Problem to load vsi file after installing ActionBar and vsi reader

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Problem to load vsi file after installing ActionBar and vsi reader

Tim VDC
Hi,

I want to use vsi files in Fiji and already installed the ActionBar plugin and the BIOP plugin containing the VSI reader. But i still get a macro error if i want load an vsi file with the VSI reader. I also updated Fiji. Can anybody give me some advice how to solve this?

Tim
Reply | Threaded
Open this post in threaded view
|

Re: Problem to load vsi file after installing ActionBar and vsi reader

Herbie
Good day Tim,

according to
<http://www.openmicroscopy.org/site/support/bio-formats5.2/formats/cellsens-vsi.html>
Bioformats should open ".vsi" files.

Now and because Bioformats is part of the Fiji-Distribution, there
appears to be no need for special VSI-Reader for opening ".vsi" files.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
Am 14.10.16 um 12:43 schrieb Tim VDC:

> Hi,
>
> I want to use vsi files in Fiji and already installed the ActionBar plugin
> and the BIOP plugin containing the VSI reader. But i still get a macro error
> if i want load an vsi file with the VSI reader. I also updated Fiji. Can
> anybody give me some advice how to solve this?
>
> Tim
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Problem-to-load-vsi-file-after-installing-ActionBar-and-vsi-reader-tp5017384.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
Reply | Threaded
Open this post in threaded view
|

Re: Problem to load vsi file after installing ActionBar and vsi reader

Swayne, Theresa C.
@Herbie, When I open a VSI using Bio-Formats, I only get the overview and can’t access the full dataset. So the VSI Reader is still necessary in my hands (plus it has many useful features for working with these files).

@Tim, I am able to open VSI files with the latest versions of Fiji, Action Bar, & VSI Reader.

Can you give details about the steps you are following and the error you are getting?

Are you able to open the sample dataset on the BIOP website (http://biop.epfl.ch/TOOL_VSI_Reader.html)?

Regards,
Theresa

On Oct 14, 2016, at 9:12 AM, Herbie <[hidden email]<mailto:[hidden email]>> wrote:

Good day Tim,

according to
<http://www.openmicroscopy.org/site/support/bio-formats5.2/formats/cellsens-vsi.html>
Bioformats should open ".vsi" files.

Now and because Bioformats is part of the Fiji-Distribution, there appears to be no need for special VSI-Reader for opening ".vsi" files.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
Am 14.10.16 um 12:43 schrieb Tim VDC:
Hi,

I want to use vsi files in Fiji and already installed the ActionBar plugin
and the BIOP plugin containing the VSI reader. But i still get a macro error
if i want load an vsi file with the VSI reader. I also updated Fiji. Can
anybody give me some advice how to solve this?

Tim




--
View this message in context: http://imagej.1557.x6.nabble.com/Problem-to-load-vsi-file-after-installing-ActionBar-and-vsi-reader-tp5017384.html
Sent from the ImageJ mailing list archive at Nabble.com<http://nabble.com>.

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


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

------------------------------------
Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: 212-851-4613
[hidden email]<mailto:[hidden email]>


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Problem to load vsi file after installing ActionBar and vsi reader

Herbie
Dear Theresa,

that's why I included the link. It tells us that Bioformats support of
vsi-files isn't perfect yet...

Furthermore and because Tim couldn't work with VSI-Reader at all, I
thought Bioformats could be worth a try.

Best

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 14.10.16 um 15:57 schrieb Swayne, Theresa C.:

> @Herbie, When I open a VSI using Bio-Formats, I only get the overview
> and can’t access the full dataset. So the VSI Reader is still
> necessary in my hands (plus it has many useful features for working
> with these files).
>
> @Tim, I am able to open VSI files with the latest versions of Fiji,
> Action Bar, & VSI Reader.
>
> Can you give details about the steps you are following and the error
> you are getting?
>
> Are you able to open the sample dataset on the BIOP website
> (http://biop.epfl.ch/TOOL_VSI_Reader.html)?
>
> Regards, Theresa
>
> On Oct 14, 2016, at 9:12 AM, Herbie
> <[hidden email]<mailto:[hidden email]>> wrote:
>
> Good day Tim,
>
> according to
> <http://www.openmicroscopy.org/site/support/bio-formats5.2/formats/cellsens-vsi.html>
>
>
Bioformats should open ".vsi" files.

