Open Microscopy Environment

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

Hi Sheila

Bio-Formats does not have a specific reader for "qptiff" files but will instead attempt to read them as a standard Tiff. This should be suitable for opening the images and reading the associated TIFF metadata. From what I can tell specific PerkinElmer metadata fields will be stored in the ImageDescription tag.

The error you are seeing is due to the size one of the images which cannot open the entire frame. Using showinf you should be able to open the remaining images using the range option. In this case the largest image will have to be opened using tiled or cropped reading.

David Gault