Opened issues in bf repo - check with this reader

[NicoKiaru]

[x] ome/bioformats#4110

• Files: in dropbox, cf linked issue
• Result:
  • Issue confirmed with the current bf reader
  • Issue not observed with the quick start reader

[x] ome/bioformats#4102

• Files: in dropbox, cf linked issue, and https://zenodo.org/records/8423633
• Result:
  • Issue not confirmed with the current bf reader and TEST 2023_10_10__1046 > skip
  • Issue confirmed (but is it the same issue) with the current bf reader and 20231016_dia1mthspax7DIApax7 1mthsA
  • Issue not observed with the quick start reader and 20231016_dia1mthspax7DIApax7 1mthsA

[] ome/bioformats#4086 (enhancement)

• Files: no file provided, but it should be doable to find one in the examples
• Not worked on

[] ome/bioformats#4029

• Files: no file provided, but it should be doable to find one in the examples
• Not worked on

[] ome/bioformats#3996

• Files: not available
• Can't be worked on

[] ome/bioformats#3921

• Files: no file provided, but it's not a problem to find one
• Not worked on

[] ome/bioformats#3919

• Files: not available (weshare link expired)
• Can't be worked on

[] ome/bioformats#3858

• problem with native lib loading - not relevant with the reader rewrite

[] ome/bioformats#3854

• Files: it's possible to artificially make a dataset to reproduce the issue
• Not worked on

[] ome/bioformats#3845

• Files: dropbox link (https://forum.image.sc/t/some-channel-names-not-importing-from-czi-files/69243)
• (Note: look at the background)
• Result:
  • Issue confirmed with the current bf reader
  • Issue also observed with the quick start reader

[] ome/bioformats#3790

• Files: expired link
• Result:
• Can't be worked on

[] ome/bioformats#3789

• Files: not available
• Result:
• Can't be worked on

[] ome/bioformats#3785

• Files: not available (expired link, and it's my fault!
• Result:
• Can't be worked on

[] ome/bioformats#3648

• Files: not available (expired link)
• Result:
• Can't be worked on

[] ome/bioformats#3591
Not sure this issue is still valid

[] ome/bioformats#3560

• Files: not available (expired link)
• Result:
• Can't be worked on

[*] ome/bioformats#3525

• Files: a still valid dropbox link
  (Note: this file takes forever to open)
• Result:
  • Issue confirmed with the current bf reader
  • Issue not observed with the quick start reader

[] ome/bioformats#3459
It's a question, not really an issue

[] ome/bioformats#3397

• Files: a still valid dropbox link
  I couldn't really understand what the issue is -

[] ome/bioformats#3381

• Files: not available (expired link)
• Result:
• Can't be worked on

[] ome/bioformats#3323

• Files: not available (expired link)
• Result:
• Can't be worked on

[] ome/bioformats#2975

• Files: not available
• Result:
• Can't be worked on

[] ome/bioformats#2962

• Files: not available
• Result:
• Can't be worked on

[] ome/bioformats#2946

• Files: not available
• Result:
• Can't be worked on

[] ome/bioformats#2467

• Files: not available
• Result:
• Can't be worked on

[psobolewskiPhD]

@NicoKiaru Just came across this while trying to find a way to read some JPEG-XR CZI Axioscans.
Can you clarify if:

[] https://github.com/ome/bioformats/issues/3858

problem with native lib loading - not relevant with the reader rewrite

means that this reader works around the jxrlib issue on arm64 macOS?

Edit: example file Zeiss-5-JXR.czi from https://openslide.cs.cmu.edu/download/openslide-testdata/Zeiss/

[NicoKiaru]

means that this reader works around the jxrlib issue on arm64 macOS?

If only! Nope unfortunately this reader suffers from the same limitations than the original bf reader. None of the decompression is done Java side - it's just delegated to the native decompressor. If no native is available, this reader will not fix it.

(NB: I have a slow connection, I couldn't open your link)