Open Microscopy Environment

Dear Melissa,

Thanks for the update. Like I said on my previous post, the issue was solved with the last version of bioformats at the time of writing.

New super fun bug:

When opening a .VSI file using bioformats importer directly, there is no problem. I can see all the series and open them.

However opening it with the following code:

Code: Select all

run("Bio-Formats Macro Extensions");
id = File.openDialog("VSI File");
Ext.getFormat(id, format);
print(format);
Ext.setId(id);


Causes a lovely error as seen below. the part
Ext.getFormat works and outputs "CellSens VSI" to the log window.

Would it be possible for you to upload the VSI file causing the problem using https://www.openmicroscopy.org/qa2/qa/upload/ so that we can try to reproduce the problem and investigate what's happening here in more detail?


Many thanks,
Roger Leigh

It's probably not necessary to upload an image, so feel free to hold off on that for the moment. This is possibly something to do with logging (see http://imagej.1557.x6.nabble.com/segmen ... l#a5004746 for a previous problem), so we'll look into this in a bit more detail and get back to you once we've done a bit more investigation.

If you haven't done so already, trying with the latest (5.0.2) version of the bioformats plugin would be worth doing.


Thanks,
Roger

Hi Oli,

This looks identical to a recently reported Fiji bug:

http://fiji.sc/bugzilla/show_bug.cgi?id=770

Does the solution outlined there help at all? The issue is that some other installed plugin contains a version of the slf4j library that is incompatible with the version used by Bio-Formats.

Regards,
-Melissa

Dear Melissa,

Indeed the bug was fixed and there was no longer a problem. Thank you very much!


We do have a new dataset for you to try out, as the extraction of the images is proving to be troublesome.

When viewed with OlyVIA, the sections are not cropped and usually quite well centered.

Opening these series with the VSI reader, some images end up getting cropped.

You should be able to download it here:

https://documents.epfl.ch/groups/p/pt/p ... D25_09.zip

If you need more information please let me know.

Best

Oli

Hi Oli,

As always, thank you for the bug report!

There is now a ticket for this on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/12433

You have been CC'd as usual, and so will be automatically notified of updates (just let us know if you would rather not be updated).

-Melissa

Hi Melissa

Thank you for the ticket. We will have a look once this is updated and get back to you.

Otherwise I am here to offer a new dataset that for some reason does not open at all with BioFormats. BioFormats importer just hangs with no error or changes. Looking at the thread killer we see that there is something running but no output at all is generated. This is Image_27.vsi and associated folder.

Something else: The Image_6 seems to open properly but complains of problems when generating a thumbnail for one of the series. I am unsure if this is linked to a problem with corrupted data or something different in BioFormats. Resaving the file on the original software does not solve either of the two issues. But importing and opening seem OK.


I have provided a link here as your SEND IMAGES link does not accept .VSI files yet
https://documents.epfl.ch/groups/p/pt/p ... etBIOP.zip

All the best

Hi Oli,

Thank you for uploading additional datasets. We're working on a fix here:

https://github.com/openmicroscopy/bioformats/pull/1381

There isn't yet a build with those changes, but the "latest" build should include them once the pull request shows as being merged.

-Melissa

Hi Melissa,

Thank you for the reply. Looking forward to testing out the new build when it comes out.

Best

Oli

Hi Melissa!

I figured I'd try out the latest version of BioFormats on VSI files.
There was a mention on it handling metadata better, which indeed seems to be the case

However, I was curious regarding the multiple resolutions that one could get using getResolutionCount().

So far, I have tested this on a dataset where I can still see the count being over 20 series, when there are actually 4 in store. using r.setSeries(k) and outputting r.getResolutionCount() returns 1 all the time. Looking at the series it is clear that they are linked and scaled down versions of each other.
https://documents.epfl.ch/groups/p/pt/p ... ataset.zip

Is there a different way to access this data or is this field not fully implemented yet?

As always thank you for your time.

Best

Oli