Open Microscopy Environment

Hi,

it seams that BioFormats (and thus OMERO) does not support the version of MSR used by the current generation of Abberior Instruments STED/RESOLFT devices via their image acquisition software Imspector.

When I try to open the MSR in ImageJ/Fiji with the current package of the Bioformats plugin, I get an "Unknown Stack Format" exception.

BioFormats however lists Imspector MSR as an supported format.

Any help would be most welcome. I attached an example MSR file for testing.

Tristan

Hi Tristan,

Thank you for the bug report. Unfortunately, it looks like the file attachment was not successful - could you please try zipping the file before attaching it, or uploading via our QA system?

https://www.openmicroscopy.org/qa2/qa/upload/

-Melissa

Hi Melissa,

the attachment () should be there now.

Hi Tristan,

Thank you for attaching the file. We now have a fix for this under review for inclusion in 5.1.0:

https://github.com/openmicroscopy/bioformats/pull/1480

-Melissa

Hi Melissa,

is there an ETA for the 5.1.0 release?

Hi Tristan,

5.1.0 is currently scheduled for February 2015. If that changes at all, we'll certainly announce it on the forums and mailing lists.

-Melissa

Hi Melissa,

I just updated OMERO to 5.1.0 and also installed the latest Fiji updates. Our AI Imspector's MSRs are now properly imported everywhere, which is great for our users.

However, Bioformats seems to ignore the Colormap (for our STED images, that's usually "Fire" (or "Red Hot" in ImageJ) for now and only show grey-scale image per default. Can this be changed in future updates?

Best,

Tristan

Hi Tristan,

We can certainly work on adding color/lookup table support for Imspector files, but as far as I know we don't currently have files with a non-grey color. Would you be willing to upload a small example to https://www.openmicroscopy.org/qa2/qa/upload/ (you may need to zip the file first)?

Regards,
-Melissa

Hi Melissa,

I uploaded a sample MSR-file that uses the "Red Hot" (Imspector calls it "Fire") standard STED lookup table. While using OMERO 5.1.0 today to import a few new Imspector MSRs, we also came across two other issues:

1) For every open measurement (which can consist of several images/channels), there was another "Line Plot" imported, often with the additional title suffix "[Pop]". I added a screenshot to illustrate this. These images were definitely not part of the original MSRs. Strangely, this did not happen with the last batch of MSRs I imported.

2) I think I mentioned this before for the Leica LIF format, but users really expect that comments are imported into OMERO if they add them to an image in Imspector. This should be pretty straight forward since a lot of the meta data is already used during an import anyway.

3) Some of the very interesting meta data of Imspector, especially the laser power used to take the measurement, is not available in the "Original Metadata" tab in OMERO (nor anywhere else that I am aware of). Could this be adapted to include all the metadata and not just a part of it?

Regards,

Tristan

[img]Exmaple.jpg[/img]

PS: Another, very important issue is this:

4) Channels are not detected during MSR-Import, i.e. every image of a multi-channel measurement is imported as a single image.