Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / AllenCellModeling/aicsimageio issues and pull requests

#558 - Extract Physical Pixel Size from SEM TIFF metadata.

Issue - State: open - Opened by gyger about 1 month ago - 1 comment

#556 - Documentation/typo in dim_order documentation

Pull Request - State: open - Opened by alanocallaghan 4 months ago

#555 - tifffile dependency: version pin outdated?

Issue - State: closed - Opened by m-albert 4 months ago - 4 comments

#554 - Importing fails

Issue - State: closed - Opened by onurserce 4 months ago - 2 comments

#552 - Remove ceiling on dependencies

Issue - State: open - Opened by joshua-gould 5 months ago

#551 - add doc for ome zarr writer

Pull Request - State: open - Opened by jackyko1991 5 months ago

#550 - Large timing overhead on TiffReader

Issue - State: open - Opened by Armavica 6 months ago - 6 comments

#549 - TimeStamps

Issue - State: open - Opened by ant-trullo 6 months ago

#548 - Move test resources to new bucket

Pull Request - State: closed - Opened by SeanLeRoy 7 months ago

#547 - Bugfix/Bfio unpin tifffile

Pull Request - State: closed - Opened by jplumail 7 months ago - 1 comment

#546 - Allow more channels in metadata than in data

Pull Request - State: closed - Opened by SeanLeRoy 7 months ago - 1 comment

#545 - support cache file system

Pull Request - State: open - Opened by joshua-gould 8 months ago - 1 comment

#543 - Remove ceiling on Pillow; adjust default reader expectations

Pull Request - State: closed - Opened by SeanLeRoy 8 months ago - 2 comments

#542 - Try newest imageio

Pull Request - State: closed - Opened by SeanLeRoy 8 months ago - 1 comment

#541 - main[base-imageio] failing due to Pillow

Issue - State: closed - Opened by SeanLeRoy 8 months ago

#540 - Move test files out of old modeling AWS account

Issue - State: open - Opened by SeanLeRoy 8 months ago

#539 - Specify resolution level for reading OME-Zarr

Issue - State: closed - Opened by tischi 8 months ago - 6 comments

#538 - Move off Node12

Pull Request - State: closed - Opened by SeanLeRoy 8 months ago - 1 comment

#537 - Adjust bfio & fsspec versions to avoid bugs

Pull Request - State: closed - Opened by SeanLeRoy 8 months ago - 1 comment

#536 - Limit fsspec version for now due to glob bug

Pull Request - State: closed - Opened by SeanLeRoy 9 months ago - 1 comment

#535 - Adjust pydantic import

Pull Request - State: closed - Opened by SeanLeRoy 9 months ago - 1 comment

#534 - pydantic user warning on import

Issue - State: closed - Opened by winnubstj 9 months ago

#533 - Feature/nd2reader-xarray-ome-metadata

Pull Request - State: closed - Opened by yichechang 9 months ago - 18 comments

#532 - czi number of channels can be out of sync and is reported as error

Issue - State: closed - Opened by toloudis 10 months ago - 2 comments
Labels: bug

#531 - test - ignore this

Pull Request - State: closed - Opened by SeanLeRoy 10 months ago

#530 - Drop py3.8 support; upgrade dependencies to support new min py

Pull Request - State: closed - Opened by SeanLeRoy 11 months ago - 1 comment

#529 - Revert to pre-2023.3.15 tifffile to avoid mm_stack issue

Pull Request - State: closed - Opened by SeanLeRoy 11 months ago - 1 comment

#528 - Fix publish task according to pypi rec for 2fa accounts

Pull Request - State: closed - Opened by SeanLeRoy 11 months ago - 2 comments

#527 - Limit numpy and dask

Pull Request - State: closed - Opened by SeanLeRoy 11 months ago - 1 comment

#526 - current dask no longer supports Python 3.8

Issue - State: closed - Opened by toloudis 11 months ago

#524 - ome_metadata fro czi file

Issue - State: closed - Opened by TomPJWyatt 12 months ago - 10 comments

#523 - tifffile min version incorrect, and now incompatible with bfio extra

Issue - State: closed - Opened by tlambert03 12 months ago - 6 comments

#522 - DependencyFix/Upgrade ome-types to 0.3.4

Pull Request - State: closed - Opened by Armavica 12 months ago - 14 comments

#521 - Feature/ome_metadata-for-nd2

Pull Request - State: closed - Opened by tlambert03 12 months ago - 3 comments

#520 - `Dimensions` typing

Issue - State: closed - Opened by multimeric 12 months ago - 2 comments

#519 - Feature/OmeZarr Chunk Dims

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 2 comments

#518 - Latest version of aicsimageio cannot read some czi images

Issue - State: closed - Opened by christinab12 about 1 year ago - 5 comments
Labels: duplicate, third party dependency

#517 - same Example_FLIM.lif has 32 bit images in it that aicsimageio cannot read

Issue - State: closed - Opened by ronnkling about 1 year ago - 3 comments
Labels: third party dependency

#516 - OmeZarrWriter: allow user choice of chunk sizes!

