BioFormats does not read Zeiss Axiovision ROIs anymore?

[lechristophe]

Hi,

This is a BioFormats question (hence the CC to Melissa Linkert), but I
figured maybe people here would be interested in the issue.

I used to be able to import Zeiss Axiovision .zvi images that contain drawn
overlays as ROIs in ImageJ/Fiji. I even included this in my batch import
macro. I didn't use this feature for quite some time, but I just tried to
use it today and see that it is not working anymore. using "Display ROIs"
in BF import dialog does not import the zvi overlay anymore.

You can find an exemple .zvi file (that contains a single line ROI) here:
http://www.cleterrier.net/up/Exemple_Zeiss_ROI.zvi

Does anyone use this feature or know if it's supposed to be working, or if
the functionnality has been removed on purpose? I remember it slowed the
import process a lot so it could have been removed I guess.

Thanks for your help,

Christophe Leterrier

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[Melissa Linkert-2]

Hi Christophe,

> I used to be able to import Zeiss Axiovision .zvi images that contain drawn
> overlays as ROIs in ImageJ/Fiji. I even included this in my batch import
> macro. I didn't use this feature for quite some time, but I just tried to
> use it today and see that it is not working anymore. using "Display ROIs"
> in BF import dialog does not import the zvi overlay anymore.
>
> You can find an exemple .zvi file (that contains a single line ROI) here:
> http://www.cleterrier.net/up/Exemple_Zeiss_ROI.zvi
>
> Does anyone use this feature or know if it's supposed to be working, or if
> the functionnality has been removed on purpose? I remember it slowed the
> import process a lot so it could have been removed I guess.

Thank you for the bug report.  This is a known problem, as documented here:

http://trac.openmicroscopy.org.uk/ome/ticket/10522

We expect to have this fixed in next week's 4.4.7 release of Bio-Formats.

Regards,
-Melissa


On Tue, Apr 16, 2013 at 02:56:50PM +0200, Christophe Leterrier wrote:

> Hi,
>
> This is a BioFormats question (hence the CC to Melissa Linkert), but I
> figured maybe people here would be interested in the issue.
>
> I used to be able to import Zeiss Axiovision .zvi images that contain drawn
> overlays as ROIs in ImageJ/Fiji. I even included this in my batch import
> macro. I didn't use this feature for quite some time, but I just tried to
> use it today and see that it is not working anymore. using "Display ROIs"
> in BF import dialog does not import the zvi overlay anymore.
>
> You can find an exemple .zvi file (that contains a single line ROI) here:
> http://www.cleterrier.net/up/Exemple_Zeiss_ROI.zvi
>
> Does anyone use this feature or know if it's supposed to be working, or if
> the functionnality has been removed on purpose? I remember it slowed the
> import process a lot so it could have been removed I guess.
>
> Thanks for your help,
>
> Christophe Leterrier

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