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NGFF-Converter 1.1.4 fails to convert CZI file which opens normally in Fiji using BioFormats #194

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zeissmicroscopy opened this issue Mar 11, 2023 · 1 comment
Open

NGFF-Converter 1.1.4 fails to convert CZI file which opens normally in Fiji using BioFormats #194

zeissmicroscopy opened this issue Mar 11, 2023 · 1 comment
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ngff/zarr Requires upstream updates to Zarr or OME-NGFF

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@zeissmicroscopy
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The issue is decribed here:

https://forum.image.sc/t/ngff-converter-1-1-4-fails-to-convert-czi-file-which-open-normally-in-fiji/78408?u=sebi06

Hi all,

I just tried to convert a CZI file using the OME-NGFF converter tool, but it fails immediately complaing that "series 96 is not present". But when opening in Fiji via BioFomats one can clearly see, that there are 96 series.

https://www.dropbox.com/s/uuh8ktgk5lz7e7d/testwell96_test.czi?dl=0

Any ideas?

image

image

17:11:36 DEBUG l.f.FormatHandler - loci.formats.in.ZeissCZIReader.initFile(image.czi)
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getParent()
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1460572002 OPEN
17:11:36 TRACE l.f.FormatHandler - plane #0 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 3296, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=2645, size=421, startCoordinate=0.0, storedSize=421; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=0, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#1 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 858240, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=2267, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=1, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#2 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 1717248, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=1889, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=2, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#3 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 2576256, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=1511, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=3, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#4 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 3435264, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=1133, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=4, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#5 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 4294272, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=755, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=5, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#6 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 5153280, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=377, size=423, startCoordinate=0.0, storedSize=423; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=6, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.f.FormatHandler - plane glencoesoftware/NGFF-Converter#7 = coreIndex=0, planeIndex=0, resolutionIndex=0, x=0, y=0, row=0, col=0, metadata=<METADATA />, attachmentSize=0, directoryEntry=schemaType = DV, pixelType = 0, filePosition = 6012288, filePart = 0, compression = 0, pyramidType = 0, dimensionCount = 3, dimensions = [dimension=X, start=0, size=422, startCoordinate=0.0, storedSize=422; dimension=Y, start=0, size=2030, startCoordinate=0.0, storedSize=2030; dimension=M, start=7, size=1, startCoordinate=0.0, storedSize=1]
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 858450849 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 858450849 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1303715745 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1303715745 CLOSE
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, C:\Program Files\NGFF-Converter\image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - getParent()
17:11:36 TRACE l.c.Location - Location(null, C:\Program Files\NGFF-Converter)
17:11:36 TRACE l.c.Location - list(true)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(C:\Program Files\NGFF-Converter, app)
17:11:36 TRACE l.c.Location - isHidden()
17:11:36 TRACE l.c.Location - Location(C:\Program Files\NGFF-Converter, NGFF-Converter.exe)
17:11:36 TRACE l.c.Location - isHidden()
17:11:36 TRACE l.c.Location - Location(C:\Program Files\NGFF-Converter, NGFF-Converter.ico)
17:11:36 TRACE l.c.Location - isHidden()
17:11:36 TRACE l.c.Location - Location(C:\Program Files\NGFF-Converter, runtime)
17:11:36 TRACE l.c.Location - isHidden()
17:11:36 TRACE l.c.Location -   returning 4 files
17:11:36 TRACE l.f.FormatHandler - rotations = 1
17:11:36 TRACE l.f.FormatHandler - illuminations = 1
17:11:36 TRACE l.f.FormatHandler - phases = 1
17:11:36 TRACE l.f.FormatHandler -     assigned plane index = 0; series index = 0; coreIndex = 0
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1341850139 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1341850139 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1814946073 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1814946073 CLOSE
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, image.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 146696414 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 146696414 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1838364287 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1838364287 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 2062486028 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 2062486028 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 2034833761 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 2034833761 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 38434318 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 38434318 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1990101238 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1990101238 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1956860739 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1956860739 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = image.czi, writable = false)
17:11:36 TRACE l.c.Location - Location.getHandle: image.czi -> loci.common.ByteArrayHandle@60b5a65a
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1158733479 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1158733479 CLOSE
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1460572002 CLOSE
17:11:36 DEBUG l.c.Location - Location.mapFile: image.czi -> null
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getName()

...

17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@143b3a0d
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@143b3a0d
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 375445828 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 375445828 CLOSE
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@78b7b980
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@78b7b980
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 991016407 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 991016407 CLOSE
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()

...

17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@76370bea
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@76370bea
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1712146065 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1712146065 CLOSE
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 598968425 OPEN
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 598968425 CLOSE
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()

...

