bioio-devs bioio issues

bioio-devs / 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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issues

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ubuntu 18.04 support (GLIBC >= 2.28)

#76 toloudis opened 1 month ago
4
admin/move-doc-publishing-to-release-cycle

#75 evamaxfield closed 2 months ago
0
Update ome_tiff_writer.py to remove reference to `image_names`

#74 TimMonko closed 2 months ago
0
image_name parameter in OmeTiffWriter should be clearly accessible with BioImage

#73 TimMonko opened 2 months ago
0
unpin zarr max version

#72 joshua-gould closed 2 months ago
6
cannot read file from S3 within parallelized loop

#71 cfrick13 closed 2 months ago
11
Remove numpy<2.0.0 restriction

#70 pgarrison opened 3 months ago
2
add channel selections to writer

#69 toloudis closed 4 weeks ago
1
User Warning due to dask dependency discrepancy and ND2File()

#68 felixS27 closed 2 months ago
1
Support public s3 files automatically

#67 SeanLeRoy closed 3 months ago
5
`AttributeError` no `_plugin` with custom `Reader`

#66 sea-shunned closed 2 months ago
2
Plans to drop py39 and add py312

#65 evamaxfield closed 2 months ago
3
bugfix/correct-version-in-doc-builds

#64 evamaxfield closed 4 months ago
1
feature/reader-surface-info

#63 BrianWhitneyAI closed 4 months ago
0
feature/plugin-registry

#62 BrianWhitneyAI closed 4 months ago
3
Read from public `s3://` paths without authentication, without requiring any code change from users

#61 pgarrison closed 3 months ago
1
Reader-specific documentation can be hard to discover

#60 pgarrison closed 4 months ago
1
bugfix/missing-plugin-metadata

#59 BrianWhitneyAI closed 4 months ago
2
generated docs are getting wrong version number

#58 toloudis closed 2 months ago
7
Bioio plugin dump unable to report plugins

#57 BrianWhitneyAI closed 4 months ago
0
Plugin Reader Metadata Does Not Standardize Supported Suffixes

#56 evamaxfield closed 3 months ago
3
bugfix/longest-suffix-wins

#55 evamaxfield closed 3 months ago
9
bioio-tifffile takes precedence over bioio-ome-tiff for ome-tiffs

#54 evamaxfield closed 3 months ago
2
remove zarr<2.18.0 constraint

#53 toloudis closed 2 months ago
1
add resolution_level_dims

#52 BrianWhitneyAI closed 4 months ago
0
Check reader for image typing

#51 BrianWhitneyAI closed 4 months ago
2
Admin: update pre-commit to `ruff`

#50 evamaxfield opened 4 months ago
1
Centralized guess dim order

#49 BrianWhitneyAI closed 4 months ago
2
Feature/ome zarr writer v2

#48 toloudis closed 4 months ago
1
feature/array-like-reader

#47 BrianWhitneyAI closed 4 months ago
0
Add new ome-zarr-writer

#46 toloudis closed 4 months ago
0
Clarify that the equivalent of aicsimageio.types.PhysicalPixelSizes is bioio_base.types.PhysicalPixelSizes

#45 SergeEParent opened 6 months ago
0
Update MIGRATION.md

#43 toloudis closed 5 months ago
0
relax the enforce_exists check because it will be done later

#42 toloudis closed 7 months ago
1
HTTP URL for ZARR fails to be validated by `determine_plugin` for bioio-ome-zarr

#41 pgarrison closed 7 months ago
6
Support ZARRs via https

#40 pgarrison closed 7 months ago
0
Add ArrayLikeReader

#39 toloudis closed 4 months ago
0
bioio-tifffile and bioio-ome-tiff parse ome-tiff metadata differently

#38 TimMonko closed 2 months ago
2
ci(dependabot): bump extractions/setup-just from 1 to 2

#37 dependabot[bot] closed 9 months ago
0
writer compression parameter

#36 toloudis opened 9 months ago
1
read physical time metadata

#35 toloudis opened 9 months ago
1
ci(dependabot): bump codecov/codecov-action from 3 to 4

#34 dependabot[bot] closed 10 months ago
0
reader chunk_dims are too coarse-grained for dask

#33 toloudis opened 10 months ago
0
ci(dependabot): bump actions/setup-python from 4 to 5

#32 dependabot[bot] closed 10 months ago
1
Unable to open czi line-scan kymographs - missing raw frame(t) pixel data

#31 cudmore opened 11 months ago
1
add resolution levels implementation

#30 toloudis closed 11 months ago
1
can't instantiate BioImage in v1.0

#29 toloudis closed 8 months ago
3
Improve error message on UnsupportedFileFormatError

#27 tlambert03 closed 4 months ago
7
Surface more information during reader/plugin selection

#26 SeanLeRoy closed 4 months ago
7
Add units to PhysicalPixelSizes

#25 SeanLeRoy opened 1 year ago
0