Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of ez-zarr

ez-zarr - v0.4.1

What's Changed

  • future proofing ez-zarr by @mbstadler in https://github.com/fmicompbio/ez_zarr/pull/51

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.4.0...v0.4.1

Scientific Software - Peer-reviewed - Python
Published by mbstadler 7 months ago

ez-zarr - v0.4.0

What's Changed

  • Add CITATION.cff file with reference to JOSS paper in https://github.com/fmicompbio/ez_zarr/pull/48
  • Zarr3 support in https://github.com/fmicompbio/ez_zarr/pull/26

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.8...v0.4.0

Scientific Software - Peer-reviewed - Python
Published by mbstadler 7 months ago

ez-zarr - v0.3.8

What's Changed

  • This is the version accepted by the Journal of Open Source Software (JOSS), reviewed at https://github.com/openjournals/joss-reviews/issues/7882
  • Add verbose argument by @csoneson in https://github.com/fmicompbio/ez_zarr/pull/42
  • use omezarr instead of hcswrappers in main.py by @mbstadler in https://github.com/fmicompbio/ez_zarr/pull/43
  • Expand vignette section on example data by @csoneson in https://github.com/fmicompbio/ez_zarr/pull/44
  • Check OME-Zarr version, document supported version by @csoneson in https://github.com/fmicompbio/ez_zarr/pull/46

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.7...v0.3.8

Scientific Software - Peer-reviewed - Python
Published by mbstadler 10 months ago

ez-zarr - v0.3.7

What's Changed

  • Support 5d OME-Zarrs by @csoneson in https://github.com/fmicompbio/ez_zarr/pull/32
  • Added examples and changes to the documentation

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.6...v0.3.7

Scientific Software - Peer-reviewed - Python
Published by mbstadler 11 months ago

ez-zarr - v0.3.6

What's Changed

  • Pin zarr version to <3.0.0a0 (for compatibility with anndata).
  • Add JOSS manuscript.

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.5...v0.3.6

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 1 year ago

ez-zarr - v0.3.5

What's Changed

  • Add support for python 3.13 by @csoneson in https://github.com/fmicompbio/ez_zarr/pull/25
  • Add support for single-channel image plotting using selected colormaps, e.g. img.plot(channels=[0], channel_colors=['viridis'])

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.4...v0.3.5

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 1 year ago

ez-zarr - v0.3.4

What's Changed

  • add conda installation instructions
  • search also higher resolution pyramid levels if label_value is not found on the lower-resolution label
  • fix use of constantvalue in plotting.padimage
  • add imagetransform, titlefontsize and scalebarfontsize arguments to plotting.plotimage (and therefore also to Image.plot and ImageList.plot)

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.3...v0.3.4

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.3.3

What's Changed

  • add reference to ezzarr
  • use lowest resolution pyramid level to get bounding box for label_value (may lead to significant speed-ups)
  • raise exception if labelvalue does not exist in getboundingboxforlabelvalue

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.2...v0.3.3

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.3.2

What's Changed

  • Remove createnameplateA1 (always use createnameplateA01 for empty wells)
  • get names from .zattr for non-empty wells

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.3.1...v0.3.2

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.3.0

What's Changed

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.2.3...v0.3.0

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.2.3

What's Changed

  • Sort layout and imgpaths jointly by @csoneson in https://github.com/fmicompbio/ezzarr/pull/13

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.2.2...v0.2.3

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.2.2

What's new

  • Add ome_zarr.ImageList class to represent a set of ome_zarr.Image objects
  • Add ome_zarr.import_Fractal_plate helper function that creates an ome_zarr.ImageList from a Fractal output with fully configured plate layout
  • Minor fixes and improvements

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.2.1...v0.2.2

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.2.1

What's new

  • minor fixes
  • add plotting.plot_image(..., restrict_to_label_values) argument, allowing to mask out regions outside of the selected label

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.2.0...v0.2.1

Scientific Software - Peer-reviewed - Python
Published by mbstadler over 1 year ago

ez-zarr - v0.2.0

What's new

Much of the issues described in #9, including:

  • move some helper functions to new module utils
  • create new module ome_zarr
  • add new class ome_zarr.Image to represent a single image (implements most of the well-level functionality in hcs_wrappers.plate, and in addition adds a few new tricks, like automated scaling of intensity and label arrays)
  • mark hcs_wrappers classes as "legacy" in the documentation

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.1.5...v0.2.0

Scientific Software - Peer-reviewed - Python
Published by mbstadler almost 2 years ago

ez-zarr - v0.1.5

What's Changed

  • add pyramidlevelcoord argument to plotwell() by @silvbarb in https://github.com/fmicompbio/ezzarr/pull/5
  • add scalebarlabel argument to plotwell() and plot_image()
  • update quickstart.qmd to use the new plotting features

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.1.4...v0.1.5

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago

ez-zarr - v0.1.4

What's new

  • add pyramid_level_coord parameter to get_image_ROI() and get_label_ROI(), allowing to extract by coordinates that refer to another pyramid_level than the one the image data is being extracted from.

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.1.3...v0.1.4

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago

ez-zarr - v0.1.3

What's Changed

  • Add plotting functionality (for example plot_plate() and plot_well methods for FractalZarr and plot_image() for any image arrays)
  • See all changes in https://github.com/fmicompbio/ez_zarr/pull/4

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.1.2...v0.1.3

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago

ez-zarr - v0.1.2

What's Changed

  • minor updates to documentation
  • add package deployment of tagged pushes to pypi.org

Full Changelog: https://github.com/fmicompbio/ez_zarr/compare/v0.1.1...v0.1.2

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago

ez-zarr - v0.1.1

What's Changed

  • Renaming of image retrieval functions in https://github.com/fmi-basel/gbioinfo-ez_zarr/pull/3
  • consistent use of coordinates: (z,y,x) or (y,x)

Full Changelog: https://github.com/fmi-basel/gbioinfo-ez_zarr/compare/v0.1.0...v0.1.1

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago

ez-zarr - Initial release

What's Changed

  • Initial release of ez_zarr, meant for testing and collecting feedback on design
  • minimal feature set has been implemented but may be subject to change

Full Changelog: https://github.com/fmi-basel/gbioinfo-ez_zarr/commits/v0.1.0

Scientific Software - Peer-reviewed - Python
Published by mbstadler about 2 years ago