Dear @OMETeam ,
Happy new year! I hope you are all well
We noticed an issue when using OMERO.insight to download *.vsi images recorded on an Olympus Spinning Disk system acquired with CellSens.
- Images on your demo server https://demo.openmicroscopy.org/webclient/?show=dataset-5245
- OMERO.insight version used: OMERO.insight-5.5.14.msi downloaded today from OMERO Downloads | Open Microscopy Environment (OME)
- How we download: select images in the tree view with shift-click. Then, right-click and choose “download” from the context menu.
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!