Ecosyste.ms: Issues

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

GitHub / ome/bioformats issues and pull requests

#4141 - CZI: fix image naming, especially for attachments

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

#4140 - Efficiency of Jpeg compression in TiffSaver

Issue - State: open - Opened by iwbh15 9 months ago

#4139 - Imspector MSR: NumberFormatException when parsing timepoints

Issue - State: open - Opened by dgault 9 months ago - 4 comments

#4138 - Issues 4150 + 4110: Consider ZSTD with pyramid levels and fix integer arithmetic scale problem

Pull Request - State: closed - Opened by swg08 9 months ago - 19 comments
Labels: include

#4136 - CVE-2022-1471

Issue - State: closed - Opened by Sravani-K 9 months ago - 2 comments
Labels: question

#4135 - TiffReader: mark order as certain if metadata is read from ImageJ tag

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

#4134 - mitosis.tif: wrong uncertain order

Issue - State: closed - Opened by NicoKiaru 10 months ago

#4131 - VirtualImagePlus: Retain B&C settings for each slice

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

#4129 - Bump version to 7.2.0-SNAPSHOT

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

#4128 - Update version numbers to 7.1.0

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

#4127 - parseOptions strips characters after "]"

Issue - State: open - Opened by CFGrote 10 months ago - 3 comments

#4126 - Bump dependency versions

Pull Request - State: closed - Opened by dgault 10 months ago - 1 comment

#4125 - Remove duplicate org.json:json dependency declaration

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

#4124 - Bump logbook version to 1.3.14

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

#4123 - Bump org.json:json from 20230227 to 20231013 in /components/formats-bsd

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 2 comments
Labels: dependencies

#4122 - Support mixed codecs with precompressed tiles

Issue - State: open - Opened by melissalinkert 10 months ago - 1 comment

#4121 - Add precompressed tile support for additional readers and writers

Issue - State: open - Opened by melissalinkert 10 months ago - 2 comments

#4119 - Gha update

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

#4118 - Dont check for update if FormatTools.VERSION is "(unknown version)"

Issue - State: open - Opened by CGDogan 10 months ago - 2 comments
Labels: enhancement

#4117 - Work-around for breaking change in CellSens 4.1

Pull Request - State: closed - Opened by ed-scanlon 11 months ago - 6 comments
Labels: include

#4116 - Change in CellSens 4.1 causing exception in VSI format reader.

Issue - State: closed - Opened by ed-scanlon 11 months ago - 2 comments
Labels: reader:VSI

#4115 - Revert RunTimeException when JPEGTurbo cannot be loaded

Pull Request - State: closed - Opened by dgault 11 months ago - 3 comments

#4114 - Add test for image names when resolutions are not flattened

Pull Request - State: closed - Opened by melissalinkert 11 months ago - 3 comments

#4113 - TiffWriter: incorrect BigTIFF threshold

Issue - State: open - Opened by dgault 11 months ago - 1 comment

#4112 - Imaris HDF: populate channel names

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

#4111 - OIR: channel order and missing pixel block fixes

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

#4110 - Opening CZI compressed with ZSTD does not allow access to series (pyramid levels)

Issue - State: closed - Opened by sebi06 12 months ago - 3 comments
Labels: reader:ZeissCZI

#4109 - #4090 breaks support for Apple Silicon for formats that don't need TurboJPEG

Issue - State: closed - Opened by petebankhead 12 months ago - 4 comments
Labels: bug

#4108 - nd2: UnknownFormatException

Issue - State: closed - Opened by dominikl 12 months ago - 1 comment

#4107 - Bump version to 7.1.0-SNAPSHOT

Pull Request - State: closed - Opened by dgault 12 months ago

#4106 - Bump org.json:json from 20230227 to 20231013 in /components/formats-gpl

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago
Labels: dependencies

#4105 - Bump version to 7.0.1

Pull Request - State: closed - Opened by dgault 12 months ago

#4104 - Micromanger: Add support for alternative metadata field names

Issue - State: open - Opened by dgault 12 months ago - 1 comment

#4103 - CZI: Label and macro image incorrectly labelled

Issue - State: closed - Opened by dgault 12 months ago - 1 comment
Labels: reader:ZeissCZI

#4102 - CZI: Autostich fails

Issue - State: open - Opened by dgault 12 months ago - 10 comments
Labels: reader:ZeissCZI

