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I noticed, each time I had to connect again to the OMERO server via ICE api, that the first image import from OMERO is very long. Same for the image opening. When the connection seems to be well established between QuPath and OMERO (i.e. second import or second opening), then it goes way faster.
In order to quantify this time, I did a benchmark of the extension.
It turns out that the time to open the OMERO browser is around 8 times slower and the time to do a first import between 5 to 10 times slower than doing the same with the OMERO-BIOP extension. This is a real bottleneck for us.
The different tests were done using a RJ45 connection, with the qupath-extension-omero-v0.1.0-rc5 and qupath-extension-biop-omero-1.0.3. I listed below everything you may need to redo the tests.
Export to OME-TIFF
The script and the image used are the same as the ones mentionned in that post
Downsample
scaled Downsample
OMERO BIOP Extension
OMERO extension
2
4
83.31s
88.97s
2
4
81.38s
84.11s
1
4
330.84s
345.76s
1
4
359.53s
335.74s
Double-clicking on an image to open it (first opening)
I noticed, each time I had to connect again to the OMERO server via ICE api, that the first image import from OMERO is very long. Same for the image opening. When the connection seems to be well established between QuPath and OMERO (i.e. second import or second opening), then it goes way faster.
In order to quantify this time, I did a benchmark of the extension.
It turns out that the time to open the OMERO browser is around 8 times slower and the time to do a first import between 5 to 10 times slower than doing the same with the OMERO-BIOP extension. This is a real bottleneck for us.
The different tests were done using a RJ45 connection, with the
qupath-extension-omero-v0.1.0-rc5
andqupath-extension-biop-omero-1.0.3
. I listed below everything you may need to redo the tests.Export to OME-TIFF
The script and the image used are the same as the ones mentionned in that post
Double-clicking on an image to open it (first opening)
Brightfield H-DAB Dataset
EdU+_RFP+
Opening an OMERO browser
Importing an image from the browser (first import)
Importing an image from the browser (second import)
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