Ecosyste.ms: Issues

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

GitHub / ome/ZarrReader issues and pull requests

#96 - Multiple PlateAcquisitions: Images in wrong Wells

Issue - State: open - Opened by will-moore 25 days ago - 1 comment

#95 - Class cast exception when parsing metadata

Pull Request - State: open - Opened by dgault about 1 month ago - 7 comments

#94 - `java.lang.ClassCastException` on ZARR import

Issue - State: open - Opened by jo-mueller about 2 months ago - 8 comments

#93 - Bump version to 0.5.3-SNAPSHOT

Pull Request - State: closed - Opened by dgault 2 months ago

#92 - Bump version to 0.5.2

Pull Request - State: closed - Opened by dgault 2 months ago

#91 - Bump Bio-Formats version to 7.3.1

Pull Request - State: closed - Opened by dgault 2 months ago

#90 - Bump version to 0.5.2-SNAPSHOT

Pull Request - State: closed - Opened by dgault 4 months ago

#89 - Bump version to 0.5.1

Pull Request - State: closed - Opened by dgault 4 months ago

#88 - Add Change Log for 0.5.1

Pull Request - State: closed - Opened by dgault 4 months ago

#87 - Bump formats-api version to 7.3.0

Pull Request - State: closed - Opened by dgault 4 months ago

#86 - Bumping version to 0.5.1-SNAPSHOT

Pull Request - State: closed - Opened by dgault 4 months ago

#85 - Bump version to 0.5.0

Pull Request - State: closed - Opened by dgault 4 months ago

#84 - ChangeLog: Add missing entry for PR #75

Pull Request - State: closed - Opened by dgault 4 months ago

#82 - Reintroduce S3FileSystemStore

Pull Request - State: closed - Opened by dgault 7 months ago - 32 comments

#81 - add Java 17 to testing matrix

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

#80 - Review action

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

#78 - Reduce number of fields in memo file

Pull Request - State: open - Opened by dgault 8 months ago - 4 comments

#77 - Index Out Of Bounds when importing to OMERO docker

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

#76 - blosc problem on import of ome.zarr into OMERO

Issue - State: open - Opened by pwalczysko 8 months ago - 3 comments

#75 - Update handling and parsing of acquisition metadata

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

#74 - JZarr: Add jackson.core and jackson-databind to exclsions

Pull Request - State: closed - Opened by dgault 10 months ago - 3 comments

#73 - Update ReadMe and Change Log

Pull Request - State: closed - Opened by dgault 10 months ago - 4 comments

#72 - OMEZarrReader.jar download link to artifactory

Issue - State: closed - Opened by will-moore 10 months ago

#71 - Bump Bio-Formats to version 7.1.0

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

#70 - Bump version to 0.4.1-SNAPSHOT

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

#69 - Bump version to 0.4.0

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

#68 - Future API updates

Issue - State: open - Opened by dgault 10 months ago

#67 - NGFF Testing

Issue - State: closed - Opened by dgault 11 months ago - 8 comments

#66 - Bump dev.zarr:jzarr to 0.4.2

Pull Request - State: closed - Opened by sbesson 11 months ago - 5 comments

#65 - Bumping Bio-Formats version to 7.0.0

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

#64 - ZarrReader performance improvements

Pull Request - State: closed - Opened by dgault about 1 year ago - 61 comments

#63 - Memo file generation - performance

Issue - State: closed - Opened by will-moore about 1 year ago - 1 comment

#62 - Update README.md

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

#61 - Deps missing from B-F update site

Issue - State: open - Opened by joshmoore about 1 year ago - 1 comment

#60 - Correct README regarding jzarr library

Issue - State: closed - Opened by joshmoore about 1 year ago - 1 comment

#59 - Actions update

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

#58 - Add new option to list pixels in getUsedFiles

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

#57 - Use canonical path for calls to ZarrService

Pull Request - State: closed - Opened by dgault over 1 year ago - 9 comments

#56 - remove duplicate declaration

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

#55 - ClassCastException when parsing acqusition start time

Issue - State: open - Opened by dgault over 1 year ago - 1 comment

#54 - Move to dev.zarr:jzarr

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

#53 - Reorder group keys

Pull Request - State: closed - Opened by dgault over 1 year ago - 15 comments

#52 - Try to reproduce Well reordering issue with Fileset swapping

Issue - State: open - Opened by will-moore over 1 year ago - 6 comments

#51 - Bump version to 0.3.2-SNAPSHOT

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

#50 - Bump version to 0.3.1

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

#49 - ZarrReader: Update handling of pre-existing plate metadata

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

#48 - NPE: Using idr0138

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

#47 - upgrade setup-java action. Current version uses set-output

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