>
> Now and because Bioformats is part of the Fiji-Distribution, there
> appears to be no need for special VSI-Reader for opening ".vsi"
> files.
>
> HTH
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::: Am 14.10.16 um 12:43 schrieb
> Tim VDC: Hi,
>
> I want to use vsi files in Fiji and already installed the ActionBar
> plugin and the BIOP plugin containing the VSI reader. But i still get
> a macro error if i want load an vsi file with the VSI reader. I also
> updated Fiji. Can anybody give me some advice how to solve this?
>
> Tim
>
>
>
>
> -- View this message in context:
> http://imagej.1557.x6.nabble.com/Problem-to-load-vsi-file-after-installing-ActionBar-and-vsi-reader-tp5017384.html
>
>
Sent from the ImageJ mailing list archive at Nabble.com<http://nabble.com>.

>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------------ Theresa Swayne, Ph.D. Manager
> Confocal and Specialized Microscopy Shared
> Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>
>
>  Herbert Irving Comprehensive Cancer Center Columbia University
> Medical Center 1130 St. Nicholas Ave., Room 222A New York, NY 10032
> Phone: 212-851-4613
> [hidden email]<mailto:[hidden email]>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Problem to load vsi file after installing ActionBar and vsi reader

Herbie
In reply to this post by Swayne, Theresa C.
Dear Tim and Theresa,

I just dropped the file "Test.vsi" from the "VSI Sample Dataset" onto
the icon of _plain_ ImageJ (BioFormats-plugin not installed) and it
opened as 620x212 RGB image (513kB). The file is about 1MB however,
which means that there is indeed something missing...

ImageJ with BioFormats-plugin opens the file "Test.vsi" as 3-color
channel image (overview with 128kB per channel) with scale data and the
VSI-metadata.

I recommend a request at OME.

Best

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 14.10.16 um 15:57 schrieb Swayne, Theresa C.:

> @Herbie, When I open a VSI using Bio-Formats, I only get the overview
> and can’t access the full dataset. So the VSI Reader is still
> necessary in my hands (plus it has many useful features for working
> with these files).
>
> @Tim, I am able to open VSI files with the latest versions of Fiji,
> Action Bar, & VSI Reader.
>
> Can you give details about the steps you are following and the error
> you are getting?
>
> Are you able to open the sample dataset on the BIOP website
> (http://biop.epfl.ch/TOOL_VSI_Reader.html)?
>
> Regards, Theresa
>
> On Oct 14, 2016, at 9:12 AM, Herbie
> <[hidden email]<mailto:[hidden email]>> wrote:
>
> Good day Tim,
>
> according to
> <http://www.openmicroscopy.org/site/support/bio-formats5.2/formats/cellsens-vsi.html>
>
>
Bioformats should open ".vsi" files.

>
> Now and because Bioformats is part of the Fiji-Distribution, there
> appears to be no need for special VSI-Reader for opening ".vsi"
> files.
>
> HTH
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::: Am 14.10.16 um 12:43 schrieb
> Tim VDC: Hi,
>
> I want to use vsi files in Fiji and already installed the ActionBar
> plugin and the BIOP plugin containing the VSI reader. But i still get
> a macro error if i want load an vsi file with the VSI reader. I also
> updated Fiji. Can anybody give me some advice how to solve this?
>
> Tim
>
>
>
>
> -- View this message in context:
> http://imagej.1557.x6.nabble.com/Problem-to-load-vsi-file-after-installing-ActionBar-and-vsi-reader-tp5017384.html
>
>
Sent from the ImageJ mailing list archive at Nabble.com<http://nabble.com>.

