OMETIFF.jl

OMETIFF v0.4.4

Diff since v0.4.3

Closed issues:

• Potentially a major performance dropoff when lazy-loading multi-file OMETIFFs (#103)
• Border slice lost when loading OOM multi-file image (#104)

Merged pull requests:

• handle multiple positions breaking unevenly across files (#105) (@tlnagy)

OMETIFF v0.4.3

Diff since v0.4.2

Closed issues:

• Add DocStringExtensions compat for 0.9? (#100)

Merged pull requests:

• update docstringextensions, fixes #100 (#101) (@tlnagy)
• increase flexibility around the file extension, see #99 (#102) (@tlnagy)

OMETIFF v0.4.2

Diff since v0.4.1

Merged pull requests:

• bump tiffimages to 0.6 (#97) (@tlnagy)

OMETIFF v0.4.1

Diff since v0.4.0

Merged pull requests:

• Fix multi-image BoundsError (#94) (@HsupoLeng)

OMETIFF v0.4.0

Diff since v0.3.14

Closed issues:

• Extract general TIFF code into a separate package and only keep OMETIFF specific stuff here (#12)
• Update strip read code on Julia 1.4 (#68)
• Support for Big-TIFF (#71)
• Large micromanager stack gives ReadOnlyMemoryError (#90)
• Error in loading some images from TestImages.jl (#91)

Merged pull requests:

• Integrate the TiffImages engine (#92) (@tlnagy)
• Remove unnecessary extension of load (#93) (@tlnagy)

OMETIFF v0.3.14

Diff since v0.3.13

Closed issues:

• reduce package size (#87)

Merged pull requests:

• use exampletiffs as testdata source (#88) (@johnnychen94)
• mimic git submodule using plain git command (#89) (@johnnychen94)

OMETIFF v0.3.13

Diff since v0.3.12

Merged pull requests:

• CompatHelper: bump compat for "ImageCore" to "0.9" (#85) (@github-actions[bot])
• Bump dependency version compatibility (#86) (@tlnagy)

OMETIFF v0.3.12

Diff since v0.3.11

Closed issues:

• suspicious ImageShow dependency (#83)

Merged pull requests:

• remove imageshow dep, fixes #83 (#84) (@tlnagy)

OMETIFF v0.3.11

Diff since v0.3.10

Merged pull requests:

• Fix crash when attempting to reopen a stream on mmap access (#80) (@tlnagy)

OMETIFF v0.3.10

Diff since v0.3.9

Merged pull requests:

• fix empty namespace warning (#78) (@tlnagy)

OMETIFF v0.3.9

Diff since v0.3.8

Closed issues:

• Use new runtime parsing API from unitful (#66)

Merged pull requests:

• CompatHelper: bump compat for "DataStructures" to "0.18" (#74) (@github-actions[bot])
• Switch to using Unitful's parsing API (#75) (@tlnagy)
• Improve support for FileIO v1.6 (#76) (@tlnagy)
• Switch to github ci (#77) (@tlnagy)

OMETIFF v0.3.8

Diff since v0.3.7

Closed issues:

• Suitable for general use on TIFFs? (#56)
• Tracking of IFD offset across separate files is very brittle (#72)

Merged pull requests:

• rework per-file IFD offset tracking, fixes #72 (#73) (@tlnagy)

OMETIFF v0.3.7

Diff since v0.3.6

Merged pull requests:

• CompatHelper: bump compat for "Unitful" to "1.0" (#67) (@github-actions[bot])

OMETIFF v0.3.6

Diff since v0.3.5

Closed issues:

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

Merged pull requests:

• switch to using uuids and internal names for file tracking (#62) (@tlnagy)

OMETIFF v0.3.5

Diff since v0.3.4

Closed issues:

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

Merged pull requests:

• CompatHelper: bump compat for "AxisArrays" to "0.4" (#58) (@github-actions[bot])
• CompatHelper: bump compat for "ImageMetadata" to "0.9" (#59) (@github-actions[bot])
• fix accidental transposition that broke rectangular image loading (#61) (@tlnagy)

OMETIFF v0.3.4

Diff since v0.3.3

Closed issues:

• add lazy loading of larger files/split files (#3)

Merged pull requests:

• Add support for memory mapping Tiff files (#51) (@tlnagy)
• Add testing on windows (#54) (@tlnagy)
• Obtain Colors&FixedPointNumbers via ImageCore (#57) (@timholy)

v0.3.3 (2019-12-18)

• Add support for memory-mapping TIFF files
• Flesh out documentation

v0.3.2 (2019-11-23)

Diff since v0.3.1

Closed issues:

• Add support for dumping internal micromanager imaging JSON (#40)
• Incomplete micromanager acquisitions cause out of bounds error (#38)

Merged pull requests:

• add support for compathelper tracking of deps (#43) (tlnagy)
• Support variable axis lengths across positions and reduce memory footprint (#41) (tlnagy)
• add ability to output embedded OME-XML inside a OMETIFF (#39) (tlnagy)

v0.3.1 (2019-09-11)

Diff since v0.3.0

Merged pull requests:

• switch to the lightweight ImageShow for show funcs (#37) (tlnagy)
• verify that an error is thrown when loading non-ometiff files (#35) (tlnagy)

v0.3.0 (2019-06-16)

Diff since v0.2.1

Closed issues:

• Update to Pkg3 format (#31)
• Extract and report actual elapsed time information (#27)
• Annotate spatial axes with spatial units if available (#26)
• Switch to new Julian iteration protocol. (#21)

Merged pull requests:

• transition package to pkg3 format, fixes #31 (#34) (tlnagy)
• add support for extracting elapsed time from the omexml (#33) (tlnagy)
• return unitful spatial axes, fixes #26 (#28) (tlnagy)
• switch to julian iteration protocol for ifds (#24) (tlnagy)