Hi all,
I have a 3GB sample image in PerkinElmer "qptiff" format. Based on the OMERO/Bio-Formats documentation, it wasn't clear to me whether or not the "qptiff" format is actually a different/unsupported format or is essentially the same as other PerkinElmer TIFF files.
Running "showinf" like this (after increasing the max mem size to 12G):
$ ./showinf ~/Downloads/scan.qptiff -debug
eventually ended with:
Reading tile Length 148950 Offset 3345390000
Reading tile Length 111990 Offset 3345464475
Reading tile Length 1752 Offset 3345520470
Reading tile Length 1752 Offset 3345521346
Read 5/8 planes (62%)
Exception in thread "main" loci.formats.FormatException: Sorry, ImageWidth x ImageLength x SamplesPerPixel x BitsPerSample > 2147483647 is not supported (36480 x 43200 x 3 x 8)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:819)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:779)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:296)
at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
at loci.formats.FormatReader.openBytes(FormatReader.java:886)
at loci.formats.ImageReader.openBytes(ImageReader.java:441)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86)
at loci.formats.tools.ImageInfo.readPixels(ImageInfo.java:818)
at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1051)
at loci.formats.tools.ImageInfo.main(ImageInfo.java:1117)
running the same withou -debug but with -nopix produces:
Checking file format [Tagged Image File Format]
Initializing reader
TiffDelegateReader initializing /Users/sheila/Downloads/scan.qptiff
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
Initialization took 0.095s
Reading core metadata
filename = /Users/sheila/Downloads/scan.qptiff
Series count = 1
Series #0 :
Image count = 8
RGB = false (1)
Interleaved = false
Indexed = false (false color)
Width = 36480
Height = 43200
SizeZ = 1
SizeT = 8
SizeC = 1
Thumbnail size = 108 x 128
Endianness = intel (little)
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
Plane #2 <=> Z 0, C 0, T 2
Plane #3 <=> Z 0, C 0, T 3
Plane #4 <=> Z 0, C 0, T 4
Plane #5 <=> Z 0, C 0, T 5
Plane #6 <=> Z 0, C 0, T 6
Plane #7 <=> Z 0, C 0, T 7
Reading global metadata
?xml version: "1.0" encoding="utf-16"?
Bands ref: "ref120"
Bands-i ref: "ref121"
BitsPerSample: 8
Compression: LZW
DateTime: 2017:04:23 11:48:35
EmissionFilter ref: "ref116"
ExcitationFilter ref: "ref127"
Exposure ref: "ref148" dim="3"
Exposure-iCSBEQwkgREMJIERDCSBEQwkgREMJIERDCSBEQw: =/Exposure-i
Exposure-iU8k8Q1PJPENTyTxDU8k8Q1PJPENTyTxDU8k8Qw: =/Exposure-i
Exposure-ibmvsQW5r7EFua+xBbmvsQW5r7EFua+xBbmvsQQ: =/Exposure-i
Exposure-if8L3QX/C90F/wvdBf8L3QX/C90F/wvdBf8L3QQ: =/Exposure-i
FilterColors ref: "ref149"
FilterPair ref: "ref115" /
FixedFilter ref: "ref128"
ImageLength: 43200
ImageWidth: 36480
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
MsiBands ref: "ref133"
MsiBands-i ref: "ref146" subtype="SpectralSegmentBasis"
MsiResolution ref: "ref2"
NewSubfileType: 0
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
PlanarConfiguration: Chunky
ResolutionUnit: Centimeter
SMinSampleValue: 0
SampleFormat: unsigned integer
SamplesPerPixel: 1
ScanBands ref: "ref3"
ScanBands-i ref: "ref114" subtype="SpectralSegmentBasis"
ScanResolution ref: "ref1"
Software: PerkinElmer-QPI
TileLength: 512
TileWidth: 512
TransmissionBands ref: "ref129" dim="1"
TransmissionBands-i ref: "ref130"
TunableFilterStates ref: "ref123" /
TunableFilterStates-i ref: "ref126"
WavelengthGroup ref: "ref147"
XPosition: 0
XResolution: 20115.529564667588
YPosition: 3
YResolution: 20115.529564667588
root s_v: "1" ref="ref0"
Reading metadata
and finally, running like this:
$ ./showinf ~/Downloads/scan.qptiff -range 0 0
does let me see an image -- but I'm not familiar with these images so I'm not 100% sure that what I'm getting is good/accurate
Does anyone have more experience with "qptiff" files from PerkinElmer? any additional information would be very helpful.
thanks!
Sheila
