[ome-devel] Generating large two-dimensional images tiles in OMERO

[S Simard]

Hi,

We are in the process of importing a number of large (9200 * 9200) TIFF 
image mosaics into OMERO 5.
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.
Since we have 200 such 3-channel images to upload into OMERO, we are 
looking for ways to improve the tiles processing delays.

Our current setup is as follows:
- OMERO 5.0.0-beta1-ice34-b3470 / Java 1.6.0_45 / 8 CPUs @ 2.40GHz
- default tile size / omero.pixeldata.threads=8

Would you have some recommendations on server configuration parameters 
or alternative deployment options that could be susceptible to yield 
faster processing times?
Are you aware of any pre-optimization we could use when generating the 
image mosaics (as they are stiched together from automated analysis 
results)?

Thank you

Regards
Sébastien


PS. Output from the Bio-Formats "showinf" tool and snippets from 
PixelData-0.log below:

1 - Test with RGB image:

INFO  [ ome.services.pixeldata.PixelDataHandler] (3-thread-1) HANDLED 
EventLog:165303(entityId=3802) [16624002 ms.]
ERROR [        ome.services.util.ServiceHandler] (3-thread-1) Method 
interface ome.services.util.Executor$Work.doWork invocation took 16624046

Reading core metadata
Filename = LameH24f1_40X_B1_C_GFP_Nodes1.tif
Series count = 1
Series #0 :
         Image count = 1
         RGB = true (3)
         Interleaved = false
         Indexed = false (false color)
         Width = 9200
         Height = 9200
         SizeZ = 1
         SizeT = 1
         SizeC = 3 (effectively 1)
         Thumbnail size = 128 x 128
         Endianness = intel (little)
         Dimension order = XYCZT (certain)
         Pixel type = uint8
         Valid bits per pixel = 8
         Metadata complete = true
         Thumbnail series = false
         -----
         Plane #0 <=> Z 0, C 0, T 0

Reading pixel data (0-0)
         Read 1/1 planes (100%)
[done]
9.093s elapsed (9093.0ms per plane)

Launching image viewer

Reading global metadata
BitsPerSample: 8
Compression: Uncompressed
ImageLength: 9200
ImageWidth: 9200
MetaDataPhotometricInterpretation: RGB
MetaMorph: no
NumberOfChannels: 3
PhotometricInterpretation: RGB
ResolutionUnit: Inch
SamplesPerPixel: 3
XResolution: 72
YResolution: 72


2 - Test with grayscale image:

INFO  [ ome.services.pixeldata.PixelDataHandler] (3-thread-1) HANDLED 
EventLog:165296(entityId=3801) [475136 ms.]
ERROR [        ome.services.util.ServiceHandler] (3-thread-1) Method 
interface ome.services.util.Executor$Work.doWork invocation took 475150

Reading core metadata
Filename = LameH24f1_40X_B1_C_GFP.tif
Series count = 1
Series #0 :
         Image count = 1
         RGB = false (1)
         Interleaved = false
         Indexed = false (false color)
         Width = 9200
         Height = 9200
         SizeZ = 1
         SizeT = 1
         SizeC = 1
         Thumbnail size = 128 x 128
         Endianness = motorola (big)
         Dimension order = XYCZT (certain)
         Pixel type = uint16
         Valid bits per pixel = 16
         Metadata complete = true
         Thumbnail series = false
         -----
         Plane #0 <=> Z 0, C 0, T 0

Reading pixel data (0-0)
         Read 1/1 planes (100%)
[done]
2.633s elapsed (2633.0ms per plane)

Launching image viewer

Reading global metadata
BitsPerSample: 16
Compression: Uncompressed
ImageJ: 1.47q
ImageLength: 9200
ImageWidth: 9200
MetaDataPhotometricInterpretation: Monochrome
MetaMorph: no
NewSubfileType: 0
NumberOfChannels: 1
PhotometricInterpretation: BlackIsZero
ResolutionUnit: Inch
SamplesPerPixel: 1
Unit: inch
XResolution: 96
YResolution: 96
max: 65535.0
min: 0.0
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