Olympus .vsi download bug using OMERO.insight

Dear @OMETeam ,

Happy new year! I hope you are all well :slight_smile:

We noticed an issue when using OMERO.insight to download *.vsi images recorded on an Olympus Spinning Disk system acquired with CellSens.

The vsi file format consists of a small .vsi file accompanied by a folder of the same name (flanked by underscores) with a nested subfolder (“stack1”) that then contains a .ets file with the pixel data. Hence the download from OMERO results in multiple files and folders.

OMERO.insight packs each such package in its own folder with the *.vsi image file name. However, for some of the images, this folder naming fails and is instead “frame_t_0.ets”, i.e. the *.ets filename, see screenshot below.

While this creates unfortunately confusion for our users.

For us, a possible fix would be to either:

  • name all “packaging” folders according to the *.vsi filename, OR
  • skip the packaging folders altogether

The latter idea is of particular interest to us, since in this example use case all *.vsi images are part of a tiled image and hence belong together. We therefore would do this “unpacking” manually.

Thank you for your time and help!
Cheers,
Kai

:heart:

re: How do you store original raw data as saved from the microscopes? - #22 by lguerard

Is the representation in OMERO (not as downloaded) what you would expect?

Are there any message in the insight log?


For reference, clicking on “Download” in the web for https://demo.openmicroscopy.org/webclient/?show=image-149046 also offers a file named ....ets.

Using omero-download I see for one of the ones that I think is broken (e.g. 3):

Repository//56/kschleicher_1132/2021-01/11/13-14-38.020/Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_03.vsi
Repository//56/kschleicher_1132/2021-01/11/13-14-38.020/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_03_
Repository//56/kschleicher_1132/2021-01/11/13-14-38.020/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_03_/stack1
Repository//56/kschleicher_1132/2021-01/11/13-14-38.020/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_03_/stack1/frame_t_0.ets

where as for 2:

Repository//56/kschleicher_1132/2021-01/11/13-14-27.317/Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_02.vsi
Repository//56/kschleicher_1132/2021-01/11/13-14-27.317/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_02_
Repository//56/kschleicher_1132/2021-01/11/13-14-27.317/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_02_/stack1
Repository//56/kschleicher_1132/2021-01/11/13-14-27.317/_Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_02_/stack1/frame_t_0.ets

~J.

Hi @joshmoore ,

Thanks for looking into it !

I’m not exactly sure what’s the difference for you in the 3 and 2 that you posted. This is exactly how it should be.

However, as you can see from Kai’s screenshot, if you try to download them alll at once some are working while others are downloaded in a folder called frame_t_0.ets while it should have been called Brain_DAPI_GFAP-488_IBA3-Cy3_MBP-647_coronal10x_coronal-slideA_03.vsi . It seems that OMERO is renaming this folders somehow while others work.

Hope this is clear.

Best,
Laurent

I opened an issue on github for it: Olympus .vsi download bug · Issue #188 · ome/omero-insight · GitHub I could replicate the problem too.
Kind Regards,
Dominik