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camicroscope / caMicroscope

Digital pathology image viewer with support for human/machine generated annotations and markups.
BSD 3-Clause "New" or "Revised" License
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HTTP 404 attempting to load TileSource #1037

Open 2grep opened 2 days ago

2grep commented 2 days ago

Describe the bug caMicroscope viewer launches and fails to find TileSource for 5 seconds: in white in the background "Unable to open [object Object]: HTTP 404 attempting to load TileSource" and in black over the top "HTTP 404 attempting to load TileSource" then aborts back to SLIDE view (/apps/table.html)

Selected lines from browser console Uncaught ReferenceError: module is not defined at DrawHelper.js:354:1

GET http://192.168.86.16:4010/img/IIP/raw/?DeepZoom=/images/CAP2014BP-01b.svs.dzi 404 (Not Found) (anonymous) @ CaMic.js:175 Promise.then loadImg @ CaMic.js:164 initCore @ init.js:197 (anonymous) @ init.js:130 setInterval initialize @ init.js:125

Following that 404'd URL Error opening '/images/CAP2014BP-01b.svs' with BioFormats, error loci.formats.FormatException: No IFDs found loci.formats.FormatException: No IFDs found at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:470) at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:609) at loci.formats.FormatReader.setId(FormatReader.java:1466) at loci.formats.ImageReader.setId(ImageReader.java:863) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:660) at loci.formats.Memoizer.setId(Memoizer.java:726) at org.camicroscope.BFBridge.BFOpen(BFBridge.java:218)

To Reproduce Steps to reproduce the behavior:

  1. Reformat machine, install Ubuntu, install Docker, install Distro per directions
  2. Visit caMicroscope site on local intranet
  3. Upload batch of 24 slides, check all slides, note 3 green checks on all slides. Click done
  4. Visit SLIDES
  5. On any slide, click Open

Expected behavior Slide viewer opens and starts rendering tiles

Server (please complete the following information):

Desktop

Additional context

2grep commented 2 days ago

Note: I do not have this problem with Distro installed on my local Mac.

Installed a desktop environment on the server and I have the same problem on the server. Why is this happening on Ubuntu and not my Mac?

birm commented 1 day ago

Thank you for reaching out. This could be a ARM/x86_64 issue, which would explain the ubuntu/macos difference for tileserver behavior.

Can you tell me a little bit about the svs files? It's surprising to me that it's returning bioformats error traces over openslide. The logic for that is here (https://github.com/camicroscope/iipImage/blob/10e6732bfc2aba926be73f42f00ec7728523758f/iipsrv/src/IIPImage.cc#L128) and usually openslide can read svs files.

2grep commented 1 day ago

Hmmm... there may be some operator error here. I got success with a batch of 2 files. The real issue may be that the batch upload workflow is not terribly transparent once you're in it, so it's hard to understand what's going on. For example, a per-file upload progress bar might be helpful.