ome/bioformats

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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

Stars: 429
Forks: 260
Open beginner issues: 0
Indexed issues: 150
Avg merge: 6d 21h
Merged PRs (30d): 4

Dominant language: Java
License: GPL-2.0
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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150 open issues indexed

Migration of the Bio-Formats artifacts to Maven Central Open

ome/bioformats#4477 · 1 reaction · 2 assignees · Opened Aug 11, 2026
Memoizer tests leak readers and temporary cache directories on failures Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

ome/bioformats#4475 · Opened Aug 8, 2026
Memoizer reports successful save when temporary memo rename fails Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

ome/bioformats#4474 · Opened Aug 8, 2026
Memoizer returns stale reader state after companion files change Open

Difficulty 4/5 3-5 days Newbie friendliness 64/100

ome/bioformats#4473 · Opened Aug 8, 2026
Memoizer reuses readers initialized with different DynamicMetadataOptions Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

ome/bioformats#4472 · Opened Aug 8, 2026
Standard flattened data tests enable Memoizer unpredictably on Java 25 Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

ome/bioformats#4471 · Opened Aug 8, 2026
Standardize Maven versions across components Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

ome/bioformats#4469 · Opened Aug 7, 2026
CellSensReader: NoClassDefFoundError: Could not initialize class com.sun.imageio.plugins.jpeg.JPEGImageReader Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4456 · 1 comment · Opened Jul 27, 2026
BioFormats metadata format breaks ImageJ's "getInfo" functionality for DICOM Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ome/bioformats#4449 · 4 comments · Opened Jul 2, 2026
OperettaReader importing transmitted light channels ("Brightfield" and "Digital Phase Contrast") in colored mode in magenta Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

ome/bioformats#4443 · 3 comments · Opened Jun 17, 2026
TIFF image data not supported for .vsi datasets Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

ome/bioformats#4433 · Opened May 28, 2026
ND2 with incorrect Z/T/series dimensions Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ome/bioformats#4431 · 1 comment · Opened May 18, 2026
ImageJ plugin: >8 bit data in a virtual stack cannot be projected Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

ome/bioformats#4422 · 1 comment · Opened Mar 25, 2026
Review build warnings Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

ome/bioformats#4407 · Opened Jan 27, 2026
Nikon NEF distorted image Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ome/bioformats#4389 · 5 comments · Opened Nov 25, 2025
OBFReader: Corrupted zlib compression Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4333 · 1 comment · Opened Jun 25, 2025
CZI: Take PixelShift into account Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ome/bioformats#4320 · 3 comments · Opened Jun 4, 2025
Review use of file modification times Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ome/bioformats#4300 · Opened Apr 21, 2025
nd2: some global metadata should actually be series metadata Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ome/bioformats#4287 · 1 comment · Opened Mar 6, 2025
Leica (.LIF) files importing colors incorrectly Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4281 · 2 comments · Opened Feb 26, 2025
.vmic reader Open

reader:new

Difficulty 5/5 Over a week Newbie friendliness 25/100

ome/bioformats#4264 · 6 comments · Opened Jan 16, 2025
Fiji Plugin: Bio-Formats with GUI Importer Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ome/bioformats#4246 · Opened Oct 15, 2024
Large JP2 Read Error Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4244 · 5 comments · Opened Sep 30, 2024
Consider more thorough comparison of image data in automated tests Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4238 · Opened Sep 11, 2024
Consider adding test that loads memo file from previous release Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ome/bioformats#4237 · 1 comment · Opened Sep 11, 2024
Bug: MicroManager 2.0.0 Division by 0 Open

ome/bioformats#4236 · 5 comments · 1 assignee · Opened Sep 10, 2024
IMOD: store one Shape per ROI Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

ome/bioformats#4230 · Opened Sep 5, 2024
SimplePCI TIFF: evaluate metadata mappings Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ome/bioformats#4228 · Opened Sep 4, 2024
Nikon TIFF channel metadata Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ome/bioformats#4227 · 2 comments · Opened Sep 4, 2024
FluoviewReader: Timepoints split over multiple files not recognized as single dataset Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ome/bioformats#4223 · 1 comment · Opened Aug 15, 2024
Float/double data not supported by `DicomWriter` Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ome/bioformats#4218 · 1 comment · Opened Aug 6, 2024
FEATURE REQUEST: BioFormats support for CZI Multi Scene images Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

ome/bioformats#4194 · 3 comments · Opened Jun 7, 2024
CZI Incorrect Pixel Physical Size (For pyramidal image series) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ome/bioformats#4191 · Opened May 24, 2024
Loading of indica tiff files Open

reader:new

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ome/bioformats#4189 · 2 comments · Opened May 14, 2024
DicomJSONProvider JSON format Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ome/bioformats#4174 · Opened Mar 28, 2024
libturbojpeg.dylib does not pass the macOS notarization check Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ome/bioformats#4170 · 1 comment · Opened Mar 20, 2024
Add method to add custom DicomJSONProvider Open

ome/bioformats#4169 · 1 assignee · Opened Mar 19, 2024
SVS: Incorrect image colour Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4166 · 2 comments · Opened Mar 14, 2024
bug: bfconvert generates bad DICOMs from SVS files Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4161 · 3 comments · Opened Mar 8, 2024
Convert several timepoints and/or channels at the same time Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4241 · 2 comments · Opened Mar 8, 2024
native-lib-loader: UnsatisfiedLinkError when calling library is in a different classloader Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

ome/bioformats#4137 · 1 comment · Opened Jan 3, 2024
parseOptions strips characters after "]" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ome/bioformats#4127 · 3 comments · Opened Dec 8, 2023
Support mixed codecs with precompressed tiles Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

ome/bioformats#4122 · 1 comment · Opened Dec 4, 2023
Add precompressed tile support for additional readers and writers Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4121 · 2 comments · Opened Dec 4, 2023
Enable reporting/discovery of readers and writers that support precompressed tiles Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

ome/bioformats#4120 · Opened Dec 4, 2023
Dont check for update if FormatTools.VERSION is "(unknown version)" Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

ome/bioformats#4118 · 2 comments · Opened Nov 22, 2023
Micromanger: Add support for alternative metadata field names Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4104 · 1 comment · Opened Oct 11, 2023
CZI: Autostich fails Open

reader:ZeissCZI

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4102 · 10 comments · Opened Oct 10, 2023
MetaMorph nd file - Invalid image number Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ome/bioformats#4095 · 2 comments · Opened Sep 11, 2023
QuickTime: images may not be readable when using Memoizer Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ome/bioformats#4091 · Opened Aug 30, 2023

ome/bioformats

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