#46 - Document blosc requirement

Issue - State: open - Opened by joshmoore over 1 year ago

#45 - "Unable to load library 'blosc'" error when reading pixel data

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

#44 - Multiple multiscales

Issue - State: open - Opened by will-moore almost 2 years ago - 6 comments

#43 - Fail on import of a plate

Issue - State: open - Opened by pwalczysko almost 2 years ago - 1 comment

#42 - switch to new output command

Pull Request - State: closed - Opened by jburel almost 2 years ago - 1 comment

#41 - ZarrReader: Update getUsedFiles to use the noPixels flag

Pull Request - State: closed - Opened by dgault about 2 years ago - 3 comments

#40 - NGFF Plate import - slow and OOM due to many files

Issue - State: open - Opened by will-moore about 2 years ago - 4 comments

#39 - Import of zarr into OMERO merge-ci latest-ci

Issue - State: closed - Opened by pwalczysko about 2 years ago - 4 comments

#38 - Dependency updates

Pull Request - State: closed - Opened by dgault over 2 years ago - 9 comments

#37 - Import of zarr is slower

Issue - State: open - Opened by pwalczysko over 2 years ago - 1 comment

#36 - naming of images in omero

Issue - State: open - Opened by pwalczysko over 2 years ago - 3 comments

#35 - Test xarray compatible datasets

Issue - State: open - Opened by joshmoore over 2 years ago - 1 comment

#34 - No original metadata

Issue - State: closed - Opened by pwalczysko over 2 years ago - 1 comment

#33 - HCS and handling of row/column index keys

Issue - State: closed - Opened by sbesson over 2 years ago - 1 comment

#32 - Integration with Bio-Formats

Issue - State: open - Opened by sbesson over 2 years ago

#31 - ZarrReader: Add support for OME-XML from bf2raw

Pull Request - State: closed - Opened by dgault over 2 years ago - 30 comments

#30 - Minor adjustments

Pull Request - State: closed - Opened by jburel over 2 years ago - 2 comments

#29 - Remove dependency

Pull Request - State: closed - Opened by jburel over 2 years ago

#28 - ZarrReader: Add support for OME-XML from bf2raw

Pull Request - State: closed - Opened by dgault over 2 years ago - 2 comments

#27 - Wrong pixel values in ome.zarr made from ome.tiff

Issue - State: closed - Opened by pwalczysko over 2 years ago - 2 comments

#25 - Multi-file images do not import correctly if nested in a .zarr folder

Issue - State: open - Opened by pwalczysko over 2 years ago - 7 comments

#24 - ZarrReader: HCS validation fixes

Pull Request - State: closed - Opened by dgault over 2 years ago - 15 comments

#23 - Fixes for dimension and tiling issues

Pull Request - State: closed - Opened by dgault over 2 years ago

#22 - HCS validation errors

Issue - State: closed - Opened by sbesson over 2 years ago

#21 - ZarrReader: Fix for plates with no acquisitions

Pull Request - State: closed - Opened by dgault over 2 years ago

#20 - ZarrReader: Use chunk API

Pull Request - State: open - Opened by dgault over 2 years ago - 3 comments

#19 - Plates with no acquisitions metadata throw a NPE

Issue - State: closed - Opened by sbesson over 2 years ago

#18 - Incorrect handling of images with labels

Issue - State: open - Opened by sbesson over 2 years ago

#17 - Incorrectly detected dimensions and tile sizes

Issue - State: closed - Opened by sbesson over 2 years ago - 1 comment

#16 - OS X arm64 support (jna dependency)

Issue - State: open - Opened by sbesson over 2 years ago

#15 - Unidata dependency unification

Issue - State: closed - Opened by sbesson over 2 years ago - 1 comment

#14 - Add standard build metadata to the JAR manifest

Pull Request - State: closed - Opened by sbesson over 2 years ago - 1 comment

#13 - Add BSD-2 license

Pull Request - State: closed - Opened by sbesson over 2 years ago - 1 comment

#12 - Small jar deployment

Pull Request - State: closed - Opened by joshmoore almost 3 years ago - 6 comments

#11 - Activate tests in maven

Pull Request - State: closed - Opened by joshmoore almost 3 years ago - 1 comment

#10 - Drop uber jar ?

Issue - State: open - Opened by joshmoore almost 3 years ago - 1 comment

#9 - Extend workflow to upload built JAR as a CI artifact

Pull Request - State: closed - Opened by sbesson almost 3 years ago - 1 comment

#8 - ZarrReader: Update to support 0.4.0 datasets

Pull Request - State: closed - Opened by dgault about 3 years ago - 29 comments

#7 - Replace Doubles with Integers

Pull Request - State: closed - Opened by joshmoore about 3 years ago - 1 comment

#6 - Pass 'level' to CompressorFactory

Pull Request - State: closed - Opened by joshmoore about 3 years ago - 1 comment

#5 - ZarrReader: NPE and parsing fixes

Pull Request - State: closed - Opened by dgault about 3 years ago - 2 comments

#4 - Bump to SNAPSHOT for merge build

Pull Request - State: closed - Opened by joshmoore about 3 years ago - 8 comments

#3 - ZarrReader: Add Unit tests

Pull Request - State: closed - Opened by dgault over 3 years ago - 3 comments

#2 - Actions

Pull Request - State: closed - Opened by jburel over 3 years ago - 5 comments

#1 - Initial Prototype ZarrReader

Pull Request - State: closed - Opened by dgault over 3 years ago