André Pedersen

> Basically, the worker is passed "the" image file, but VSI is a multi file format, and the worker doesn't have all of it to work with inside the docker....

Just tried running the [Nuclei Detection](https://github.com/DigitalSlideArchive/HistomicsTK/tree/master/histomicstk/cli/NucleiDetection) algorithm which is part of HistomicsTK on the full [CMU-1.tiff](https://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/) WSI from the OpenSlide test data. With default settings without setting the bounding box...

> Can you look in the actual girder log file (info.log) Below I have shared you the girder log file. Seems like a GirderException was raised due to `Read exceeds...

> See [girder/large_image#1075](https://github.com/girder/large_image/pull/1075) for a fix but not a total solution. Apparently that restriction wasn't there before we made a change to better support S3 assetstores -- it could just...

Oh, note that after the job is done, it takes quite long until the annotation becomes available under `Annotations`. Is the JSON format threadsafe? Could it be possible to speed...

Thank you for sharing your performance benchmarks. They seem similar to what I am observing on the desktop I was testing this on. If I understand it correctly, are all...

> I'd have to hunt through the metadata that bioformats exposes to find where it exposes the microns per pixel or the magnification. Sadly, bioformats is not as consistent between...

> See [girder/large_image#1074](https://github.com/girder/large_image/pull/1074) which uses data exposed a different way but should work. Oh, OK. I was not aware that you have found a fix for that issue. Then I...

What's the status on this issue? That is having proper cellSens VSI support during compute with HistomicsTK and girder worker. @markusdrange who made the issue https://github.com/DigitalSlideArchive/digital_slide_archive/issues/257, also needs this to...

Minor bump @manthey @dgutman. This is a feature that is of great interest for our project as most of our WSIs are stored in the `.vsi` format.