tlnagy/OMETIFF.jl issues and pull requests

#112 - EzXML error when trying to load ome.tiff

Issue - State: open - Opened by elmbeech 28 days ago

#111 - Change in tiff reading since 0.3.5

Issue - State: open - Opened by warnerwarner 3 months ago - 1 comment
Labels: bug

#110 - bump tiffimages compat

Pull Request - State: closed - Opened by tlnagy 6 months ago - 1 comment

#109 - BoundsError when accessing Tag

Issue - State: closed - Opened by RpfR2000 6 months ago - 6 comments
Labels: bug

#107 - bump deps

Pull Request - State: closed - Opened by tlnagy 9 months ago - 1 comment

#106 - Re: error with opening a ome.tiff file.

Issue - State: open - Opened by mdhe1248 about 1 year ago - 8 comments
Labels: bug

#105 - handle multiple positions breaking unevenly across files

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

#104 - Border slice lost when loading OOM multi-file image

Issue - State: closed - Opened by tlnagy over 1 year ago - 3 comments
Labels: bug

#103 - Potentially a major performance dropoff when lazy-loading multi-file OMETIFFs

Issue - State: closed - Opened by tlnagy about 2 years ago - 1 comment
Labels: performance

#102 - increase flexibility around the file extension, see #99

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

#101 - update docstringextensions, fixes #100

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

#100 - Add DocStringExtensions compat for 0.9?

Issue - State: closed - Opened by BioTurboNick about 2 years ago

#99 - Opening OME TIFF files without `.ome.tif` extension

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

#98 - Broken JSON metadata blocks file loading

Issue - State: open - Opened by tlnagy about 2 years ago
Labels: bug

#97 - bump tiffimages to 0.6

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

#96 - first attempt to write OMETIFF

Pull Request - State: open - Opened by JiangXL over 2 years ago

#95 - Add examples to docs

Issue - State: open - Opened by tlnagy over 2 years ago
Labels: help wanted, good-first-issue

#94 - Fix multi-image BoundsError

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

#93 - Remove unnecessary extension of load

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

#92 - Integrate the TiffImages engine

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

#91 - Error in loading some images from TestImages.jl

Issue - State: closed - Opened by a-r-n-o-l-d almost 3 years ago - 3 comments
Labels: waiting on author

#90 - Large micromanager stack gives ReadOnlyMemoryError

Issue - State: closed - Opened by jowch about 3 years ago - 7 comments
Labels: waiting on author

#89 - mimic git submodule using plain git command

Pull Request - State: closed - Opened by johnnychen94 about 3 years ago - 2 comments

#88 - use exampletiffs as testdata source

Pull Request - State: closed - Opened by johnnychen94 about 3 years ago - 12 comments

#87 - reduce package size

Issue - State: closed - Opened by johnnychen94 over 3 years ago - 3 comments

#86 - Bump dependency version compatibility

Pull Request - State: closed - Opened by tlnagy over 3 years ago - 1 comment
Labels: needs version bump

#85 - CompatHelper: bump compat for "ImageCore" to "0.9"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 4 comments

#84 - remove imageshow dep, fixes #83

Pull Request - State: closed - Opened by tlnagy over 3 years ago - 1 comment

#83 - suspicious ImageShow dependency

Issue - State: closed - Opened by johnnychen94 over 3 years ago - 3 comments

#82 - Imspectorpro ome.tif file: ERROR: KeyError: key "Type" not found

Issue - State: open - Opened by james-a-mcmanus over 3 years ago - 6 comments
Labels: bug

#81 - CompatHelper: bump compat for "ImageShow" to "0.3"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago

#80 - Fix crash when attempting to reopen a stream on mmap access

Pull Request - State: closed - Opened by tlnagy over 3 years ago - 1 comment
Labels: bug

#79 - TagBot trigger issue

Issue - State: closed - Opened by JuliaTagBot over 3 years ago - 12 comments

#78 - fix empty namespace warning

Pull Request - State: closed - Opened by tlnagy over 3 years ago - 1 comment

#77 - Switch to github ci

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

#76 - Improve support for FileIO v1.6

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

#75 - Switch to using Unitful's parsing API

Pull Request - State: closed - Opened by tlnagy almost 4 years ago

#74 - CompatHelper: bump compat for "DataStructures" to "0.18"

