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Recent Releases of dlup

dlup - v0.7.0

In this release the build tools have been modified. If you have issues installing dlup, please create an issue

What's Changed

  • Allow annotation files with raster type (yet not supported) in https://github.com/NKI-AI/dlup/pull/245
  • Add a C++ TIFF writer https://github.com/NKI-AI/dlup/pull/249

- Python
Published by jonasteuwen over 1 year ago

dlup - v0.6.1

What's Changed

  • Annotation filter bugfix by @EricMarcus-ai in https://github.com/NKI-AI/dlup/pull/246

New Contributors

  • @EricMarcus-ai made their first contribution in https://github.com/NKI-AI/dlup/pull/246

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.6.0...v0.6.1

- Python
Published by jonasteuwen over 1 year ago

dlup - v0.6.0

This release has performance and testing improvements. Backward incompatibility issues are not to be expected.

What's Changed

  • Feature/speedup masking https://github.com/NKI-AI/dlup/pull/242
  • Increased test coverage in https://github.com/NKI-AI/dlup/pull/242

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.5.3...v0.6.0

- Python
Published by jonasteuwen over 1 year ago

dlup - v0.5.3

What's Changed

  • Fix annotations not being cropped #241

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.5.2...v0.5.3

- Python
Published by jonasteuwen over 1 year ago

dlup - v0.5.2

What's Changed

  • Properly close open file handlers with PYVIPS image backend by @AjeyPaiK in https://github.com/NKI-AI/dlup/pull/238

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.5.1...v0.5.2

- Python
Published by jonasteuwen over 1 year ago

dlup - v0.5.1

What's Changed

Two small, but important bugs have been fixed

  • Bugfix/multiclass flag by @AjeyPaiK in https://github.com/NKI-AI/dlup/pull/234
  • Implement proper serialization of the dlup.annotations.Polygon and dlup.annotations.Polygon objects to ensure correct pickling by @AjeyPaiK in https://github.com/NKI-AI/dlup/pull/236

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.5.0...v0.5.1

- Python
Published by jonasteuwen almost 2 years ago

dlup - v0.5.0

What's Changed

  • Support multiclass in convert_annotations (#228)
  • Support colors and z_indices in Annotations (#228)
  • Several performance improvements and bugfixes

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.38...v0.5.0

- Python
Published by jonasteuwen almost 2 years ago

dlup - v0.4.0

Update with breaking changes

Next to several bugfixes, a major change is that the SlideImage and the dataset classes now output a pyvips.Image. For a simple fix, you can do the following: python pil_image = PIL.Image.fromarray(np.asarray(sample["image"])) Note that calling np.asarray() on the image returns the same data as was previously the case with PIL. This changes has led to several performance improvements

Bugfixes

  • TiffWriter did not work properly when using a pyramid. This has now been fixed.

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.38...v0.4.0

- Python
Published by jonasteuwen almost 2 years ago

dlup - v0.3.38

What's Changed

  • Enlarge scope backends by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/225

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.37...v0.3.38

- Python
Published by jonasteuwen almost 2 years ago

dlup - v0.3.37

What's Changed

  • Implement mode in backends by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/207
  • Enlarge scope of possible backends by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/219
  • Implement Halo annotations @rharkes in https://github.com/NKI-AI/dlup/pull/220
  • Update github actions by @rharkes in https://github.com/NKI-AI/dlup/pull/220

New Contributors

  • @rharkes made their first contribution in https://github.com/NKI-AI/dlup/pull/220

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.36...v0.3.37

- Python
Published by jonasteuwen about 2 years ago

dlup - v0.3.36 - bug fixes

What's Changed

  • Fix annotation order of WsiAnnotations when sorting is None by @BPdeRooij in https://github.com/NKI-AI/dlup/pull/215

New Contributors

  • @BPdeRooij made their first contribution in https://github.com/NKI-AI/dlup/pull/215

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.35...v0.3.36

- Python
Published by jonasteuwen about 2 years ago

dlup - v0.3.35 - Removing untested functionality. Extend behavior of TiffWriter

A few small breaking changes and an update

Breaking changes

Removed utilities to move towards version 1.0, which should have only tested functionality. The masking utility will be replaced by ahcore as the FESI methods are, in general, not very good.

  • Remove mask utility by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/209
  • Remove multiscale dataset by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/211

What's New

  • Add an optional colormap parameter while writing tiff files. by @AjeyPaiK in https://github.com/NKI-AI/dlup/pull/213

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.34...v0.3.35

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.34 - ICC profiles, code streamlined, improved HaloXML parsing

What's Changed

  • Improve logic of limit_bounds together with rois by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/201
  • Added complete tests for convert_annotations by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/199
  • Bug/fix annotation sorting by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/203
  • Implement offset for HaloXML by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/204
  • Implement ICC profile in the pyvips backend by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/206

New Contributors

  • @moerlemans made their first contribution in https://github.com/NKI-AI/dlup/pull/198

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.32...v0.3.34

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.3 - bug fixes, minor enhancements

What's Changed

  • Improve logic of limit_bounds together with rois by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/201
  • Added complete tests for convert_annotations by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/199
  • The behavior of annotations has changed. An empty annotation list from a TiledWsiDataset with an annotation based WsiAnnotations.read_region() means that the are no annotations for this tile, while None means no annotations are given. This is also encapsulated in the exceptions raised.

