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GitHub / CellProfiler/python-bioformats issues and pull requests

#176 - Failed install

Issue - State: closed - Opened by bill-connelly about 2 months ago - 1 comment

#175 - Release plans

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

#174 - Support for WSI pyramids?

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

#172 - python-bioformats support qptiff file?

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

#170 - Bumpy to 4.1.0

Pull Request - State: closed - Opened by gnodar01 11 months ago

#167 - Can't get well plate information from OMEXML

Issue - State: open - Opened by JKelle over 1 year ago

#165 - Upgrade bioformats_package.jar

Issue - State: open - Opened by Sravani-K over 1 year ago

#164 - Array too large Exception when using reader.read()

Issue - State: open - Opened by nishantshakya almost 2 years ago

#163 - extract metadata from VSI files

Issue - State: open - Opened by LibbyLi667 about 2 years ago

#161 - How to get the tile images in multiprocessing

Issue - State: open - Opened by InfinityBox over 2 years ago

#160 - Make dependencies on boto3 optional

Issue - State: open - Opened by jhnnsrs almost 3 years ago

#159 - Unable to load CH5 File

Issue - State: open - Opened by roshankern about 3 years ago - 8 comments

#158 - Update link: OME-XML schema documentation

Issue - State: open - Opened by YoussefAyachii over 3 years ago

#157 - Improve image reader selection function

Pull Request - State: open - Opened by DavidStirling over 3 years ago

#156 - Long and possibly multiple exceptions while using the package

Issue - State: open - Opened by vbmade2000 over 3 years ago - 2 comments

#155 - Update to latest java version?

Issue - State: open - Opened by kmccormickTetra over 3 years ago - 2 comments

#154 - swap from log4j to logback

Pull Request - State: closed - Opened by bethac07 over 3 years ago - 3 comments

#153 - Remove outdated references to log4j

Issue - State: closed - Opened by bethac07 over 3 years ago

#152 - log4j security issue

Issue - State: closed - Opened by claycoleman over 3 years ago - 5 comments

#151 - How to extract metadata?

Issue - State: open - Opened by vbmade2000 almost 4 years ago - 1 comment

#150 - Add the 3i SlideBook jar to the list of jars if present

Pull Request - State: closed - Opened by ehrenfeu about 4 years ago - 1 comment

#149 - Tests/physical size

Pull Request - State: closed - Opened by ehrenfeu about 4 years ago - 1 comment

#148 - Generate version info from git tags

Pull Request - State: closed - Opened by ehrenfeu about 4 years ago - 1 comment

#146 - Instantiate file reader with stream instead of path

Issue - State: open - Opened by evan-anderson-ts about 4 years ago

#145 - Failing to extract OIR metadata

Issue - State: open - Opened by bethac07 over 4 years ago

#144 - How to install in readme

Issue - State: open - Opened by wimpomp over 4 years ago

#143 - Bioformats not finding Python Javabridge?

Issue - State: open - Opened by u2056710 over 4 years ago

#142 - Conda fails to install python-bioformats- incompatible with python 3?

Issue - State: open - Opened by markemus over 4 years ago - 5 comments

#140 - Having a trouble to install it in ubuntu?

Issue - State: closed - Opened by Yuvi-416 over 4 years ago - 3 comments

#139 - Trouble converting .bif slides into .png

Issue - State: closed - Opened by rashindrie almost 5 years ago

#138 - It´s related about .ndpi file extension?

Issue - State: open - Opened by Yuvi-416 almost 5 years ago

#137 - Suppressing debug and info logging?

Issue - State: open - Opened by markemus almost 5 years ago - 5 comments

#136 - Trying to log an error results in another error

Issue - State: open - Opened by manthey almost 5 years ago

#135 - AttributeError: 'OMETiffWriter' object has no attribute 'class_name'

Issue - State: open - Opened by markemus almost 5 years ago - 1 comment

#134 - slide functions

Pull Request - State: closed - Opened by 0x00b1 about 5 years ago

#132 - Bright field Images Are Pink

Issue - State: open - Opened by arielleleon about 5 years ago

#131 - Update bioformats package JAR to 6.5.1

Pull Request - State: closed - Opened by alejoe91 about 5 years ago - 1 comment

#130 - Pin dependencies

Pull Request - State: closed - Opened by DavidStirling about 5 years ago

#129 - Incorrect Image Reader Selected

Issue - State: open - Opened by Nicholas-Schaub about 5 years ago

#128 - BioFormats 6.5.0

Pull Request - State: closed - Opened by 0x00b1 about 5 years ago - 4 comments

#127 - Bump .jar to something in the 6 family

Issue - State: closed - Opened by bethac07 about 5 years ago

#125 - reading tif with >3 channels returns just 3 channels

Issue - State: open - Opened by tamkaho over 5 years ago

#124 - Added rectangle ROIs and TiffData to omexml.py

Pull Request - State: closed - Opened by thomasmfish almost 6 years ago - 3 comments

#123 - Install on windows 10 fails

Issue - State: open - Opened by jaydoc almost 6 years ago - 4 comments

#122 - bioformats.write_image pixels problem

Issue - State: open - Opened by goodjs1 almost 6 years ago

#121 - OMETiffWriter Error - has no attribute 'class_name'

Issue - State: closed - Opened by Nicholas-Schaub almost 6 years ago

#120 - Getting Exact Time Values for Timeseries Image Stack

Issue - State: open - Opened by sbowerma almost 6 years ago

#119 - Error opening Tif file with bioformats?