17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getAbsolutePath()
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - getName()
17:11:36 DEBUG l.c.Location - Location.mapFile: embedded-stream.raw -> null
17:11:36 DEBUG l.c.Location - Location.mapFile: embedded-stream.raw -> null
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 43023822 CLOSE
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - lastModified()
17:11:36 DEBUG l.f.Memoizer - loaded memo file: F:\Testdata_Zeiss\CZI_Testfiles\.testwell96_test.czi.bfmemo (8817839 bytes)
17:11:36 DEBUG l.f.Memoizer - start[1678464696498] time[34] tag[loci.formats.Memoizer.loadMemo]
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@5136de40
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@5136de40
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1634768657 OPEN
17:11:36 DEBUG l.f.Memoizer - start[1678464696498] time[34] tag[loci.formats.Memoizer.setId]
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - lastModified()
17:11:36 DEBUG l.f.Memoizer - loaded memo file: F:\Testdata_Zeiss\CZI_Testfiles\.testwell96_test.czi.bfmemo (8817839 bytes)
17:11:36 DEBUG l.f.Memoizer - start[1678464696534] time[33] tag[loci.formats.Memoizer.loadMemo]
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@7d75a378
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@7d75a378
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 773527809 OPEN
17:11:36 DEBUG l.f.Memoizer - start[1678464696534] time[34] tag[loci.formats.Memoizer.setId]
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - lastModified()
17:11:36 DEBUG l.f.Memoizer - loaded memo file: F:\Testdata_Zeiss\CZI_Testfiles\.testwell96_test.czi.bfmemo (8817839 bytes)
17:11:36 DEBUG l.f.Memoizer - start[1678464696568] time[32] tag[loci.formats.Memoizer.loadMemo]
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@6e0c015c
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@6e0c015c
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1499170649 OPEN
17:11:36 DEBUG l.f.Memoizer - start[1678464696568] time[33] tag[loci.formats.Memoizer.setId]
17:11:36 TRACE l.c.Location - Location(null, F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi)
17:11:36 TRACE l.c.Location - lastModified()
17:11:36 DEBUG l.f.Memoizer - loaded memo file: F:\Testdata_Zeiss\CZI_Testfiles\.testwell96_test.czi.bfmemo (8817839 bytes)
17:11:36 DEBUG l.f.Memoizer - start[1678464696602] time[30] tag[loci.formats.Memoizer.loadMemo]
17:11:36 TRACE l.c.Location - getHandle(id = F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi, writable = false)
17:11:36 TRACE l.c.Location - no handle was mapped for this ID
17:11:36 TRACE l.c.Location - Created new handle F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@32aff37f
17:11:36 TRACE l.c.Location - Location.getHandle: F:\Testdata_Zeiss\CZI_Testfiles\testwell96_test.czi -> loci.common.NIOFileHandle@32aff37f
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 280616683 OPEN
17:11:36 DEBUG l.f.Memoizer - start[1678464696601] time[31] tag[loci.formats.Memoizer.setId]
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.DichroicRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.DichroicRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 DEBUG o.x.m.ManufacturerSpec - Unable to handle reference of type: class ome.xml.model.EmissionFilterRef
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 773527809 CLOSE
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1499170649 CLOSE
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 280616683 CLOSE
17:11:36 TRACE l.c.RandomAccessInputStream - RandomAccessInputStream 1634768657 CLOSE
17:11:36 ERROR c.g.c.ConverterTask - java.lang.IllegalArgumentException: Series 96 not present in metadata!
17:11:36 INFO  c.g.c.ConverterTask - Failed with Exit Code 1 : testwell96_test.zarr

17:11:36 INFO  c.g.c.ConverterTask - Completed conversion of 0 files.
@sbesson sbesson transferred this issue from glencoesoftware/NGFF-Converter Mar 13, 2023
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sbesson commented Mar 13, 2023

Thanks @zeissmicroscopy for the report. I can reproduce both using the converter and the command-line bioformats2raw utility (both 0.6.0 as well as the latest 0.6.1 release) so I am migrating this issue as it's effectively unrelated to the GUI component itself.

The source of the issue is that by default Bio-Formats reads the data as a combination of 96 well samples within a plate plus one label image outside the HCS structure. While this representaton is fully legit from the perspective of the OME data model, there is no OME-NGFF specification for the handling of a mixture of HCS and non HCS data. In the absence of such, bioformats2raw will decide whether the data is HCS or not based on a combination of input options and metadata.

There is possibly a wider support conversation to be had at the OME-NGFF specification level but trying to revolve your immediate conversion issue, there are two options which should work with NGFF-Converter 1.1.4:

1- if you do not care about the high-content screening layout (i.e. the Fiji scenario where there is no metadata relationship between the individual images), you should be able to specify --no-hcs in the Extra arguments list. This will create an OME-Zarr dataset with 97 multiscale groups

2- if you want to preserve the HCS metadata, you should be able to specify --options=zeissczi.attachments=false (see the options) in the Extra arguments list. This will ignore the label image and create an OME-Zarr according to the plate specification. Note in this second case, you may have to manually delete the dangling .testwell96_test.czi.bfmemo file left from the failing conversion which would be at the same level as the original CZI file

@sbesson sbesson self-assigned this Mar 13, 2023
@melissalinkert melissalinkert added the ngff/zarr Requires upstream updates to Zarr or OME-NGFF label Mar 31, 2023
@sbesson sbesson removed their assignment May 30, 2023
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ngff/zarr Requires upstream updates to Zarr or OME-NGFF
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