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bioio-devs
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bioio
Image reading, metadata management, and image writing for Microscopy images in Python
https://bioio-devs.github.io/bioio/OVERVIEW.html
BSD 3-Clause "New" or "Revised" License
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ubuntu 18.04 support (GLIBC >= 2.28)
#76
toloudis
opened
2 hours ago
0
admin/move-doc-publishing-to-release-cycle
#75
evamaxfield
closed
3 weeks ago
0
Update ome_tiff_writer.py to remove reference to `image_names`
#74
TimMonko
closed
4 weeks ago
0
image_name parameter in OmeTiffWriter should be clearly accessible with BioImage
#73
TimMonko
opened
4 weeks ago
0
unpin zarr max version
#72
joshua-gould
closed
3 weeks ago
6
cannot read file from S3 within parallelized loop
#71
cfrick13
closed
1 week ago
11
Remove numpy<2.0.0 restriction
#70
pgarrison
opened
1 month ago
1
add channel selections to writer
#69
toloudis
opened
1 month ago
1
User Warning due to dask dependency discrepancy and ND2File()
#68
felixS27
closed
1 week ago
1
Support public s3 files automatically
#67
SeanLeRoy
closed
1 month ago
5
`AttributeError` no `_plugin` with custom `Reader`
#66
sea-shunned
closed
2 weeks ago
2
Plans to drop py39 and add py312
#65
evamaxfield
closed
2 weeks ago
3
bugfix/correct-version-in-doc-builds
#64
evamaxfield
closed
2 months ago
1
feature/reader-surface-info
#63
BrianWhitneyAI
closed
2 months ago
0
feature/plugin-registry
#62
BrianWhitneyAI
closed
2 months ago
3
Read from public `s3://` paths without authentication, without requiring any code change from users
#61
pgarrison
closed
1 month ago
1
Reader-specific documentation can be hard to discover
#60
pgarrison
closed
2 months ago
1
bugfix/missing-plugin-metadata
#59
BrianWhitneyAI
closed
2 months ago
2
generated docs are getting wrong version number
#58
toloudis
closed
3 weeks ago
7
Bioio plugin dump unable to report plugins
#57
BrianWhitneyAI
closed
2 months ago
0
Plugin Reader Metadata Does Not Standardize Supported Suffixes
#56
evamaxfield
closed
2 months ago
3
bugfix/longest-suffix-wins
#55
evamaxfield
closed
2 months ago
9
bioio-tifffile takes precedence over bioio-ome-tiff for ome-tiffs
#54
evamaxfield
closed
2 months ago
2
remove zarr<2.18.0 constraint
#53
toloudis
closed
1 week ago
1
add resolution_level_dims
#52
BrianWhitneyAI
closed
2 months ago
0
Check reader for image typing
#51
BrianWhitneyAI
closed
2 months ago
2
Admin: update pre-commit to `ruff`
#50
evamaxfield
opened
3 months ago
1
Centralized guess dim order
#49
BrianWhitneyAI
closed
2 months ago
2
Feature/ome zarr writer v2
#48
toloudis
closed
2 months ago
1
feature/array-like-reader
#47
BrianWhitneyAI
closed
3 months ago
0
Add new ome-zarr-writer
#46
toloudis
closed
2 months ago
0
Clarify that the equivalent of aicsimageio.types.PhysicalPixelSizes is bioio_base.types.PhysicalPixelSizes
#45
SergeEParent
opened
4 months ago
0
Update MIGRATION.md
#43
toloudis
closed
3 months ago
0
relax the enforce_exists check because it will be done later
#42
toloudis
closed
5 months ago
1
HTTP URL for ZARR fails to be validated by `determine_plugin` for bioio-ome-zarr
#41
pgarrison
closed
5 months ago
6
Support ZARRs via https
#40
pgarrison
closed
5 months ago
0
Add ArrayLikeReader
#39
toloudis
closed
3 months ago
0
bioio-tifffile and bioio-ome-tiff parse ome-tiff metadata differently
#38
TimMonko
closed
1 week ago
2
ci(dependabot): bump extractions/setup-just from 1 to 2
#37
dependabot[bot]
closed
7 months ago
0
writer compression parameter
#36
toloudis
opened
7 months ago
1
read physical time metadata
#35
toloudis
opened
7 months ago
1
ci(dependabot): bump codecov/codecov-action from 3 to 4
#34
dependabot[bot]
closed
8 months ago
0
reader chunk_dims are too coarse-grained for dask
#33
toloudis
opened
8 months ago
0
ci(dependabot): bump actions/setup-python from 4 to 5
#32
dependabot[bot]
closed
8 months ago
1
Unable to open czi line-scan kymographs - missing raw frame(t) pixel data
#31
cudmore
opened
9 months ago
1
add resolution levels implementation
#30
toloudis
closed
9 months ago
1
can't instantiate BioImage in v1.0
#29
toloudis
closed
6 months ago
3
Improve error message on UnsupportedFileFormatError
#27
tlambert03
closed
2 months ago
7
Surface more information during reader/plugin selection
#26
SeanLeRoy
closed
2 months ago
7
Add units to PhysicalPixelSizes
#25
SeanLeRoy
opened
11 months ago
0
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