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
#4204 - PyramidOMETiffWriter `close()` duration scales as a (number of planes)^2
Issue -
State: open - Opened by NicoKiaru 4 days ago
- 1 comment
#4203 - CV7000/8000: fix used files list when TIFFs are in a subdirectory
Pull Request -
State: open - Opened by melissalinkert 5 days ago
#4202 - SVS: update isThisType to reject files with a single IFD
Pull Request -
State: open - Opened by melissalinkert 5 days ago
#4201 - Bug(?): IJ exported OME-TIFFs lack original metadata
Issue -
State: open - Opened by joshmoore 11 days ago
#4200 - Allow processing multiple files sequentially in a single run, with file names read from stdin.
Pull Request -
State: open - Opened by tstoeter 11 days ago
- 6 comments
#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
#4191 - CZI Incorrect Pixel Physical Size (For pyramidal image series)
Issue -
State: open - Opened by ian-coccimiglio about 1 month ago
#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
#4180 - Columbus: update to use micrometers instead of `reference frame` for positions
Pull Request -
State: open - Opened by melissalinkert 3 months ago
#4179 - Fix Java 9+ deprecation warnings in smaller components
Pull Request -
State: closed - Opened by melissalinkert 3 months ago
- 1 comment
#4178 - Fix most Java 9+ deprecation warnings in bio-formats-plugins component
Pull Request -
State: closed - Opened by melissalinkert 3 months ago
#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
#4170 - libturbojpeg.dylib does not pass the macOS notarization check
Issue -
State: open - Opened by conradkun 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
#4165 - BioFormats DICOM WSI reader problem with nested Pixel Data in private data element and/or offset tables
Issue -
State: closed - Opened by dclunie 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
#4149 - bfconvert: Using channel option does not remove additional channel elements from OME-XML
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
#4145 - CZI: use alternate source for well identifiers when available
Pull Request -
State: closed - Opened by melissalinkert 5 months ago
#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
#4142 - Argument #1 to org.joda.time.DateTime is declared as a long but an int is being passed in MetamorphReader.decodeTime(int millis).
Issue -
State: open - Opened by scuniff 6 months ago
- 1 comment
#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
#4137 - native-lib-loader: UnsatisfiedLinkError when calling library is in a different classloader
Issue -
State: open - Opened by dgault 6 months ago
- 1 comment
#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
#4133 - HCImage cxd: IllegalArgumentException: -20 must be neither null nor strictly negative
Issue -
State: closed - Opened by dominikl 6 months ago
- 3 comments
#4132 - Olympus OIR: MetadataTools.populatePixelsOnly: 0 must be non-null and strictly positive.
Issue -
State: open - Opened by dominikl 6 months ago
#4131 - VirtualImagePlus: Retain B&C settings for each slice
Pull Request -
State: open - Opened by dgault 7 months ago
- 3 comments
#4130 - matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)
Pull Request -
State: open - Opened by carandraug 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
#4121 - Add precompressed tile support for additional readers and writers
Issue -
State: open - Opened by melissalinkert 7 months ago
- 2 comments
#4120 - Enable reporting/discovery of readers and writers that support precompressed tiles
Issue -
State: open - Opened by melissalinkert 7 months ago
#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