Bfconvert error with *.vsi file

Dear @OMETeam,

I’m trying to convert a vsi file using bfconvert (6.5.0) and the command line :

bfconvert -pyramid-resolutions 2 -pyramid-scale 3 -series 0 -tilex 512 -tiley 512 -noflat -bigtiff JPEG-90pct.vsi JPEG-90.ome.tiff

or without the -series :

bfconvert -pyramid-resolutions 2 -pyramid-scale 3  -tilex 512 -tiley 512 -noflat -bigtiff JPEG-90pct.vsi JPEG-90.ome.tiff

I get an FormatException error :

CellSensReader initializing JPEG-90pct.vsi
[CellSens VSI] -> JPEG-90.ome.tiff [OME-TIFF]
Tile size = 512 x 512
        Converted 1/1 planes (100%)
Tile size = 512 x 512
Exception in thread "main" loci.formats.FormatException: (w:512 + x:3584) must be <= 3892
        at loci.formats.FormatWriter.checkParams(FormatWriter.java:464)
        at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:229)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:218)
        at loci.formats.out.PyramidOMETiffWriter.saveBytes(PyramidOMETiffWriter.java:89)
        at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:923)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:791)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:719)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:1096)

I found this topic but it’s a different error message.

Am I missing something?

Thank you for your help,

Romain

1 Like

Hi @romainGuiet,

a similar error message has been reported in this topic and is related to the bfconvert issue with multi-series images which should be addressed with this Pull Request.

We are hoping to release Bio-Formats 6.5.1 to the community next week including this fix. If you need a working solution until then, you could either downgrading temporarily to Bio-Formats 6.3.1 or consume the latest SNAPSHOT version of Bio-Formats from the OME artifactory.

Best,
Sebastien

1 Like