#4101 - Bump ome-common version to 6.0.20

Pull Request - State: closed - Opened by dgault 12 months ago - 1 comment

#4099 - TIFF: check IFD entry offset before seeking

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

#4098 - TIFF: throw exception on 64-bit int data

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

#4096 - Update GitHub Actions from checkout v2 to v3

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

#4095 - MetaMorph nd file - Invalid image number

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

#4094 - File header update

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

#4092 - Commits an alternative Zeiss CZI Reader

Pull Request - State: open - Opened by NicoKiaru about 1 year ago - 46 comments
Labels: exclude

#4090 - Throw error when cannot load library

Pull Request - State: closed - Opened by CGDogan about 1 year ago - 2 comments
Labels: include

#4089 - Loading 64-bit int TIFFs

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

#4088 - CZI: unify channel color parsing

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

#4087 - ZeissCZIReader get lut error

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

#4086 - CZI: interpret ContrastMethod field under Channel and map to OME-XML

Issue - State: open - Opened by dsudar about 1 year ago - 1 comment
Labels: enhancement

#4085 - CV7000 improvements

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

#4084 - CZI: Wrong dimensions

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

#4083 - NDPI: correct for potential integer overflow in stored restart marker tag

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

#4082 - NDPI: incorrect pixels at bottom of full-resolution image

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

#4081 - SVS: fix a variety of small issues

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

#4080 - Exporter plugin: remove any extra Channel elements

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

#4079 - Leica LIF: throw a nicer exception if no images are found

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

#4078 - OIR: fix off-by-one in XML block reading

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

#4077 - TillVision: fix some metadata parsing and .pst detection issues

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

#4076 - VSI: fix uncompressed BGR data

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

#4075 - Photoshop TIFF: fix plane reading with memoization

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

#4074 - Gel: check IFD count in isThisType

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

#4073 - OME-TIFF: optionally fail fast if an invalid file is encountered

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

#4072 - Ventana: fix tile arithmetic for smallest resolutions

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

#4071 - IVision: improve version and data type checks in isThisType

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

#4070 - Gatan DM3: be more defensive in parsing acquisition mode

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

#4069 - bfconvert misreports stage position when converting from metamorph tiff ND

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

#4068 - czi files with mixed confocal and airyscan channels cannot be uploaded on OMERO

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

#4067 - Mouse over triggers an exception while saving virtual stack (Metamorph)

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

#4066 - Slidebook: ArrayIndexOutOfBoundsException

Issue - State: open - Opened by dgault about 1 year ago - 5 comments

#4065 - CellSens IndexOutOfBoundsException

Issue - State: closed - Opened by jburel about 1 year ago - 4 comments

#4064 - Jpegturboserviceimpl sometimes doesnt like restartinterval and dimensions

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

#4063 - Bump version to 7.0.1-SNAPSHOT

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

#4062 - Bump version to 7.0.0

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

#4061 - Don't fail on non-4:4:4 JPEG

Pull Request - State: closed - Opened by CGDogan about 1 year ago - 13 comments
Labels: include

#4060 - Bump ome-common, ome-codecs and ome-stubs

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

#4059 - TiffSaver: produce valid 4-channel RGBA images

Pull Request - State: closed - Opened by CGDogan about 1 year ago - 4 comments
Labels: include

#4057 - Add CodecOptions.disableChromaSubsampling

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

#4056 - DNG file only displays as a single channel

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

#4055 - Legacy QT removal

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

#4054 - Legacy ND2 removal

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

#4053 - Fixes a NPE in OperettaReader.

Pull Request - State: closed - Opened by NicoKiaru about 1 year ago - 2 comments
Labels: include

#4052 - Allow finding potential readers when the file extension is not known

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

#4051 - fix aplreader throwing nullptrexception

Pull Request - State: closed - Opened by CGDogan about 1 year ago - 9 comments
Labels: include

#4050 - Flex: ignore files where compression cannot be identified

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

#4049 - Remove LegacyND2Reader and options

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

#4047 - Remove Woolz support

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

#4046 - Build is broken when OME servers are down

Issue - State: open - Opened by aubreyrjones about 1 year ago - 3 comments

#4045 - May I have access to the data repository please ; I need this for GraalVM

Issue - State: open - Opened by CGDogan about 1 year ago - 2 comments

#4044 - ARM64 libturbojpeg linux

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

#4043 - FlowSightReader: Tried to read past end of IFD data

Issue - State: closed - Opened by jburel about 1 year ago - 4 comments