>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ------------------------------------ Theresa Swayne, Ph.D. Manager
> Confocal and Specialized Microscopy Shared
> Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>
>
>  Herbert Irving Comprehensive Cancer Center Columbia University
> Medical Center 1130 St. Nicholas Ave., Room 222A New York, NY 10032
> Phone: 212-851-4613
> [hidden email]<mailto:[hidden email]>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: Problem to load vsi file after installing ActionBar and vsi reader

Swayne, Theresa C.
Dear Herbie,

You are right there is something missing — in fact, much more than 1 MB. The whole sample dataset is 250 MB, stored in a (presumably) pyramid-like format.

If you use drag and drop, you see only the overview.

However, if you call the Bio-Formats importer from the ImageJ menu, you can see and open different areas and magnification levels (presented as “Series”).

It looks like you can access all the pixels in this way, but actually using the images is hard — you can’t tell what each “Series” corresponds to, and you may have memory problems with opening very large single-plane images.

IMHO a major benefit of the BIOP's VSI Reader is that it is more user-friendly and memory-friendly — you can make an ROI on the overview and extract just that area at full resolution.

Maybe there is some trick to using Bio-Formats with pyramid images that I don’t know. But I agree, VSI users probably should request/contribute to better support by Bio-Formats.

Best,
Theresa


On Oct 14, 2016, at 11:16 AM, Herbie <[hidden email]<mailto:[hidden email]>> wrote:

Dear Tim and Theresa,

I just dropped the file "Test.vsi" from the "VSI Sample Dataset" onto the icon of _plain_ ImageJ (BioFormats-plugin not installed) and it opened as 620x212 RGB image (513kB). The file is about 1MB however, which means that there is indeed something missing...

ImageJ with BioFormats-plugin opens the file "Test.vsi" as 3-color channel image (overview with 128kB per channel) with scale data and the VSI-metadata.

I recommend a request at OME.

Best

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 14.10.16 um 15:57 schrieb Swayne, Theresa C.:
@Herbie, When I open a VSI using Bio-Formats, I only get the overview
and can’t access the full dataset. So the VSI Reader is still
necessary in my hands (plus it has many useful features for working
with these files).

@Tim, I am able to open VSI files with the latest versions of Fiji,
Action Bar, & VSI Reader.

Can you give details about the steps you are following and the error
you are getting?

Are you able to open the sample dataset on the BIOP website
(http://biop.epfl.ch/TOOL_VSI_Reader.html)?

Regards, Theresa

On Oct 14, 2016, at 9:12 AM, Herbie
<[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:

Good day Tim,

according to
<http://www.openmicroscopy.org/site/support/bio-formats5.2/formats/cellsens-vsi.html>


Bioformats should open ".vsi" files.

Now and because Bioformats is part of the Fiji-Distribution, there
appears to be no need for special VSI-Reader for opening ".vsi"
files.

HTH

Herbie

::::::::::::::::::::::::::::::::::::: Am 14.10.16 um 12:43 schrieb
Tim VDC: Hi,

I want to use vsi files in Fiji and already installed the ActionBar
plugin and the BIOP plugin containing the VSI reader. But i still get
a macro error if i want load an vsi file with the VSI reader. I also
updated Fiji. Can anybody give me some advice how to solve this?

Tim




-- View this message in context:
http://imagej.1557.x6.nabble.com/Problem-to-load-vsi-file-after-installing-ActionBar-and-vsi-reader-tp5017384.html


Sent from the ImageJ mailing list archive at Nabble.com<http://nabble.com><http://nabble.com>.

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


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

------------------------------------ Theresa Swayne, Ph.D. Manager
Confocal and Specialized Microscopy Shared
Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center Columbia University
Medical Center 1130 St. Nicholas Ave., Room 222A New York, NY 10032
Phone: 212-851-4613
[hidden email]<mailto:[hidden email]><mailto:[hidden email]>


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


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

------------------------------------
Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: 212-851-4613
[hidden email]<mailto:[hidden email]>


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