Open Microscopy Environment

Dear Oli,

This should all work. I think the behaviour you have observed might be because you can open the VSI file with or without the pyramids being "flattened" into individual series. If you use:

http://downloads.openmicroscopy.org/bio ... boolean%29

i.e. call r.setFlattenedResolutions(false) before you call r.setId() this will instruct the reader to keep the pyramids as resolution levels within a series rather than making them into separate series'. This should make r.getResolutionCount() return the sub-resolutions for the selected series (and the series count will decrease appropriately).


Regards,
Roger

Dear Roger,

Thanks for the update, I seem to be able to access these resolutions now, thank you!

However I noticed that some datasets that used to work are now giving me an error when I open them

Code: Select all

java.lang.IllegalArgumentException: Invalid C index: 1/1
   at loci.formats.FormatTools.getIndex(FormatTools.java:412)


If needed I can provide a copy of this file.

Best

Oli

As a sidenote, it would appear that the latest bioformats cannot open VSI files with more than 1 fluorescent channel.

Hi Oli,

Uploading a sample VSI file that causes this failure to https://www.openmicroscopy.org/qa2/qa/upload/ would certainly help us track down the source of the bug.
As always, thanks for the feedback.

Best regards,
Sebastien

Dear Sebastien,

Thanks for the reply. I have uploaded a zip file containint the VSI and its associated folder.
https://www.openmicroscopy.org/qa2/qa/feedback/11039

Best

Oli

Hi Oli,

Thank you very much for uploading your sample file. There is now a ticket:

https://trac.openmicroscopy.org/ome/ticket/12848

and as usual, you have been CC'd.

Best regards,
Sebastien

hi Sebastien,

Thanks for the update. However, could you suggest a way for me to regress the bioformats library within fiji to a state about 2-3 weeks ago when the reader was working?
I've tried getting the 4.4 version from your website as a full package and installed it into a vanilla ImageJ for testing purposes and still get the error...

Best

Oli

Hi Oli,

did you try setting up the Life-Line version of Fiji as suggested by Curtis on the ImageJ thread?

Best regards,
Sebastien

Hi Sebastian,

The lifeline version is a bit too old with the included bioformats. Installing the bioformats_package.jar of version 5.0.8 gives us the original functionality back, sor now.

But we really appreciate the extra metadata that you are able to provide in the latest version of the CellSens reader
If I wanted diving into the source code for the error, where would I start looking?

HI Oli,

The ticket created for the VSI error in the case of fluorescent multi-channel images is definitely on our radar and assigned to the 5.1.2 milestone due by the end of May.

We will likely have a Pull request opened for review in the upcoming weeks. Once this PR is merged, we will make sure this forum thread is also updated and you should be able to use the Bio-Formats 5.1.x update site.

Best,
Sebastien