elf

What's Changed

• Fix issues in parallel processing code by @constantinpape in https://github.com/constantinpape/elf/pull/100

Full Changelog: https://github.com/constantinpape/elf/compare/0.5.1...0.5.2

What's Changed

• Use zarr over z5py by @JonasHell in https://github.com/constantinpape/elf/pull/92
• Minor typo in msa docstring by @anwai98 in https://github.com/constantinpape/elf/pull/95
• Update to io files by @constantinpape in https://github.com/constantinpape/elf/pull/96
• Improve elf.paralel and misc changes by @constantinpape in https://github.com/constantinpape/elf/pull/97
• Update version.py by @constantinpape in https://github.com/constantinpape/elf/pull/98

New Contributors

• @JonasHell made their first contribution in https://github.com/constantinpape/elf/pull/92

Full Changelog: https://github.com/constantinpape/elf/compare/0.5.0...0.5.1

What's Changed

• Implement tracking based on motile by @constantinpape in https://github.com/constantinpape/elf/pull/82
• Parallel distance transform implementation by @constantinpape in https://github.com/constantinpape/elf/pull/84
• Refactor tracking so that utility functionality can be used independe… by @constantinpape in https://github.com/constantinpape/elf/pull/86
• Start implementing nifti file wrapper by @constantinpape in https://github.com/constantinpape/elf/pull/79
• Fix Loading Nifti data by @anwai98 in https://github.com/constantinpape/elf/pull/87

New Contributors

• @anwai98 made their first contribution in https://github.com/constantinpape/elf/pull/87

Full Changelog: https://github.com/constantinpape/elf/compare/0.4.8...0.5.0

What's Changed

• Implement parallel seeded watershed by @constantinpape in https://github.com/constantinpape/elf/pull/73
• Hotfix mean_average_precision by @constantinpape in https://github.com/constantinpape/elf/pull/74
• Make the image stack wrapper and knossos wrapper iterable by @constantinpape in https://github.com/constantinpape/elf/pull/76
• Use threadctl to set numpy thread limits in scope by @constantinpape in https://github.com/constantinpape/elf/pull/77
• Raise errors for not thread-safe acces in elf.parallel by @constantinpape in https://github.com/constantinpape/elf/pull/78

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

What's Changed

• Add CLI for viewing hdf5 etc containers by @constantinpape in https://github.com/constantinpape/elf/pull/69
• Extend paralle.size_filter functionality to also relabel the result. by @constantinpape in https://github.com/constantinpape/elf/pull/70
• Update mrc_wrapper.py by @martinschorb in https://github.com/constantinpape/elf/pull/67
• Make running napari in view_container optional by @constantinpape in https://github.com/constantinpape/elf/pull/71
• Implement segmentation stitching by @constantinpape in https://github.com/constantinpape/elf/pull/72

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

What's Changed

• Naive tracking by @constantinpape in https://github.com/constantinpape/elf/pull/61
• Add vis functionality for simple grid views by @constantinpape in https://github.com/constantinpape/elf/pull/63
• Two pass ws by @constantinpape in https://github.com/constantinpape/elf/pull/64
• Improve and extend parallel functionality by @constantinpape in https://github.com/constantinpape/elf/pull/65
• Fix ci by @constantinpape in https://github.com/constantinpape/elf/pull/66

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

What's Changed

• Add support for ngff transformations by @constantinpape in https://github.com/constantinpape/elf/pull/59

Full Changelog: https://github.com/constantinpape/elf/compare/0.4.4...0.4.5

What's Changed

• fixed computation of scores for non-continuous label ids by @k-dominik in https://github.com/constantinpape/elf/pull/55
• Implement plate visualization for htm by @constantinpape in https://github.com/constantinpape/elf/pull/56
• Htm by @constantinpape in https://github.com/constantinpape/elf/pull/57
• Add parser for simple htm layout by @constantinpape in https://github.com/constantinpape/elf/pull/58

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

What's Changed

• fix mrc import axes by @martinschorb in https://github.com/constantinpape/elf/pull/52

New Contributors

• @martinschorb made their first contribution in https://github.com/constantinpape/elf/pull/52

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

What's Changed

• expose available multicut solver names by @k-dominik in https://github.com/constantinpape/elf/pull/53

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

What's Changed

• Extend mesh format import / export by @constantinpape in https://github.com/constantinpape/elf/pull/49
• Support passing kwargs to open_file

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

What's Changed

• Reactivate tests with affogato on mac by @constantinpape in https://github.com/constantinpape/elf/pull/44
• Gasp by @abailoni in https://github.com/constantinpape/elf/pull/46
• Fix lint by @constantinpape in https://github.com/constantinpape/elf/pull/47

New Contributors

• @abailoni made their first contribution in https://github.com/constantinpape/elf/pull/46

Full Changelog: https://github.com/constantinpape/elf/compare/0.3.1...0.4.0

What's Changed

• Add segmentation functionality for embeddings in elf.segmentation.embeddings
• Fix tests by @constantinpape in https://github.com/constantinpape/elf/pull/40
• Add cloud protocol support for elf.io.open_file, starting with BossDB by @j6k4m8 in https://github.com/constantinpape/elf/pull/41

New Contributors

• @j6k4m8 made their first contribution in https://github.com/constantinpape/elf/pull/41

Full Changelog: https://github.com/constantinpape/elf/compare/0.3.0...0.3.1

Add grid-graph functionality for pixel-wise segmentation

• Add roi functionality to elf.parallel
• Use nifty affine transformation for all dtypes in elf.transformation.affine

Add elf.io.LabelMultisetWrapper, to allow arbitrary slicing for label multiset datasets.
Also extend nifty transformation functionality to more dtypes.

• Improved IO functionality (thanks to @clbarnes)
• Implement parallel module for parallel and larger than memory array processing
• Generalize coordinate_transformation logic and implement affine transformations