OMERO.figure Max Projections Problem

I’m sorry that I’ve asked this before, but I can’t find the old thread.

I’m still having an issue where I cannot see the preview of a max projected image when I’m using OMERO Figure on the web. I can work with single planes without problem, but when I select the max projection button the preview goes white and I can’t work with the image (if more than 3 planes are selected) for up to 10 seconds. If I increase the number of slices that I’m trying to project to the complete stack, it will break the preview until I bring the sliders back closer together. So, my users are having to generate previews by gradually moving the sliders apart to avoid this issue. This is with a simple 2424x2424 pixel monochrome Z-stack of 41 slices. So, nothing exotic. Do I need to have more processor power or memory allocated to the machine running my server? Is this an issue with the browser? Please advise as more and more of my users are adopting the web figure interface for making figures for publication.

Hi,
I’m afraid that the Max-Intensity projection is happening ‘on the fly’ on the OMERO server and this is quite an intensive process. Performance of reading data from disk will depend on hardware as well as the file format (since data is arranged in different ways for different formats). I don’t have a similar image to test with, but on our production OMERO server, a 512 x 512 3-channel image takes around 0.5 - 1 seconds to project. Given that this is 8 x smaller than yours, the times seem comparable, although you see much longer times with larger ranges.

This may be useful if you’ve not read it before:
https://docs.openmicroscopy.org/omero/5.5.0/sysadmins/system-requirements.html
Could you check how much memory and CPU is being used by OMERO during projection?

OMERO.figure doesn’t save the projected images, and will always re-project when you re-open the File or refresh the page.
One option is to save the Projected image as a new Image (you can do this in the OMERO.iviewer under File > Save Projection as new Image . EDIT: iviewer won’t project a tiled image of this size, but you can still do this in the OMERO.insight desktop client).
Then the projected Image can be used in Figure without having to re-project each time (although you won’t be able to adjust the projection in Figure).

Regards,
Will.

Thanks Will! We’re more than satisfying the server requirements. I was thinking that creating the max first would be the way to go. My only regret is losing the dynamism of working with the native data. This is especially true when I’m working with data where something will be moving in Z so the range to project will be different in different T points. I think we’ll work with a combination of creating max projections and doing slow maxes within OMERO.figure.

1 Like