Pull Request - State: closed - Opened by github-actions[bot] about 4 years ago

#73 - rework per-file IFD offset tracking, fixes #72

Pull Request - State: closed - Opened by tlnagy over 4 years ago

#72 - Tracking of IFD offset across separate files is very brittle

Issue - State: closed - Opened by tlnagy over 4 years ago
Labels: bug

#71 - Support for Big-TIFF

Issue - State: closed - Opened by JiangXL over 4 years ago - 3 comments
Labels: enhancement

#70 - [WIP] Add support for streaming files as they are being acquired

Pull Request - State: open - Opened by tlnagy over 4 years ago - 1 comment
Labels: enhancement

#69 - Should striping be encoded in the type?

Issue - State: open - Opened by tlnagy over 4 years ago
Labels: enhancement, question

#68 - Update strip read code on Julia 1.4

Issue - State: closed - Opened by tlnagy over 4 years ago
Labels: enhancement, low priority

#67 - CompatHelper: bump compat for "Unitful" to "1.0"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago - 1 comment

#66 - Use new runtime parsing API from unitful

Issue - State: closed - Opened by tlnagy over 4 years ago
Labels: upstream

#65 - bump EzXML versions

Pull Request - State: closed - Opened by tlnagy over 4 years ago - 1 comment
Labels: no changelog

#64 - CompatHelper: bump compat for "EzXML" to "1.1"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago - 1 comment

#63 - CompatHelper: bump compat for "EzXML" to "1.0"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago - 1 comment

#62 - switch to using uuids and internal names for file tracking

Pull Request - State: closed - Opened by tlnagy over 4 years ago - 1 comment
Labels: enhancement

#61 - fix accidental transposition that broke rectangular image loading

Pull Request - State: closed - Opened by tlnagy over 4 years ago - 1 comment

#60 - DimensionMismatch("array could not be broadcast to match destination")

Issue - State: closed - Opened by JiangXL over 4 years ago - 7 comments
Labels: bug

#59 - CompatHelper: bump compat for "ImageMetadata" to "0.9"

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago - 1 comment
Labels: no changelog

#58 - CompatHelper: bump compat for "AxisArrays" to "0.4"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#57 - Obtain Colors&FixedPointNumbers via ImageCore

Pull Request - State: closed - Opened by timholy almost 5 years ago - 3 comments

#56 - Suitable for general use on TIFFs?

Issue - State: closed - Opened by IanButterworth almost 5 years ago - 3 comments

#55 - CompatHelper: bump compat for "ImageMetadata" to "0.8"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 2 comments

#54 - [WIP] Add testing on windows

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment
Labels: no changelog

#53 - CompatHelper: bump compat for "Colors" to "0.11"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#52 - Add setters to memory-mapped arrays

Issue - State: open - Opened by tlnagy almost 5 years ago
Labels: enhancement

#51 - Add support for memory mapping Tiff files

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment
Labels: enhancement, performance

#50 - CompatHelper: bump compat for "Colors" to "0.10"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#49 - CompatHelper: bump compat for "FixedPointNumbers" to "0.7"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#48 - Add documentation of internals

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment

#47 - CompatHelper: bump compat for "Unitful" to "0.18"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#46 - add support for preserving unused dimensions, fixes #45¬

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment

#45 - Add option for preserving dimensions of length 1

Issue - State: closed - Opened by tlnagy almost 5 years ago
Labels: enhancement

#44 - CompatHelper: bump compat for "Unitful" to "0.17"

Pull Request - State: closed - Opened by github-actions[bot] almost 5 years ago - 1 comment
Labels: no changelog

#43 - add support for compathelper tracking of deps

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment

#42 - Spin out the position axis and return a list of (N-1)D images instead of a ND image

Issue - State: open - Opened by tlnagy almost 5 years ago - 1 comment
Labels: enhancement

