loci.formats.FormatException while converting series to tiff format

[de9821]

my current version bftools is below

Version: 7.3.1
Build date: 11 July 2024
VCS revision: 41e12f6

I am getting below error while converting vsi file series into tiff

../bftools/bfconvert -no-upgrade -bigtiff -series 1 -pyramid-scale 1 -noflat ./DATA_022/DATA_022.vsi ./DATA_022_1.tiff
./DATA_022/DATA_022.vsi
CellSensReader initializing ./DATA_022/DATA_022.vsi
[CellSens VSI] -> ./DATA_022_1.tiff [Tagged Image File Format]
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 <= 4034
at loci.formats.FormatWriter.checkParams(FormatWriter.java:469)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:223)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:469)
at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)

Series description is below

Image count = 1
RGB = true (3)
Interleaved = true
Indexed = false (false color)
Width = 4034
Height = 4710
SizeZ = 1
SizeT = 1
SizeC = 3 (effectively 1)
Tile size = 512 x 512
Thumbnail size = 109 x 128
Endianness = motorola (big)
Dimension order = XYCZT (uncertain)
Pixel type = uint8
Valid bits per pixel = 8
Metadata complete = true
Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

I referred documentation and tried various options but still getting error.

Also tried older version of 6.3.1 as it was suggested in old discussion in forum but no luck.

please suggest if you faced similar issue and have any solution

[dgault]

Hi @de9821, thank you for reporting the issue. If you leave out the -pyramid-scale 1 option, do you still see the same error?

[de9821]

Hi @dgault thanks for the response.

I see similar error with out -pyramid-scale 1 option.

../bftools/bfconvert -no-upgrade -bigtiff -series 1 -noflat ./DATA_022/DATA_022.vsi ./DATA_022_1.tiff
./DATA_022/DATA_022.vsi
CellSensReader initializing ./DATA_022/DATA_022.vsi
[CellSens VSI] -> ./DATA_022_1.tiff [Tagged Image File Format]
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 <= 4034
at loci.formats.FormatWriter.checkParams(FormatWriter.java:469)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:223)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:469)
at loci.formats.ImageWriter.saveBytes(ImageWriter.java:260)
at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:1076)
at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:908)
at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:841)
at loci.formats.tools.ImageConverter.main(ImageConverter.java:1318)

[dgault]

Thanks @de9821 for confirming. Would you be able to share a sample file showing the error that we can test? If you need a suitable upload location then you can upload files to the Bio-Formats Zenodo community.