Update metadata in the filetypes and metadata episode#124
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Rendered Changes🔍 Inspect the changes: https://github.com/HealthBioscienceIDEAS/microscopy-novice/compare/md-outputs..md-outputs-PR-124 The following changes were observed in the rendered markdown documents: What does this mean?If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation. ⏱️ Updated at 2026-06-08 08:38:58 +0000 |
stellaprins
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Yes, same here.
Also, the rich metadata printed out with
import rich
rich.print(image.standard_metadata)
has changed for me to:
StandardMetadata(
binning='2x2',
column='2',
dimensions_present='CZYX',
image_size_c=3,
image_size_t=1,
image_size_x=672,
image_size_y=512,
image_size_z=21,
imaged_by='Zeiss',
imaging_datetime=datetime.datetime(2013, 12, 10, 17, 0, 17, 98422, tzinfo=datetime.timezone.utc),
objective='63x/1.4Oil',
pixel_size_x=0.20476190476190476,
pixel_size_y=0.20476190476190476,
pixel_size_z=0.35,
position_index=3,
row='6',
timelapse=False,
timelapse_interval=None,
total_time_duration=None
)
If this is the case for you too, you could add an updated screenshot to this PR?
The rest seems unchanged for me.
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Thanks @stellaprins - good point! I checked and I also get different output for The link checker action is currently failing due to : https://idr.openmicroscopy.org/search/?query=Name:idr0011-ledesmafernandez-dad4/screenD , but I think the website might be down at the moment? (I at least couldn't open this link in my browser or the IDR homepage: https://idr.openmicroscopy.org/) Do you get the same @stellaprins ? |
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@K-Meech I can open the links fine. I re-ran the link-checker and it is still failing (not sure whether it is the same issue?). I remember that previously I had to white list some links for this repo as they often made the link checker fail because of temporary issues. |
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Thanks for checking @stellaprins - I just tried the links and I can now open both successfully, so looks like IDR was down temporarily this morning. The Link Checker seems to be failing due to a different link, as the IDR ones now print ok. I've opened a separate issue to fix this: #127 I'll go ahead and merge this PR, as it seems un-related to any of these changes. |
Auto-generated via `{sandpaper}`
Source : 4d6953c
Branch : main
Author : Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Time : 2026-06-08 12:02:54 +0000
Message : Merge pull request #124 from HealthBioscienceIDEAS/km/update-metadata
Update metadata in the filetypes and metadata episode
Auto-generated via `{sandpaper}`
Source : 45fd68d
Branch : md-outputs
Author : GitHub Actions <actions@github.com>
Time : 2026-06-08 12:05:16 +0000
Message : markdown source builds
Auto-generated via `{sandpaper}`
Source : 4d6953c
Branch : main
Author : Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Time : 2026-06-08 12:02:54 +0000
Message : Merge pull request #124 from HealthBioscienceIDEAS/km/update-metadata
Update metadata in the filetypes and metadata episode
2 participants
Closes #120
Updates metadata output to match that from a fresh napari installation. This is mostly minor changes to field names and overall layout. I had to update one of the exercise questions, as the microscope model name no longer seems to appear in the printed metadata.
It'd be great if you could check that your output looks the same as mine.