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

#3937 - BDV reader memory issues

Issue - State: open - Opened by will-moore over 1 year ago
Labels: reader:BDV

#3936 - Added Fli 2.0 support in LiFlimReader

Pull Request - State: closed - Opened by ShaquilleLouisa-LambertInstruments over 1 year ago - 8 comments
Labels: include

#3932 - ND2: fix reading of blocks larger than 2 GB

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

#3930 - Bio-Rad Gel: fix pixel data offsets for cropped images

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

#3928 - CZI: tile stitching fixes when pyramid does not exist

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

#3927 - Ventana BIF: grid of zero pixel values at lowest resolution levels

Issue - State: closed - Opened by dgault over 1 year ago - 3 comments

#3926 - VSI: respect tile origin metadata

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

#3925 - Olympus .vsi: only read pixels from frame_*.ets files

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

#3924 - Fixes Null Pointer Exception in case no plane is present in OperettaReader

Pull Request - State: closed - Opened by NicoKiaru almost 2 years ago - 5 comments
Labels: exclude

#3922 - ICS: Fix Illegal group reference when constructing slice label

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

#3920 - .TIFF from Napari readed in omero with inversion between T and Z

Issue - State: closed - Opened by sodesset almost 2 years ago - 8 comments

#3918 - Operetta Phenix: IllegalStateException when attempting to open plane

Issue - State: closed - Opened by dgault almost 2 years ago - 3 comments

#3915 - Fix min/max calculation for RGB data

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago

#3912 - Upload one set of artifacts from the GitHub Actions ant build

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 11 comments

#3911 - DICOM writer: initial support for dual personality DICOM/TIFF

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 18 comments

#3910 - Fake: if there are RGB channels, dimension order needs to be XYC*

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 5 comments

#3909 - ND2: IllegalArgumentException during openBytes

Issue - State: closed - Opened by dgault almost 2 years ago - 1 comment
Labels: reader:NativeND2

#3908 - Operetta/Harmony: ignore any 32-bit TIFF files

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

#3907 - bfconvert: PyramidOMETiffWriter failed to close with no flat and output pattern

Issue - State: open - Opened by dgault almost 2 years ago - 2 comments

#3902 - LSID validation

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 5 comments

#3900 - MetaMorph Tiff: NullPointerException when parsing Stage Positions

Issue - State: closed - Opened by dgault almost 2 years ago

#3899 - Plugin: Handle closing of reader after exception

Issue - State: closed - Opened by dgault almost 2 years ago - 1 comment

#3898 - InCell 1000/2000 field count and plane metadata fixes

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 2 comments

#3897 - Olympus vsi: fix exposure time handling

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

#3896 - Leica LIF: Mix up of channel indexes, names, excitations

Issue - State: open - Opened by dominikl almost 2 years ago - 3 comments
Labels: reader:LeicaLIF

#3892 - QPTIFF: preserve biomarker data in channel name

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago

#3891 - NIFTI: reduce number of backwards seeks

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago

#3890 - CZI: support multiple fields in a plate

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

#3886 - Make logback dependencies optional

Pull Request - State: closed - Opened by ctrueden almost 2 years ago - 3 comments

#3883 - DICOM: fix certain types of data with multiple optical paths

Pull Request - State: closed - Opened by melissalinkert almost 2 years ago - 7 comments

#3877 - SVS: IndexOutOfBoundsException when opening lower resolutions

Issue - State: closed - Opened by dgault about 2 years ago - 2 comments
Labels: reader:SVS

#3876 - Add ReportEnabledStatus class to list files that aren't tested

Pull Request - State: closed - Opened by melissalinkert about 2 years ago - 5 comments

#3873 - LIF: ArrayIndexOutOfBoundsException when parsing offsets

Issue - State: closed - Opened by dgault about 2 years ago - 3 comments
Labels: reader:LeicaLIF

#3872 - New codec integration Jetraw

Pull Request - State: closed - Opened by arvequina about 2 years ago - 16 comments

#3869 - CZI: fix pyramid dimension calculation

Pull Request - State: closed - Opened by melissalinkert about 2 years ago

#3866 - Leica LIF: Incorrect reading of data with FLIM and TileScan

Issue - State: open - Opened by dgault about 2 years ago - 10 comments
Labels: reader:LeicaLIF

#3863 - ND2: remove chunkmap skipping logic

Pull Request - State: closed - Opened by melissalinkert about 2 years ago - 1 comment

#3860 - bfconvert: fix overwrite checking when output path is a pattern

Pull Request - State: closed - Opened by melissalinkert about 2 years ago - 1 comment

#3856 - TIFF: Incorrect PhotometricInterpretation on converted TIFF

Issue - State: closed - Opened by dgault about 2 years ago - 5 comments

#3855 - bfconvert: Image plane too large when downsampling lower resolutions

Issue - State: open - Opened by dgault about 2 years ago - 4 comments
Labels: enhancement

#3852 - NDPI: fix non-number tag handling for files > 4GB

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

#3851 - OME-TIFF: allow individual file reading for datasets with one file per series

Pull Request - State: closed - Opened by melissalinkert about 2 years ago - 1 comment

#3850 - VirtualImagePlus: retain contrast in setSlice

Pull Request - State: closed - Opened by tfarago about 2 years ago - 7 comments
Labels: include

#3849 - ND2 32-bit float

Issue - State: closed - Opened by jburel about 2 years ago - 2 comments
Labels: reader:NativeND2

#3847 - NDPI: IndexOutOfBoundsException when calling getTile in JPEGTurboServiceImpl

Issue - State: open - Opened by dgault about 2 years ago - 6 comments
Labels: reader:NDPI

#3842 - OME-TIFF: improve performance with open file handle reduction

Pull Request - State: closed - Opened by melissalinkert over 2 years ago - 5 comments

#3840 - OME-TIFF saving differently on windows vs linux?

