Error trying to convert / read MetaSystems ".vsi" image

UPDATE: I had previously thought that this image was the output of the 10xGenomics Visium assay, but now I realize that it is from the MetaSystems “Metafer” scanning platform. I found a similar question from 2018 about this, but it’s not completely clear if that was resolved or not, although someone said at the time that they “open .vsi files every day”…

I am trying to convert a .vsi image file using bfconvert, but I’m getting an error.

$ ./bfconvert -version
Version: 6.6.0
Build date: 14 December 2020
VCS revision: e0cdb3c28b52ba1b429d56c37a409fe53b5722ba

here is the error I get from bfconvert – I also get the same error from showinf and from Fiji – am I missing something in the installation?

Exception in thread "main" java.lang.IllegalArgumentException: Invalid series: 0
	at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1276)
	at loci.formats.FormatReader.setSeries(FormatReader.java:947)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:203)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:116)
	at loci.formats.in.CellSensReader.initFile(CellSensReader.java:801)
	at loci.formats.FormatReader.setId(FormatReader.java:1421)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:506)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1095)

thanks,

Sheila

I have the same exact problem with a metasystem metafer vsi file
I tried with a vsi file download online with a folder that inclueds the ets files. and it worked alright.
This time the file was a single vsi with other files (vsa, vsc, vsr and vsv).
Some of them inclued metatada about the vsi file.
With this file i have same exact error as above and i have the latest versione installed.

Hi @SheilaMReynolds and @lpizzato, the .vsi files supported through Bio-Formats will be from the CellSens software,these will be the ones with the ets files as mentioned above. So it looks as though the MetaSystems vsi may actually be a different format with the same extension as CellSens, in which case it wont currently be supported by Bio-Formats.

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thank you @dgault – that would certainly explain why it doesn’t work – I have sent a question in to MetaSystems as well, I will update here if I get any information from them

I came to the same conclusion talking to the technician since he told me he was using a Zeiss microscope and not an Olympus (the .vsi real file).

I have a contact with metasystem too and so far i still have to understand if there’s any open format available in the metafer software beside the “fake” vsi and some html5 export which already slipts the file in FOVs

I’ll wirte here too if i’ll have any updates.

I was able to get in touch with MetaSystems and they pointed me to a free download (Windows only) of their VSViewer software. Images (or portions thereof) can be exported to JPEG and TIFF (BigTIFF not supported, so very large / hi-res images may get truncated) – with optional compression. Essentially none of the metadata is included in the TIFF, though.

Thanks for the information.
Is it possible to have the same link to test the software with some of out VSI files?