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

#4253 - Operetta/Phenix: calculate physical Z size in micrometers

Pull Request - State: closed - Opened by melissalinkert 12 days ago

#4252 - Leica TCS: make sure XML file is on used files list

Pull Request - State: open - Opened by melissalinkert 13 days ago - 1 comment

#4251 - showinf image viewer broken since 8.0.0 (on OSX at least)

Issue - State: closed - Opened by dominikl 13 days ago - 3 comments

#4250 - ImageInfo: only call System.exit in batch mode

Pull Request - State: closed - Opened by sbesson 18 days ago

#4249 - Imaris Reader: support for LZ4 compression and performance improvements

Pull Request - State: open - Opened by marcobitplane 26 days ago - 4 comments

#4248 - Operetta reader: don't add directories to the used files list

Pull Request - State: closed - Opened by melissalinkert 29 days ago - 1 comment

#4247 - unable to open the images saved as qpproj

Issue - State: closed - Opened by 7Lechen322 30 days ago - 1 comment

#4246 - Fiji Plugin: Bio-Formats with GUI Importer

Issue - State: open - Opened by LPUoO about 1 month ago
Labels: enhancement

#4245 - Upgrade cdm-core (netcdf Java) to 5.6.0

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

#4244 - Large JP2 Read Error

Issue - State: open - Opened by guymac about 2 months ago - 4 comments

#4243 - Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object

Pull Request - State: open - Opened by melissalinkert about 2 months ago - 1 comment

#4242 - Some improvements to OME-TIFF write performance

Pull Request - State: closed - Opened by melissalinkert about 2 months ago - 7 comments

#4241 - Convert several timepoints and/or channels at the same time

Issue - State: open - Opened by mbahin 9 months ago - 2 comments

#4239 - Empty image.name returned by `showinf` for some Zeiss .czi file

Issue - State: open - Opened by technics3 2 months ago - 1 comment

#4237 - Consider adding test that loads memo file from previous release

Issue - State: open - Opened by melissalinkert 2 months ago - 1 comment
Labels: enhancement

#4236 - Bug: MicroManager 2.0.0 Division by 0

Issue - State: open - Opened by jburel 2 months ago - 1 comment

#4235 - Dead store to local variable

Issue - State: open - Opened by scuniff 2 months ago

#4233 - Handle UnknownFormatException for batch processing multiple files.

Pull Request - State: closed - Opened by tstoeter 2 months ago - 2 comments
Labels: include

#4232 - NULL being returned for a Boolean object

Issue - State: open - Opened by scuniff 2 months ago

#4231 - ScanR: exposure times not always populated

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

#4230 - IMOD: store one Shape per ROI

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

#4229 - Leica TCS: incorrect used files list

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

#4228 - SimplePCI TIFF: evaluate metadata mappings

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

#4227 - Nikon TIFF channel metadata

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

#4226 - Metamorph ND time-lapse no longer recognised

Issue - State: open - Opened by dominikl 3 months ago - 2 comments

#4225 - Cast to double may be needed

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

#4224 - RCPNL: add data for objective ID 18112

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

#4220 - Fix float casting when autoscaling int values to byte

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

#4219 - ImageJ exporter: save original metadata

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

#4218 - Float/double data not supported by `DicomWriter`

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

#4217 - Imaris IMS Reader: support for LZ4 compression and performance improvements

Pull Request - State: closed - Opened by marcobitplane 3 months ago - 18 comments

#4216 - loci.formats.FormatException while converting series to tiff format

Issue - State: open - Opened by de9821 4 months ago - 3 comments

#4215 - Fix DICOM export in ImageJ

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

#4214 - Fix incorrect logical operators in Zeiss LSM and OME-XML readers

Pull Request - State: closed - Opened by sbesson 4 months ago - 1 comment

#4213 - Switch clauses have same code

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

#4212 - May need to replace single | with double ||

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

#4211 - break statement always gets executed

Issue - State: open - Opened by scuniff 4 months ago

#4210 - Cast to float may be needed

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

#4209 - && needed instead of &

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

#4208 - Bump version to 8.0.0-SNAPSHOT

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

#4207 - Bump version to 7.3.1

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

#4206 - CZI: fluorescent channels not displaying

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

#4205 - OIRReader: Major performance improvement when reading a ROI within a plane

Pull Request - State: closed - Opened by NicoKiaru 5 months ago - 21 comments
Labels: include

#4204 - PyramidOMETiffWriter `close()` duration scales as a (number of planes)^2

Issue - State: closed - Opened by NicoKiaru 5 months ago - 6 comments

#4202 - SVS: update isThisType to reject files with a single IFD

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

#4201 - Bug(?): IJ exported OME-TIFFs lack original metadata

Issue - State: closed - Opened by joshmoore 5 months ago

#4200 - Allow processing multiple files sequentially in a single run, with file names read from stdin.

Pull Request - State: closed - Opened by tstoeter 5 months ago - 8 comments
Labels: include

#4199 - LIF Reader: index out of bounds

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

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

Pull Request - State: closed - Opened by cqian89 5 months ago - 2 comments
Labels: include

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

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

#4196 - DICOM: use FrameTimePointer to detect timelapse data

Pull Request - State: open - Opened by melissalinkert 5 months ago - 4 comments
Labels: exclude

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

Pull Request - State: open - Opened by WalkerKnapp 5 months ago - 8 comments
Labels: include

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

Issue - State: open - Opened by MichaelDausmann 6 months ago - 3 comments

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

Pull Request - State: closed - Opened by dgault 6 months ago - 2 comments

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

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

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

Pull Request - State: closed - Opened by melissalinkert 6 months ago - 4 comments

#4189 - Loading of indica tiff files

Issue - State: open - Opened by rharkes 6 months ago - 2 comments
Labels: reader:new

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

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

#4187 - Bump version to 8.0.0-SNAPSHOT

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

#4186 - Bump version to 7.3.0

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

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

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

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

Issue - State: closed - Opened by scuniff 7 months ago - 1 comment

#4183 - Bump lower level component versions prior to 7.3.0

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

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

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

#4181 - Add support for reading compressed NDPI tiles

Pull Request - State: closed - Opened by melissalinkert 7 months ago - 3 comments

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

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

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

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

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

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

#4175 - showinf `OutOfMemoryError` with large JPG file

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

#4174 - DicomJSONProvider JSON format

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

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

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

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

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

#4171 - Add `-quality` option to bfconvert

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

#4169 - Add method to add custom DicomJSONProvider

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

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

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

#4167 - DICOM: treat ultrasound ECG data as timelapse

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

#4166 - SVS: Incorrect image colour

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

#4164 - Reduce DICOM write time

Pull Request - State: closed - Opened by melissalinkert 8 months ago - 5 comments

#4163 - SimplePCI: fix Z position handling

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

#4162 - Remove duplicate enum check and add clarifying comment

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

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

Issue - State: open - Opened by jcupitt 9 months ago - 3 comments

#4160 - Repeated conditional test II

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

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

Pull Request - State: closed - Opened by melissalinkert 9 months ago - 2 comments

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

Pull Request - State: closed - Opened by sbesson 9 months ago - 3 comments

#4157 - OME-XML: populate original metadata table

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

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

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

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

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