Issue - State: open - Opened by noamza over 2 years ago - 1 comment
Labels: question

#3839 - ZeissCZIReader performance issue with Lattice Light Sheet

Issue - State: closed - Opened by NicoKiaru over 2 years ago - 9 comments
Labels: reader:ZeissCZI

#3835 - Zeiss CZI: use scene names as image names

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

#3831 - OME-TIFF: faster initialization when there are lots of planes

Pull Request - State: closed - Opened by melissalinkert over 2 years ago - 3 comments

#3829 - QPTIFF: update to support schema version 4

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

#3823 - Plugins: Add option for memoizer

Issue - State: open - Opened by dgault over 2 years ago - 6 comments
Labels: enhancement

#3820 - Memoizer API updates

Issue - State: closed - Opened by melissalinkert over 2 years ago - 1 comment
Labels: enhancement

#3819 - VSI: Inverted colours (RGB instead of BGR)

Issue - State: closed - Opened by dgault over 2 years ago - 1 comment
Labels: reader:VSI

#3817 - TIFF metadata fix

Pull Request - State: closed - Opened by melissalinkert over 2 years ago - 3 comments

#3816 - VSI: Only part of image displayed

Issue - State: open - Opened by dgault over 2 years ago - 2 comments
Labels: reader:VSI

#3811 - Deltavision: another fix for incorrect XY tile count detection

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

#3810 - Fake hashes fail validation

Issue - State: closed - Opened by joshmoore over 2 years ago - 5 comments

#3809 - HitachiReader updates

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

#3808 - Olympus OIR: Undetected PixelBlocks/Incorrect dimensions

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

#3807 - Metamorph: parse doubles with DataTools

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

#3805 - Automated tests: make sure the file is initialized before all tests

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

#3804 - Fake: move configurable sleep to the end of initFile

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

#3803 - Zeiss LSM: assume 32 bit data is floating point

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

#3802 - Deltavision: allow partial planes to be read from truncated files

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

#3800 - Fill color configuration

Issue - State: closed - Opened by melissalinkert over 2 years ago - 3 comments
Labels: enhancement

#3796 - Make private Pattern field transient

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

#3795 - CZI: use fill color of 255 when brightfield data is suspected

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

#3794 - Chunk API: Add new API and functionality for reading and writing chunks

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

#3791 - Add support for multi-Z images exported from Perkin Elmer Columbus

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

#3784 - OperettaReader improvements

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

#3783 - ND2 metadata updates

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

#3779 - Another No Pixel Block error

Issue - State: closed - Opened by EitNickS over 2 years ago - 4 comments

#3766 - OME-TIFF reader: reduce open file handle count during setId

Pull Request - State: closed - Opened by melissalinkert over 2 years ago - 3 comments

#3761 - ND2: Inverted LUT for RGB images

Issue - State: open - Opened by dgault over 2 years ago - 6 comments
Labels: reader:NativeND2

#3757 - SVS: Incorrect pyramid levels with 6.8.0

Issue - State: closed - Opened by dgault over 2 years ago - 16 comments
Labels: reader:SVS

#3756 - Libjpeg-turbo exception when converting/opening .ndpi file.

Issue - State: open - Opened by michaellee1 almost 3 years ago - 4 comments
Labels: reader:NDPI

#3749 - Operetta/Phenix: allow for sparse planes

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

#3744 - Allow DICOM writer to accept additional DICOM-specific metadata

Issue - State: closed - Opened by melissalinkert almost 3 years ago - 2 comments

#3743 - SVS label and macro physical sizes/positions

Issue - State: closed - Opened by melissalinkert almost 3 years ago
Labels: reader:SVS

#3742 - Support reading and writing DICOM whole slide images

Pull Request - State: closed - Opened by melissalinkert almost 3 years ago - 14 comments

#3740 - FEI TIFF: fix physical pixel sizes for Phenom data

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

#3739 - Reduce memory required to read tiles from large JPEGs

Pull Request - State: closed - Opened by melissalinkert almost 3 years ago - 2 comments

#3738 - Improve tile read speeds for some pyramid OME-TIFFs

Pull Request - State: closed - Opened by melissalinkert almost 3 years ago - 2 comments

#3726 - ND2 metadata parsing fixes

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

#3722 - ImageConverter not support openslide api

Issue - State: closed - Opened by mywsat about 3 years ago - 2 comments

#3713 - Add support for VisiView STK files

Pull Request - State: closed - Opened by dgault about 3 years ago - 5 comments
Labels: exclude

#3710 - CZI pyramid not detected / tile width not correct

Issue - State: closed - Opened by melissalinkert over 3 years ago - 1 comment
Labels: reader:ZeissCZI

#3706 - MRCReader: invert planes in Y for FEI variants

Issue - State: open - Opened by sbesson over 3 years ago - 2 comments
Labels: enhancement

#3682 - SVS: handle optional label and macro images

Issue - State: closed - Opened by sbesson over 3 years ago - 5 comments
Labels: reader:SVS

#3680 - Performance increase in writeIFD

Pull Request - State: closed - Opened by iwbh15 over 3 years ago - 36 comments
Labels: exclude

#3678 - Ventana BIF: Z stacks not supported

Issue - State: open - Opened by dgault over 3 years ago - 6 comments

#3661 - ND2: Skewed image display

Issue - State: open - Opened by dgault over 3 years ago - 10 comments
Labels: reader:NativeND2

#3636 - Opening a large (17 GB) delta vision file.

Issue - State: closed - Opened by ajasja almost 4 years ago - 11 comments

#3634 - FileStitcher: add reader.close() statement when setting the class list

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