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

#4199 - LIF Reader: index out of bounds

Issue - State: open - Opened by jburel 12 days ago - 2 comments

#4198 - SDT: fix NegativeArraySizeException when reading files recorded by SPCM64 9.90

Pull Request - State: open - Opened by cqian89 13 days ago - 2 comments
Labels: include

#4197 - ICS: Fix NPE when image name is empty

Pull Request - State: closed - Opened by dgault 17 days ago - 1 comment

#4196 - DICOM: use FrameTimePointer to detect timelapse data

Pull Request - State: open - Opened by melissalinkert 20 days ago

#4195 - Andor SIF: Support files larger than 4 GB and with non-fixed-size footers

Pull Request - State: open - Opened by WalkerKnapp 24 days ago - 4 comments

#4194 - FEATURE REQUEST: BioFormats support for CZI Multi Scene images

Issue - State: open - Opened by MichaelDausmann 24 days ago - 3 comments

#4193 - Imaris: Remove empty color entries for non 0 indexed colors

Pull Request - State: open - Opened by dgault 27 days ago - 1 comment

#4192 - SVS/MinimalTiffReader: FormatException: No IFDs found

Issue - State: closed - Opened by dominikl 27 days ago - 1 comment

#4190 - Extend precompressed support to read DICOM and write TIFF/OME-TIFF

Pull Request - State: open - Opened by melissalinkert about 1 month ago - 1 comment

#4189 - Loading of indica tiff files

Issue - State: open - Opened by rharkes about 2 months ago - 2 comments
Labels: reader:new

#4188 - Fix a few string comparisons, fixes #4184

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

#4187 - Bump version to 8.0.0-SNAPSHOT

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

#4186 - Bump version to 7.3.0

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

#4185 - Bump ome-poi to 5.3.9 and ome-metakit to 5.3.7

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

#4184 - Strings are being compared with == and !=

Issue - State: closed - Opened by scuniff 3 months ago - 1 comment

#4183 - Bump lower level component versions prior to 7.3.0

Pull Request - State: closed - Opened by dgault 3 months ago - 1 comment

#4182 - Fix Java 9+ warnings in formats-gpl component

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

#4181 - Add support for reading compressed NDPI tiles

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

#4179 - Fix Java 9+ deprecation warnings in smaller components

Pull Request - State: closed - Opened by melissalinkert 3 months ago - 1 comment

#4177 - Fix some Java 9+ warnings in formats-bsd

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

#4176 - bfconvert: issue after changing tile size in ome.tiff

Issue - State: open - Opened by alexeykurbako 3 months ago - 1 comment

#4175 - showinf `OutOfMemoryError` with large JPG file

Issue - State: open - Opened by glyg 3 months ago - 3 comments

#4174 - DicomJSONProvider JSON format

Issue - State: open - Opened by ebremer 3 months ago

#4173 - bfconvert: remove extra channels if `-channel` was used

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

#4172 - testSaneUsedFiles: check getCurrentFile is the first file in the getUsedFiles list

Pull Request - State: open - Opened by sbesson 3 months ago - 2 comments

#4171 - Add `-quality` option to bfconvert

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

#4169 - Add method to add custom DicomJSONProvider

Issue - State: open - Opened by ebremer 3 months ago

#4168 - DICOM reader: better handling of nested sequences that include pixel data

Pull Request - State: closed - Opened by melissalinkert 3 months ago - 1 comment

#4167 - DICOM: treat ultrasound ECG data as timelapse

Pull Request - State: closed - Opened by melissalinkert 4 months ago - 3 comments

#4166 - SVS: Incorrect image colour

Issue - State: open - Opened by dgault 4 months ago - 1 comment

#4164 - Reduce DICOM write time

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

#4163 - SimplePCI: fix Z position handling

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

#4162 - Remove duplicate enum check and add clarifying comment

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

#4161 - bug: bfconvert generates bad DICOMs from SVS files

Issue - State: open - Opened by jcupitt 4 months ago - 3 comments

#4160 - Repeated conditional test II

Issue - State: closed - Opened by scuniff 4 months ago - 1 comment

#4159 - Turn off file-leak-detector if tests are run with Java 21

Pull Request - State: closed - Opened by melissalinkert 4 months ago - 2 comments