Issue - State: closed - Opened by toloudis about 1 year ago

#515 - dtype error converting Olympus VSI

Issue - State: closed - Opened by dyf about 1 year ago - 8 comments

#514 - Guess dims for missing field 'axes'

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 2 comments

#513 - czi reader is very slow to get channel_names for a large file

Issue - State: closed - Opened by toloudis about 1 year ago - 2 comments

#512 - Feature/omezarrreader guess dims

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 1 comment

#511 - LIF image data ordering

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 2 comments

#510 - Admin/OmeZarrReader variable dimension unit tests

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 5 comments

#509 - OmeZarrReader physical_pixel_sizes support

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 1 comment

#508 - channel-z ordering problem when reading lif

Issue - State: closed - Opened by TomPJWyatt about 1 year ago - 7 comments
Labels: third party dependency

#507 - Admin/OmeZarrReader redundant test

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 2 comments

#506 - OmeZarrReader physical pixel resolution

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago
Labels: enhancement

#505 - OmeZarrReader Performance Benchmarks

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago - 11 comments

#504 - OmeZarrReader only has "public data or supply your own creds in env"

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago - 3 comments

#503 - OmeZarrReader dimension guess for absent field 'axes'

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago

#502 - OmeZarrReader Test with variable dimensions

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago

#501 - OmeZarrReader redundant testfile

Issue - State: closed - Opened by BrianWhitneyAI about 1 year ago
Labels: admin

#500 - Bugfix/Bfio Tifffile breaks tests

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 2 comments

#499 - Upgrade imageio to prevent bug with Pillow in 2.28.0

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 1 comment

#498 - Ignore missing Position dimension

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 2 comments

#497 - added parser="lxml"

Pull Request - State: closed - Opened by joshua-gould about 1 year ago - 2 comments

#496 - Feature/sldy reader

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 2 comments

#495 - Tifffile error when accessing dims attribute

Issue - State: closed - Opened by jplumail about 1 year ago - 9 comments
Labels: third party dependency

#494 - Admin: Update deploy process

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 4 comments

#493 - OmeZarrReader

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 6 comments

#492 - store frame metadata when reading a specific scene

Pull Request - State: closed - Opened by joshua-gould about 1 year ago - 1 comment
Labels: enhancement

#491 - does not open the latest leica formats for .lif

Issue - State: closed - Opened by ronnkling about 1 year ago - 11 comments

#490 - test aics internal nd2 files

Issue - State: closed - Opened by toloudis about 1 year ago - 3 comments

#489 - Admin/drop 3.8 support for newest xarray

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 7 comments

#488 - Nikon nd2 file causing error

Issue - State: closed - Opened by toloudis about 1 year ago - 3 comments

#487 - Adjusting tiffile versioning

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 4 comments

#486 - Bugfix/slow tile retrieval

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 2 comments

#485 - Feature/tiledtiffwriter

Pull Request - State: closed - Opened by BrianWhitneyAI about 1 year ago - 1 comment

#483 - Extract S dim from OME data

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 3 comments

#482 - get_mosaic_tile_position is prohibitively slow

Issue - State: closed - Opened by toloudis about 1 year ago - 2 comments

#481 - Restrict xarray version to support py3.8

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 2 comments

#480 - Bugfix/mosaic lif merge error

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 1 comment

#479 - aicsimageio uses ome_types in a way that causes the emission of a warning

Issue - State: closed - Opened by anntzer about 1 year ago - 3 comments

#478 - try to use optimized codepath through ome-types

Pull Request - State: closed - Opened by toloudis about 1 year ago - 1 comment

#477 - Bugfix/empty scene name

Pull Request - State: closed - Opened by BrianWhitneyAI over 1 year ago - 1 comment

#476 - Drop py3.8 support for newest xarray version

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 4 comments

#475 - Do something about xarray version issue

Issue - State: closed - Opened by SeanLeRoy over 1 year ago - 3 comments

#474 - feature/github-action-stale

Pull Request - State: closed - Opened by BrianWhitneyAI over 1 year ago - 2 comments

#473 - Bugfix: Upgrade minimum fsspec version

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 1 comment

#472 - Bugfix: Restrict tifffile version for now

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 3 comments

#471 - Bugfix: unclear warning for missing 'bfio' install.

Pull Request - State: closed - Opened by BrianWhitneyAI over 1 year ago - 3 comments

#470 - bugfix: removing 2.11.0 threshold

Pull Request - State: closed - Opened by BrianWhitneyAI over 1 year ago - 11 comments

#469 - Test passing without tifffile

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 1 comment

#468 - Bugfix: Avoid FssSpec bug

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 1 comment

#467 - Support reading ome-zarr files

Issue - State: closed - Opened by joshua-gould over 1 year ago - 2 comments

#466 - Quality of Life: Make pip install platform independent

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 4 comments

#465 - Bugfix: Dimension mismatch error + minor test fixes

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 6 comments

#464 - Bugfix: Fix tests not asserting error expected

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 3 comments

#463 - Bugfix/Docs-README-Mention-mvn/maven-requirement-for-bioformats_jar

Pull Request - State: closed - Opened by psobolewskiPhD over 1 year ago - 2 comments

#462 - OME Zarr metadata files do not have newline characters at the end of files

Issue - State: closed - Opened by galenlynch over 1 year ago - 3 comments

#461 - Fix/build fix ometypes validation

Pull Request - State: closed - Opened by toloudis over 1 year ago - 2 comments

#460 - Getting all mosaic positions at once

Issue - State: closed - Opened by yfukai over 1 year ago - 2 comments

#459 - Don't warn when opening ome.tif if bfio is not installed

Issue - State: closed - Opened by anntzer over 1 year ago - 1 comment

#458 - More descriptive scene index error message.

Pull Request - State: closed - Opened by pgarrison over 1 year ago - 1 comment

#457 - AICSImageIO fails to open OME-TIFF from Fiji which has type RGB

Issue - State: closed - Opened by sebi06 over 1 year ago - 1 comment