Issue - State: open - Opened by cudmore over 6 years ago

#117 - error messsage when writing OME-TIFF

Issue - State: open - Opened by sebi06 over 6 years ago - 1 comment

#116 - write numpy array as OME-TIFF question

Issue - State: open - Opened by sebi06 over 6 years ago

#115 - Make `set_image_count()` efficient with large values.

Pull Request - State: open - Opened by riccardomurri over 6 years ago

#113 - Import 2D+t time series

Issue - State: open - Opened by dschetel almost 7 years ago - 2 comments

#112 - Resolve five undefined names found by flake8

Pull Request - State: closed - Opened by cclauss almost 7 years ago

#111 - Undefined names may raise NameError at runtime

Issue - State: closed - Opened by cclauss almost 7 years ago

#109 - Update bioformats JAR to v5.9.0

Pull Request - State: closed - Opened by jnj16180340 about 7 years ago

#108 - write_image add PhysicalSize

Issue - State: open - Opened by tribol about 7 years ago

#107 - concatenate time series

Issue - State: open - Opened by Cumol about 7 years ago

#106 - What's the proper way to write 5D data?

Issue - State: open - Opened by morganrcu about 7 years ago - 7 comments

#105 - Fix documentation on testing

Issue - State: open - Opened by ehrenfeu over 7 years ago

#104 - Derive version info from git tags

Pull Request - State: closed - Opened by ehrenfeu over 7 years ago - 1 comment

#103 - Add methods to access units for physical pixel sizes

Pull Request - State: closed - Opened by ehrenfeu over 7 years ago

#102 - Add method to access physical size for Z axis

Pull Request - State: closed - Opened by ehrenfeu over 7 years ago

#101 - Support units of measurement

Issue - State: open - Opened by ehrenfeu over 7 years ago

#100 - Fix example in OMEXML.Pixels docstring

Pull Request - State: closed - Opened by ehrenfeu over 7 years ago

#99 - Example from OMEXML.Pixels docstring is slightly broken

Issue - State: open - Opened by ehrenfeu over 7 years ago

#98 - Download images from s3

Pull Request - State: closed - Opened by mcquin over 7 years ago

#97 - Update to class ImageReader docstring

Pull Request - State: closed - Opened by GenevieveBuckley over 7 years ago

#96 - get_PhysicalSizeZ() function missing in Pixels

Issue - State: closed - Opened by vladchimescu over 7 years ago

#95 - Heap space error

Issue - State: open - Opened by yoda-vid over 7 years ago

#94 - Documentation bug in ImageReader

Issue - State: open - Opened by omsai over 7 years ago - 3 comments
Labels: Documentation

#93 - Reading .jp2 files

Issue - State: open - Opened by jacobpennels over 7 years ago - 2 comments

#91 - Release 1.3.2

Pull Request - State: closed - Opened by mcquin almost 8 years ago

#90 - Fix demo script.

Pull Request - State: closed - Opened by mcquin almost 8 years ago

#89 - Demo file does not work

Issue - State: closed - Opened by everyones almost 8 years ago

#88 - Upgrade to BioFormats 5.7.1

Pull Request - State: closed - Opened by mcquin almost 8 years ago

#87 - Updated BioFormats to 5.7.0

Pull Request - State: closed - Opened by 0x00b1 almost 8 years ago

#86 - `bioformats.__version__` should print package version

Issue - State: closed - Opened by mcquin almost 8 years ago - 1 comment
Labels: Bug

#85 - update test url

Pull Request - State: closed - Opened by mcquin almost 8 years ago

#84 - Test failure in test_load_using_bioformats

Issue - State: closed - Opened by mcquin almost 8 years ago - 1 comment
Labels: Bug

#83 - Upgrade bioformats to 5.5.3

Pull Request - State: closed - Opened by mcquin almost 8 years ago - 2 comments

#82 - Bio-formats 5.5

Issue - State: closed - Opened by nerduno about 8 years ago - 3 comments
Labels: Enhancement

#79 - Encode both 'str' and 'unicode'

Pull Request - State: closed - Opened by BioGeek over 8 years ago - 2 comments

#78 - Incorrect namespaces detection leads to incomplete/ incorrect metadata readout

Issue - State: open - Opened by FannyGeorgi over 8 years ago - 2 comments
Labels: Needs verification

#77 - ImportError javabridge although Cellprofiler installed fine

Issue - State: closed - Opened by anou85 over 8 years ago - 5 comments

#76 - Possible strategies to include new features of BioFormats 5.3.1

Issue - State: open - Opened by sebi06 over 8 years ago - 5 comments
Labels: Enhancement

#73 - add physical pixel size

Issue - State: open - Opened by helme over 8 years ago - 1 comment