Omero iviewer shows blank for some images

Hello
My whole slide images are of svs format. Most of these images work. Some of them don’t open using omero-iviewer (I verified the size of the images that do open and that dont. They dont seem to have any correlation. The one that doesnt open is smaller than the one that opens). They open when i use omero.figure or omero.insight. I tried in chrome, safari and firefox. I was trying to debut and could see the following error. Could you please help out.

My omero instance is based on the docker-file from “omero-web-standalone” (https://hub.docker.com/r/openmicroscopy/omero-web-standalone). It doesnt use nginx (since i saw some other posts where nginx conf was a problem)

Best Regards
Vignesh

Hi,
Thanks for the report. The error URL simply says " resolutions must be sorted in descending order."

I wonder if you could go to /iviewer/image_data/ID/ on your server, where ID is the image ID for an Image that’s failing. This should give you some JSON data with a list of zoomLevelScaling (similar to e.g.
https://idr.openmicroscopy.org/iviewer/image_data/9822152/)

If you could check that list and see if any of the levels are out of order, that might explain the error, although I can’t think what the fix might be just now.

Thanks,
Will.

Hi Will

Sorry, Notifications werent on for my email. I just saw that I got a reply here. Thanks a lot for the reply. I checked the corresponding json file. It doesnt look out of order to me. What do you think? Is there a workaround for such cases

Here is the json

{“id”: 208, “meta”: {“imageName”: “data.svs [0]”, “imageDescription”: “22784x25088 [0, 100 22528x24832] (256x256) -> 22528x24832 JPEG/YCC”, “imageAuthor”: “root root”, “projectName”: “data”, “projectId”: 1, “projectDescription”: “”, “datasetName”: “set1”, “datasetId”: 152, “datasetDescription”: “”, “wellSampleId”: “”, “wellId”: “”, “imageTimestamp”: 1567772580.0, “imageId”: 208, “pixelsType”: “uint8”}, “perms”: {“canAnnotate”: true, “canEdit”: true, “canDelete”: true, “canLink”: true}, “tiles”: true, “tile_size”: {“width”: 256, “height”: 256}, “levels”: 4, “zoomLevelScaling”: {“0”: 1.0, “1”: 0.25, “2”: 0.0625, “3”: 0.0625}, “interpolate”: true, “size”: {“width”: 22528, “height”: 24832, “z”: 1, “t”: 1, “c”: 3}, “pixel_size”: {“x”: 0.277232142857143, “y”: 0.277232142857143, “z”: null, “unit_x”: 0.277232142857143, “symbol_x”: “\u00b5m”, “unit_y”: 0.277232142857143, “symbol_y”: “\u00b5m”}, “init_zoom”: 0, “pixel_range”: [0, 255], “channels”: [{“emissionWave”: null, “label”: “0”, “color”: “FF0000”, “inverted”: false, “reverseIntensity”: false, “family”: “linear”, “coefficient”: 1.0, “window”: {“min”: 0.0, “max”: 255.0, “start”: 0.0, “end”: 255.0}, “active”: true}, {“emissionWave”: null, “label”: “1”, “color”: “00FF00”, “inverted”: false, “reverseIntensity”: false, “family”: “linear”, “coefficient”: 1.0, “window”: {“min”: 0.0, “max”: 255.0, “start”: 0.0, “end”: 255.0}, “active”: true}, {“emissionWave”: null, “label”: “2”, “color”: “0000FF”, “inverted”: false, “reverseIntensity”: false, “family”: “linear”, “coefficient”: 1.0, “window”: {“min”: 0.0, “max”: 255.0, “start”: 0.0, “end”: 255.0}, “active”: true}], “split_channel”: {“g”: {“width”: 45062, “height”: 49670, “border”: 2, “gridx”: 2, “gridy”: 2}, “c”: {“width”: 45062, “height”: 49670, “border”: 2, “gridx”: 2, “gridy”: 2}}, “rdefs”: {“model”: “color”, “projection”: “normal”, “defaultZ”: 0, “defaultT”: 0, “invertAxis”: false}, “roi_count”: 0, “delta_t”: , “delta_t_unit_symbol”: null, “import_date”: “2020-10-09 15:51:02”, “acquisition_date”: “2019-09-06 13:23:00”, “families”: [“linear”, “polynomial”, “exponential”, “logarithmic”]}

Best
Vignesh

Hi,
Apologies for the delay in replying.
It would be useful if you could provide us with a sample file, so we can look at potential fixes for this issue. We have an upload site at https://www.openmicroscopy.org/qa2/qa/upload/ (apologies - this is a bit dated and requires you to enable Flash in your browser).

Thanks,
Will.

Hi Will
I provided a sample file through the upload site. It would be great if you could look into it.
Best
Vignesh

Hi
Could you please look into this issue.
Thanks
Vignesh

Hi,
Apologies for the delay.
I tested with the images you uploaded and created an issue at https://github.com/ome/omero-iviewer/pull/359 which is fixed by the PR at https://github.com/ome/omero-iviewer/pull/359.

Once tested and merged, this will be in the next iviewer release.

Regards,
Will.

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Thanks a lot. Looking forward to it