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VSI Reader, new version

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Olivier Burri

VSI Reader, new version

Dear List,
We've made a few updates to the reader for Olympus VSI Files
For the more info and documentation, please visit
http://biop.epfl.ch/INFO_completed_projects.html#vsi-reader
Updates include:

- Proper bit depth is taken when downsampling images.

- We can now fairly accurately read labels, masks, overview scans from the images. This is still based on empirical formulas to recognize which files are which, so if you have some troublesome files, feel free to let us know. When the great team at BioFormats manages to parse the metadata from the SVI files directly, we'll make sure to modify our macro accordingly.

- We've added an Update Site for our platform containing the macro, as per Johannes's suggestion.
host: http://biop.epfl.ch/Fiji-Update,
Latest versions will still be available through our website as .zip downloads, but if you want to keep up with the latest modifications, you can add an update site for our platform to the Fiji Updater, see instructions at http://fiji.sc/wiki/index.php/How_to_follow_a_3rd_party_update_site
The only issue we have is regarding the icons used for the actionbar buttons: There is an incompatibility between Fiji's Updater and the ActionBar plugin that does not allow for the upload of the icons to the update site. In the meantime, you can get the icons separately on our website if you really want them :). Note that once the icons are installed, the update site is enough, as the only thing that will change is the .ijm file.

- So far we've had no more issues with the latest LOCI installations so hopefully this is a thing of the past and it should run 'out of the box'.

All the best,

Oli

Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP

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ctrueden

Re: VSI Reader, new version

Hi Oli,

> We've added an Update Site for our platform containing the macro

Excellent, looks great! Your mail inspired me to create a page on the Fiji
wiki listing all known available update sites:

http://fiji.sc/List_of_update_sites

If anyone has an update site missing from the list, feel free to add it, or
let me know and I can do it.

In the future, we will have ImageJ2 parse this list and create a nice GUI
directly within ImageJ so that users can more easily turn on update sites
by clicking them.

Regards,
Curtis

On Tue, Mar 5, 2013 at 10:14 AM, Burri Olivier <[hidden email]>wrote:

> Dear List,
> We've made a few updates to the reader for Olympus VSI Files
> For the more info and documentation, please visit
> http://biop.epfl.ch/INFO_completed_projects.html#vsi-reader
> Updates include:
>
>
> - Proper bit depth is taken when downsampling images.
>
>
> - We can now fairly accurately read labels, masks, overview scans
> from the images. This is still based on empirical formulas to recognize
> which files are which, so if you have some troublesome files, feel free to
> let us know. When the great team at BioFormats manages to parse the
> metadata from the SVI files directly, we'll make sure to modify our macro
> accordingly.
>
>
> - We've added an Update Site for our platform containing the
> macro, as per Johannes's suggestion.
> host: http://biop.epfl.ch/Fiji-Update,
> Latest versions will still be available through our website as .zip
> downloads, but if you want to keep up with the latest modifications, you
> can add an update site for our platform to the Fiji Updater, see
> instructions at
> http://fiji.sc/wiki/index.php/How_to_follow_a_3rd_party_update_site
> The only issue we have is regarding the icons used for the actionbar
> buttons: There is an incompatibility between Fiji's Updater and the
> ActionBar plugin that does not allow for the upload of the icons to the
> update site. In the meantime, you can get the icons separately on our
> website if you really want them :). Note that once the icons are installed,
> the update site is enough, as the only thing that will change is the .ijm
> file.
>
> - So far we've had no more issues with the latest LOCI
> installations so hopefully this is a thing of the past and it should run
> 'out of the box'.
>
> All the best,
>
> Oli
>
>
> Olivier Burri
> Engineer - Image Processing
> & Software Development
> EPFL - SV - PTECH - PTBIOP
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Jerome Mutterer-3

Re: VSI Reader, new version

In reply to this post by Olivier Burri

Dear all,
I've updated the ActionBar plugin so that action bars now can be
distributed as single jar files (examples on the wiki site). This makes
them compatible with Fiji update sites.

The latest version of ActionBar can be obtained from:
http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start#downloads

Jerome

On 5 March 2013 17:14, Burri Olivier <[hidden email]> wrote:

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dscho

Re: VSI Reader, new version

Hi Jerome,

On Fri, 8 Mar 2013, Jerome Mutterer wrote:

> I've updated the ActionBar plugin so that action bars now can be
> distributed as single jar files (examples on the wiki site). This makes
> them compatible with Fiji update sites.

Thank you for the reminder that the Action Bar source code we had in
Fiji's repository was woefully obsolete. I removed it from Fiji's source
code tree today.

Thanks!
Johannes

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Jerome Mutterer-3

Re: VSI Reader, new version

Hi Johannes,
I'm terribly sorry, I wish I knew how to upgrade the version on the Fiji
repository. The source code, however, is included in the jar file, so
you're very welcome to put it back in if you want. I'm using a standard
Eclipse for writing my plugins, so if there's a simple way I can push from
there to the repository, I'm willing to learn how to do this.
Sincerely,
Jerome

On 9 March 2013 00:07, Johannes Schindelin <[hidden email]>wrote:

> Hi Jerome,
>
> On Fri, 8 Mar 2013, Jerome Mutterer wrote:
>
> > I've updated the ActionBar plugin so that action bars now can be
> > distributed as single jar files (examples on the wiki site). This makes
> > them compatible with Fiji update sites.
>
> Thank you for the reminder that the Action Bar source code we had in
> Fiji's repository was woefully obsolete. I removed it from Fiji's source
> code tree today.
>
> Thanks!
> Johannes
>

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dscho

Re: VSI Reader, new version

Hi Jerome,

On Sat, 9 Mar 2013, Jerome Mutterer wrote:

> I'm terribly sorry, I wish I knew how to upgrade the version on the Fiji
> repository. The source code, however, is included in the jar file, so
> you're very welcome to put it back in if you want. I'm using a standard
> Eclipse for writing my plugins, so if there's a simple way I can push
> from there to the repository, I'm willing to learn how to do this.

I do not want to interfere with your current development procedure. If you
already use Git to track your source code changes, it would be relatively
easy to integrate Action Bar into Fiji's source code.

But here is another idea: why not make your own update site? Then you can
easily retain your current development process and by adding your site to

http://fiji.sc/List_of_update_sites

publish your work in a way.

Ciao,
Johannes

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Niko Ehrenfeuchter

ActionBar source code (was: VSI Reader, new version)

In reply to this post by Jerome Mutterer-3

sorry, for digging out this super-old thread:

On 09.03.2013 19:37, Jerome Mutterer wrote:
> Hi Johannes,
> I'm terribly sorry, I wish I knew how to upgrade the version on the Fiji
> repository. The source code, however, is included in the jar file, so

Jerome, I wasn't able to find the source code for your ActionBar plugin
in the jar file distributed via your update site [1]. However, it is
contained in the one downloadable from the imagejdocu wiki [2]. Is there
a reason why those two differ? And do they differ in more than this
property?

Cheers
Niko

[1] http://www-ibmp.u-strasbg.fr/fijiupdates/
[2] http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start

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bgxz1985

Re: VSI Reader, new version

In reply to this post by Olivier Burri

Dear Olivia

I tried to download the new version of vsi reader and I have noted that the link http://biop.epfl.ch/INFO_completed_projects.html#vsi-reader
no longer works. Are there any other way that I can download the pluggin?

Thanks.
Bill