ZVI Duplicate Channels

[Oli]

Dear Melissa et al.

We're having problems opening .ZVI Files in Fiji using LOCI.

It opens two channels which contain the same information. It would seem that the first channel is duplicated.
These files however open OK in Imaris for example.

ZVI File Open in Imaris

Elodie_Imaris.jpg (144.29 KiB) Viewed 3338 times

I've uploaded a couple of files your sftp server.

Best!


Oli

[mlinkert]

Hi Oli,

Thank you for the bug report. We have a fix for this under review:

https://github.com/openmicroscopy/bioformats/pull/544

Just out of curiosity, were these files created by extracting a subset of the channels from larger .zvi files? It doesn't affect how we fix it, but it would explain what was going wrong.

Regards,
-Melissa

[ShoFujisawa]

The ZVI file imported using Bio-Formats plugin still duplicates the channel.

I downloaded the most recent trunk (loci_tools.jar) file and put it in the plugin folder. Now when I start FIJI, it gives me configuration errors, and the channels are still duplicated.

Am I installing the .jar file wrongly?

Sho

[mlinkert]

Hi Sho,

Installing a loci_tools.jar file in Fiji is not recommended, as it will conflict with the version of Bio-Formats installed by Fiji's updater.

I would suggest trying the instructions here:

http://lists.openmicroscopy.org.uk/pipe ... 03890.html

as that should allow you to install recent development builds of Bio-Formats into Fiji. Please note that those builds are not official stable releases, and as such are not as thoroughly tested.

-Melissa