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QuPath gets stuck when trying to open an image / opens it at low resolution only #894

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petebankhead opened this issue Jan 20, 2022 · 1 comment · Fixed by #896
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QuPath gets stuck when trying to open an image / opens it at low resolution only #894

petebankhead opened this issue Jan 20, 2022 · 1 comment · Fixed by #896
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petebankhead commented Jan 20, 2022 •
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Bug report

Describe the bug
QuPath v0.3.2 hangs when attempting to open certain images with Bio-Formats, outside of a project.

The problem occurs when:

  • Bio-Formats is the reader
  • There are multiple series (non-thumbnail) in the file
  • A project is not used to open the image

See https://forum.image.sc/t/problem-about-opening-ndpis-files-in-qupath-v0-3-1/62184/4

Update: Sometimes QuPath doesn't hang, but the image only opens at a low resolution

To Reproduce
Steps to reproduce the behavior:

  1. Launch QuPath but do not open a project
  2. Try to open an image containing multiple (non-thumbnail) series using Bio-Formats
  3. Select any series from the Open image dialog
  4. Wait... and wait.... and wait... then force quit

Expected behavior
Image opens properly, both inside and outside a project.

Desktop (please complete the following information):

  • OS: All
  • QuPath v0.3.1 and v0.3.2

Additional context
Problem was introduced in #867 so should not affect any older versions.

Solution / Workaround
Create a a project first, then open the image.

This avoids showing the 'Open image' dialog, and so should work.
@petebankhead petebankhead self-assigned this Jan 20, 2022
petebankhead added a commit to petebankhead/qupath that referenced this issue Jan 20, 2022
@petebankhead
Fix image selector/Bio-Formats bug
aaeff95 
Fixes qupath#894
There were two problems:
* ServerSelector would close the server that it returned
* BioFormatsImageServer could block forever waiting for a reader after the image was closed
@petebankhead petebankhead mentioned this issue Jan 20, 2022
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@petebankhead petebankhead mentioned this issue Mar 2, 2022
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@petebankhead petebankhead mentioned this issue Mar 12, 2022
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@petebankhead petebankhead mentioned this issue May 30, 2022
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@petebankhead petebankhead mentioned this issue Jul 16, 2022
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@petebankhead petebankhead changed the title Reading from Bio-Formats blocks forever when using multiple series outside a project QuPath gets stuck when trying to open an image Jul 17, 2022
@petebankhead petebankhead reopened this Jul 17, 2022
@petebankhead petebankhead pinned this issue Jul 17, 2022
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petebankhead commented Jul 17, 2022 •
edited

The code has been fixed, so this should work again in the next QuPath release (v0.4.0).

Until then, the workaround is to open the image through a project.

I'm leaving this issue open because the question understandably comes up quite often, and I want to make the solution easier to find.

Duplicates:

@petebankhead petebankhead mentioned this issue Jul 21, 2022
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@petebankhead petebankhead changed the title QuPath gets stuck when trying to open an image QuPath gets stuck when trying to open an image / opens it at low resolution Jul 22, 2022
@petebankhead petebankhead changed the title QuPath gets stuck when trying to open an image / opens it at low resolution QuPath gets stuck when trying to open an image / opens it at low resolution only Jul 22, 2022
@petebankhead petebankhead unpinned this issue Dec 16, 2022
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Fix image selector/Bio-Formats bug petebankhead/qupath
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