#41 - Support variable axis lengths across positions and reduce memory footprint

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment
Labels: enhancement

#40 - Add support for dumping internal micromanager imaging JSON

Issue - State: closed - Opened by tlnagy almost 5 years ago - 1 comment
Labels: enhancement

#39 - add ability to output embedded OME-XML inside a OMETIFF

Pull Request - State: closed - Opened by tlnagy almost 5 years ago - 1 comment

#38 - Incomplete micromanager acquisitions cause out of bounds error

Issue - State: closed - Opened by tlnagy almost 5 years ago
Labels: bug

#37 - switch to the lightweight ImageShow for show funcs

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

#36 - Profile loading code

Issue - State: closed - Opened by tlnagy over 5 years ago - 3 comments
Labels: performance, upstream

#35 - verify that an error is thrown when loading non-ometiff files

Pull Request - State: closed - Opened by tlnagy over 5 years ago - 3 comments

#34 - transition package to pkg3 format, fixes #31

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

#33 - add support for extracting elapsed time from the omexml

Pull Request - State: closed - Opened by tlnagy over 5 years ago - 3 comments

#32 - Use proper mapping for OME-XML time units to Unitful time units

Issue - State: closed - Opened by tlnagy over 5 years ago - 1 comment
Labels: enhancement

#31 - Update to Pkg3 format

Issue - State: closed - Opened by tlnagy over 5 years ago
Labels: enhancement

#30 - add ability to save OMETIFF files

Issue - State: open - Opened by tlnagy over 5 years ago
Labels: enhancement

#29 - document and add more examples

Issue - State: closed - Opened by tlnagy over 5 years ago - 1 comment
Labels: docs

#28 - return unitful spatial axes, fixes #26

Pull Request - State: closed - Opened by tlnagy over 5 years ago - 3 comments

#27 - Extract and report actual elapsed time information

Issue - State: closed - Opened by tlnagy over 5 years ago - 1 comment
Labels: enhancement

#26 - Annotate spatial axes with spatial units if available

Issue - State: closed - Opened by tlnagy over 5 years ago
Labels: enhancement

#25 - ERROR: OMETIFF can't be installed because it has no versions that support 0.5.2 of julia

Issue - State: closed - Opened by dns43 over 5 years ago - 1 comment
Labels: wontfix

#24 - switch to julian iteration protocol for ifds

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

#23 - use codecov instead of coveralls

Pull Request - State: closed - Opened by tlnagy almost 6 years ago - 1 comment

#22 - fix for zlib issues

Pull Request - State: closed - Opened by tlnagy almost 6 years ago

#21 - Switch to new Julian iteration protocol.

Issue - State: closed - Opened by tlnagy almost 6 years ago - 1 comment
Labels: enhancement

#20 - add support for intercalated slices in same file, fixes #19

Pull Request - State: closed - Opened by tlnagy almost 6 years ago

#19 - In multi-position files the IFDs are sometimes intercalated so the naive next function fails

Issue - State: closed - Opened by tlnagy about 6 years ago
Labels: bug

#18 - Update for Julia 1.0 and EzXML 0.8

Pull Request - State: closed - Opened by tlnagy about 6 years ago - 2 comments

#17 - Fix Micro-Manager (and other?) byte order

Pull Request - State: closed - Opened by rsrock over 6 years ago - 3 comments

#16 - Something up with MicroManager OMEs?

Issue - State: closed - Opened by rsrock over 6 years ago - 1 comment
Labels: bug

#15 - add support for bundling acquisition comments with data

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

#14 - Handle cases where file is renamed and the filepath in the OME-XML is out of date

Issue - State: closed - Opened by tlnagy almost 7 years ago - 7 comments
Labels: low priority

#13 - add prelim support for position as an additional axis

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

#12 - Extract general TIFF code into a separate package and only keep OMETIFF specific stuff here

Issue - State: closed - Opened by tlnagy almost 7 years ago - 4 comments
Labels: enhancement

GitHub / tlnagy/OMETIFF.jl issues and pull requests