the advice below and removing SCIFO as default.  However, my bioformats importer plugin is no longer working properly and the LOCI one is no longer available. Installation of the bioformats plugin said it was successful, but I just keep getting pop up boxes that don't make sense.  Not getting the usual dialog box for the importer.

Thanks,
Jordan

[ctrueden]

Hi Jordan,

> I just keep getting pop up boxes that don't make sense

We would need to see the contents of those dialog boxes in order to
diagnose the issue. You should be able to copy and paste the contents into
an email.

Have you tried downloading a fresh Fiji from http://fiji.sc/Downloads ?
If all else fails, you can download one of the "Life-line" versions which
are known to work well.

Regards,
Curtis


On Fri, Aug 15, 2014 at 10:18 AM, Jordan Cocchiaro <
[hidden email]> wrote:

> I have been having a problem similar to the one Richard describes.  I tried
> following the advice below and removing SCIFO as default.  However, my
> bioformats importer plugin is no longer working properly and the LOCI one
> is
> no longer available. Installation of the bioformats plugin said it was
> successful, but I just keep getting pop up boxes that don't make sense.
> Not
> getting the usual dialog box for the importer.
>
> Thanks,
> Jordan
>
>
>
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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