New Contributors

  • @moerlemans made their first contribution in https://github.com/NKI-AI/dlup/pull/198

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.32...v0.3.33

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.32 - bug fixes and improve tests

This release is a bug fix release. Tests to catch those bugs have also been added.

What's Changed

  • Initial work to support OpenSlide 4.0.0, implement ICC profiles in OpenSlide Backend https://github.com/NKI-AI/dlup/pull/185
  • Fix the output_tile_size which was accidentally removed (#191, #193) by @AjeyPaiK in https://github.com/NKI-AI/dlup/pull/192
  • GeoJSON annotations were not properly sorted by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/194
  • Bug/fix slide bounds in TiffFile by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/196

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.31...v0.3.32

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.31 - improve exceptions

What's Changed

  • Improve exceptions by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/181
  • Fix README.md update script @jonasteuwen in https://github.com/NKI-AI/dlup/pull/181

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.30...v0.3.31

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.30 - minor bug fixes, small enhancements

What's Changed

  • Add __iter__ to dlup.data.dataset.TiledWsiDataset and added .pre-commit-config.yaml by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/173
  • add CITATION.cff file with main contributors by @YoniSchirris in https://github.com/NKI-AI/dlup/pull/159
  • Fix bug in pyvips_backend.py by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/178
  • Implement functional interface for RenameLabels by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/176

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.29...v0.3.30

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.29 - dlup is now strongly typed

dlup now passed mypy --strict

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.28 - minor bugfixes, update mypy parsing

What's Changed

  • Minor bug fixes
  • Increase test coverage by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/165
  • Improve mypy by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/166

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.27...v0.3.28

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.27

What's Changed

  • Fix rename labels by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/164
  • Small bug fixes

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.26...v0.3.27

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.26

This release implements Darwin V7 annotations.

Breaking changes

This release implements breaking changes in dlup.annotations.WsiAnnotations. Internally, labels are not handled anymore as strings, but there is now an AnnotationClass that carries both the label and annotation type. This also affects .available_labels.

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.25...v0.3.26

- Python
Published by jonasteuwen over 2 years ago

dlup - v0.3.25

What's Changed

  • Support Halo annotations by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/153

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.24...v0.3.25

- Python
Published by jonasteuwen almost 3 years ago

dlup - v0.3.24

What's Changed

  • Support multipoint by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/148
  • Limit bounds by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/146

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.23...v0.3.24

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.23

What's Changed

  • Wsi to polygon by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/138
  • Allow selecting a different interpolator in TiffWriter by @jonasteuwen in https://github.com/NKI-AI/dlup/pull/144

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.3.20...v0.3.23

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.22

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.20

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.19

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.18

- Python
Published by jonasteuwen about 3 years ago

dlup - v0.3.17

- Python
Published by jonasteuwen over 3 years ago

dlup - v0.3.6

- Python
Published by jonasteuwen over 3 years ago

dlup - v0.3.5

- Python
Published by jonasteuwen over 3 years ago

dlup - v0.3.4

Bug fix release

- Python
Published by jonasteuwen over 3 years ago

dlup - v0.3.0

Major new version v0.3.0

This is v0.3.0 release with a new key features: * Annotations are supported in both polygons and images * Multiscale datasets now have experimental support. * Experimental backend support of openslide, pyvips and tiffile, supporting a broader range of files * Masks and images can now be written to tiffs

New Contributors

  • @Baggsy made their first contribution in https://github.com/NKI-AI/dlup/pull/32
  • @YoniSchirris made their first contribution in https://github.com/NKI-AI/dlup/pull/43
  • @AjeyPaiK made their first contribution in https://github.com/NKI-AI/dlup/pull/52
  • @Tkootstra made their first contribution in https://github.com/NKI-AI/dlup/pull/79

Full Changelog: https://github.com/NKI-AI/dlup/compare/v0.2.0...v0.3.0

- Python
Published by jonasteuwen over 3 years ago

dlup - v0.2.0

Second release of dlup

This is the second release of dlup. See below for details.

The full documentation of the API and how to use dlup can be found at the AI for Oncology documentation website.

Whole slide image utilities

  • A command-line interface dlup wsi no works on individual slides rather than folders.
  • Dataset classes have been added, that allow to directly load tile datasets from WSIs, and a dataset that can read the dlup wsi tile output (which is the same as the output from SlideImageDataset).

- Python
Published by jonasteuwen over 4 years ago

dlup - v0.2.0-dev4

- Python
Published by jonasteuwen over 4 years ago

dlup - v0.1.0

First release of DLUP

This is the first release of DLUP. This includes the following utilities. The full documentation of the API and how to use DLUP can be found at the AI for Oncology documentation website.

Whole slide image utilities

A command-line interface dlup wsi is provided that allows the tiling and extracting metadata of a directory of whole-slide images (WSI). Use dlup wsi --help for more information about the interface.

SlideScore utilities

A command-line interface dlup slidescore is provided to interface with the SlideScore API. Current support is for the downloading of WSIs, and the uploading and downloading of annotations. Use dlup slidescore --help for more information about the interface.

- Python
Published by jonasteuwen almost 5 years ago