#4158 - Bump file-leak-detector to version 1.18 for JDK 21 support

Pull Request - State: closed - Opened by sbesson 4 months ago - 3 comments

#4157 - OME-XML: populate original metadata table

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

#4155 - Prairie: look for "<PV" string instead of just "PV"

Pull Request - State: closed - Opened by melissalinkert 5 months ago

#4154 - Update GitHub actions versions and add M1/Java 21 build

Pull Request - State: closed - Opened by melissalinkert 5 months ago

#4153 - CZI single channel image is read as RGB

Issue - State: closed - Opened by will-moore 5 months ago - 2 comments

#4152 - Bump version to 8.0.0-SNAPSHOT

Pull Request - State: closed - Opened by dgault 5 months ago

#4151 - Bump version to 7.2.0

Pull Request - State: closed - Opened by dgault 5 months ago

#4150 - CZI: Auto-stitch scaling

Issue - State: closed - Opened by dgault 5 months ago - 1 comment

#4148 - JPEG: reset `useLegacy` flag to its original state upon close

Pull Request - State: closed - Opened by melissalinkert 5 months ago - 3 comments

#4147 - Added support for ColumbusReader to import data with z stacks

Pull Request - State: closed - Opened by TBlackmore 5 months ago - 3 comments
Labels: include

#4146 - Plugin: Update ND2 widget indexing to fix chunkmap exception

Pull Request - State: closed - Opened by dgault 5 months ago - 1 comment

#4144 - SVS: remove thumbnails and improve label/macro detection

Pull Request - State: closed - Opened by melissalinkert 5 months ago

#4143 - Repeated conditional tests

Issue - State: closed - Opened by scuniff 6 months ago - 2 comments

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

Pull Request - State: closed - Opened by melissalinkert 6 months ago - 1 comment

#4140 - Efficiency of Jpeg compression in TiffSaver

Issue - State: open - Opened by iwbh15 6 months ago

#4139 - Imspector MSR: NumberFormatException when parsing timepoints

Issue - State: open - Opened by dgault 6 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 6 months ago - 19 comments
Labels: include

#4136 - CVE-2022-1471

Issue - State: closed - Opened by Sravani-K 6 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 6 months ago - 1 comment

#4134 - mitosis.tif: wrong uncertain order

Issue - State: closed - Opened by NicoKiaru 6 months ago

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

Pull Request - State: open - Opened by dgault 7 months ago - 3 comments

#4129 - Bump version to 7.2.0-SNAPSHOT

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

#4128 - Update version numbers to 7.1.0

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

#4127 - parseOptions strips characters after "]"

Issue - State: open - Opened by CFGrote 7 months ago - 3 comments

#4126 - Bump dependency versions

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

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

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

#4124 - Bump logbook version to 1.3.14

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

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

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: dependencies

#4122 - Support mixed codecs with precompressed tiles

Issue - State: open - Opened by melissalinkert 7 months ago - 1 comment

#4119 - Gha update

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

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

Issue - State: open - Opened by CGDogan 7 months ago - 2 comments
Labels: enhancement

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

Pull Request - State: closed - Opened by ed-scanlon 7 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 7 months ago - 2 comments
Labels: reader:VSI

#4115 - Revert RunTimeException when JPEGTurbo cannot be loaded

Pull Request - State: closed - Opened by dgault 8 months ago - 3 comments

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

Pull Request - State: closed - Opened by melissalinkert 8 months ago - 3 comments

#4113 - TiffWriter: incorrect BigTIFF threshold

Issue - State: open - Opened by dgault 8 months ago - 1 comment

#4112 - Imaris HDF: populate channel names

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

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

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

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

Issue - State: closed - Opened by sebi06 8 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 9 months ago - 4 comments
Labels: bug

#4108 - nd2: UnknownFormatException

Issue - State: closed - Opened by dominikl 9 months ago - 1 comment

#4107 - Bump version to 7.1.0-SNAPSHOT

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

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

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#4105 - Bump version to 7.0.1

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

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

Issue - State: open - Opened by dgault 9 months ago - 1 comment