cluster_tools

What's Changed

• Always use z5py for zarr files; bump version by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/48

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.7...0.4.8

What's Changed

• implement metadata checks for downscaling by @martinschorb in https://github.com/constantinpape/cluster_tools/pull/47

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.6...0.4.7

What's Changed

• Update for elf by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/41

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.5...0.4.6

That made the ome.zarr file format written invalid

What's Changed

• Replace tail unix command with python impl by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/38

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.3...0.4.4

What's Changed

• Update copy_volume.py by @martinschorb in https://github.com/constantinpape/cluster_tools/pull/35
• Warn for unsafe uint8 conversion by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/36

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.2...0.4.3

What's Changed

• Add change from signed int to unsigned int upon copying data by @martinschorb in https://github.com/constantinpape/cluster_tools/pull/33

New Contributors

• @martinschorb made their first contribution in https://github.com/constantinpape/cluster_tools/pull/33

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.1...0.4.2

What's Changed

• Fix downscaling with ome zarr metadata format by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/32

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.4.0...0.4.1

What's Changed

• Enable inference with bioimageio models by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/29
• Update ilastik prediction workflow by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/28
• Use ome-zarr v04 format and remove bdv.ome.zarr file format by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/31

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.3.7...0.4.0

What's Changed

• Add prepare_test function and add github CI by @constantinpape in https://github.com/constantinpape/cluster_tools/pull/24
• Fix several issues in workflows
• Refactor connected components workflow

Full Changelog: https://github.com/constantinpape/cluster_tools/compare/0.3.6...0.3.7

Add statistics workflow and adapt downscaling workflow to new pybdv syntax

• Extend support for label-multisets to:
  • GraphWorkflow
  • EdgeFeaturesWorfklow
  • FindUniques
• Fix issues in multicut stitching workflow
• Add simple threshold task
• Use pybdv to extend downscaling workflow to bdv.n5 format

Change the storage layout for distributed region graphs and distributed edge feature calculation.
Now, n5 varlen chunks are used to store the properties (edges, nodes or features) for each block.

This has the advantage that storage uses less files, because less files are written per block and because the chunks are only stored for non-empty blocks.

However, data from the old storage layout cannot be read any longer with the newer version.

• Implement object distance workflow
• Implement multicut based stitching
• Multiscale network inference
• Improve functionality:
  • Various improvements in inference workflow
  • Node label workflow supports label multiset input
  • Add object sizes to region features

• Move general purpose functionality to elf
• Adapt to new nifty.distributed function signatures
• Implement label multiset functionality
• Simplify paintera conversion and downscaling workflow

Experiments in https://arxiv.org/pdf/1905.10535.pdf were done with this release.