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Unsupported TIFF compression: 7 #310

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suminwei opened this issue Jul 3, 2024 · 4 comments
Open

Unsupported TIFF compression: 7 #310

suminwei opened this issue Jul 3, 2024 · 4 comments

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@suminwei
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suminwei commented Jul 3, 2024 •
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Hi, I am getting the following error when trying to run histoqc on .svs files.

Command:
python -m histoqc -c v2.1 -n 3 "./input_svs_test/*.svs"

Error:
2024-07-03 15:43:52,680 - INFO - -----Working on: ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs 1 of 15 TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered. ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs: JPEG compression support is not configured. 2024-07-03 15:43:52,701 - ERROR - ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideError'> An error produced by the OpenSlide library. Import this from openslide rather than from openslide.lowlevel. Unsupported TIFF compression: 7

I don't quite understand why it's not recognizing the .svs files?
Thank you.
@choosehappy
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choosehappy commented Jul 3, 2024 via email

@suminwei
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suminwei commented Jul 3, 2024 •
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Hi @choosehappy , thanks for the suggestion! I checked the md5sum of the file against the original that I downloaded using a manifest file from the TCGA site and they're the same.

@choosehappy
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apologies for the delay in responding - were you able to get this working? it looks like you had another issue with the HTML report you were able to resolve which seems like it's downstream from this?

@CielAl
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CielAl commented Jul 17, 2024

apologies for the delay in responding - were you able to get this working? it looks like you had another issue with the HTML report you were able to resolve which seems like it's downstream from this?

Could be better to do some ablation study here: in the exact same environment and a different environment, can the following code parse the image.

from openslide import OpenSlide
osh = OpenSlide('./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs')
region = osh.read_region((0, 0), 0, (512, 512))
region.show()

It may as well be an issue of corrupted openslide dependencies and therefore we need to rule them out and confirm whether it's a HistoQC issue.

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3 participants
@choosehappy @CielAl @suminwei