Slow opening of big 3D images

BIOP / qupath-extension-biop-omero

QuPath extension to work with images through OMERO's Java API (raw)

GNU General Public License v3.0

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Slow opening of big 3D images #17

Open NicoKiaru opened 11 months ago

NicoKiaru commented 11 months ago

Probably there's way too many things being fetched from the server.

Example URL (internal BIOP EPFL):

https://omero.epfl.ch/webclient/?show=image-511517

NicoKiaru commented 8 months ago

@Rdornier no news on this ? (it's not urgent)

Rdornier commented 8 months ago

Hi @NicoKiaru,

Yes, I think the issue is coming from this method https://github.com/qupath/qupath/blob/main/qupath-gui-fx/src/main/java/qupath/lib/display/ImageDisplay.java#L872-L894

Basically, when an ImageData is created, a thumbnail is created for every images (nZ * nT) , so more than 600 requests for the above image ! That's why it's so long to open this image (60-120s instead of 2-3s if we skip this step)

This is a side effect of QuPath ; I'll open an issue to discuss what would be possible to do.

Rdornier commented 8 months ago

To speed up a bit, I try to always take the lowest resolution level to generate the thumbnails

200-220s with the current thumbnail generation, at the level 8 /32 of downsampling
30-40s if I take the 32/32 level of downsampling

Improves a bit but still not optimal.

Rdornier commented 8 months ago

Forum post : https://forum.image.sc/t/slow-opening-of-3d-stacks-in-qupath/90996

Rdornier commented 6 months ago

I had to go back and increase the size of the thumbnail to 1024*1024 again, so that it does not introduce bias in the histogram generation for the images coming from OMERO / local. I have speed up the general streaming of data by paralellisation ; it should be twice faster. I hope the way the histogram is generated will be modified on QuPath side.