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<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">Hi,
<br>
<br>
We are in the process of importing a number of large (9200 * 9200)
TIFF image mosaics into OMERO 5.
<br>
Some initial experiments show that the pyramids generation process
reaches completion within a few minutes (~ 10-20) for grayscale
image, but may last up to several hours (~ 4-5) with RGB images.
<br>
Since we have 200 such 3-channel images to upload into OMERO, we
are looking for ways to improve the tiles processing delays.
<br>
<br>
Our current setup is as follows:
<br>
- OMERO 5.0.0-beta1-ice34-b3470 / Java 1.6.0_45 / 8 CPUs @ 2.40GHz
<br>
- default tile size / omero.pixeldata.threads=8
<br>
<br>
Would you have some recommendations on server configuration
parameters or alternative deployment options
that could be susceptible to yield faster processing times?
<br>
Are you aware of any pre-optimization we could use when generating
the image mosaics (as they are stiched together from automated
analysis results)?
<br>
<br>
Thank you
<br>
<br>
Regards
<br>
Sébastien
<br>
<br>
<br>
PS. Output from the Bio-Formats "showinf" tool and snippets from
PixelData-0.log below:
<br>
<br>
1 - Test with RGB image:
<br>
<br>
INFO [ ome.services.pixeldata.PixelDataHandler] (3-thread-1)
HANDLED EventLog:165303(entityId=3802) [16624002 ms.]
<br>
ERROR [ ome.services.util.ServiceHandler] (3-thread-1)
Method interface ome.services.util.Executor$Work.doWork invocation
took 16624046
<br>
<br>
Reading core metadata
<br>
Filename = LameH24f1_40X_B1_C_GFP_Nodes1.tif
<br>
Series count = 1
<br>
Series #0 :
<br>
Image count = 1
<br>
RGB = true (3)
<br>
Interleaved = false
<br>
Indexed = false (false color)
<br>
Width = 9200
<br>
Height = 9200
<br>
SizeZ = 1
<br>
SizeT = 1
<br>
SizeC = 3 (effectively 1)
<br>
Thumbnail size = 128 x 128
<br>
Endianness = intel (little)
<br>
Dimension order = XYCZT (certain)
<br>
Pixel type = uint8
<br>
Valid bits per pixel = 8
<br>
Metadata complete = true
<br>
Thumbnail series = false
<br>
-----
<br>
Plane #0 <=> Z 0, C 0, T 0
<br>
<br>
Reading pixel data (0-0)
<br>
Read 1/1 planes (100%)
<br>
[done]
<br>
9.093s elapsed (9093.0ms per plane)
<br>
<br>
Launching image viewer
<br>
<br>
Reading global metadata
<br>
BitsPerSample: 8
<br>
Compression: Uncompressed
<br>
ImageLength: 9200
<br>
ImageWidth: 9200
<br>
MetaDataPhotometricInterpretation: RGB
<br>
MetaMorph: no
<br>
NumberOfChannels: 3
<br>
PhotometricInterpretation: RGB
<br>
ResolutionUnit: Inch
<br>
SamplesPerPixel: 3
<br>
XResolution: 72
<br>
YResolution: 72
<br>
<br>
<br>
2 - Test with grayscale image:
<br>
<br>
INFO [ ome.services.pixeldata.PixelDataHandler] (3-thread-1)
HANDLED EventLog:165296(entityId=3801) [475136 ms.]
<br>
ERROR [ ome.services.util.ServiceHandler] (3-thread-1)
Method interface ome.services.util.Executor$Work.doWork invocation
took 475150
<br>
<br>
Reading core metadata
<br>
Filename = LameH24f1_40X_B1_C_GFP.tif
<br>
Series count = 1
<br>
Series #0 :
<br>
Image count = 1
<br>
RGB = false (1)
<br>
Interleaved = false
<br>
Indexed = false (false color)
<br>
Width = 9200
<br>
Height = 9200
<br>
SizeZ = 1
<br>
SizeT = 1
<br>
SizeC = 1
<br>
Thumbnail size = 128 x 128
<br>
Endianness = motorola (big)
<br>
Dimension order = XYCZT (certain)
<br>
Pixel type = uint16
<br>
Valid bits per pixel = 16
<br>
Metadata complete = true
<br>
Thumbnail series = false
<br>
-----
<br>
Plane #0 <=> Z 0, C 0, T 0
<br>
<br>
Reading pixel data (0-0)
<br>
Read 1/1 planes (100%)
<br>
[done]
<br>
2.633s elapsed (2633.0ms per plane)
<br>
<br>
Launching image viewer
<br>
<br>
Reading global metadata
<br>
BitsPerSample: 16
<br>
Compression: Uncompressed
<br>
ImageJ: 1.47q
<br>
ImageLength: 9200
<br>
ImageWidth: 9200
<br>
MetaDataPhotometricInterpretation: Monochrome
<br>
MetaMorph: no
<br>
NewSubfileType: 0
<br>
NumberOfChannels: 1
<br>
PhotometricInterpretation: BlackIsZero
<br>
ResolutionUnit: Inch
<br>
SamplesPerPixel: 1
<br>
Unit: inch
<br>
XResolution: 96
<br>
YResolution: 96
<br>
max: 65535.0
<br>
min: 0.0
<br>
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