we recently bought a new Olympus spinning disk system which stores its data in the *.vsi file format as written by the cellSens Dimension 2.3 software.
These files readily open with Bio-formats, but I noticed that a few metadata fields were not or incorrectly populated. I have hence uploaded an example file including an export of the original (aka “correct”) metadata as exported directly from the cellSens software itself for comparison.
- When you open the image in Fiji with Bio-formats, the voxel depth is reported as 1, or maybe in other words it was not found. It should be 0.11 um.
- “PositionZ” in the ome-xml for each plane is correct, but a field for the z interval is missing.
- In the “Original metadata”-file as opened by Bio-formats, I did however find the correct value in line 489:
405, 561 Z incrementValue #1 0.11
- The exposure time for C1 is not correct (80ms written, but should be 100ms), but for C2 it is correct (80ms).
- In the “Original metadata”-file as opened by Bio-formats, I did however find the correct values in lines 369 & 370:
405, 561 Microscope Exposure time (microseconds) #1 100000
405, 561 Microscope Exposure time (microseconds) #2 80000
I hope this helps and that the issue can be fixed .
Thank you for your help and cheers,