Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NKI-AI/dlup issues and pull requests

#255 - Use dynamic annotation reader and writers

Pull Request - State: closed - Opened by jonasteuwen 7 days ago

#254 - Revert "Implement WsiAnnotations in C++"

Pull Request - State: closed - Opened by jonasteuwen 7 days ago - 1 comment

#253 - Multithreaded TIFF writer

Issue - State: open - Opened by jonasteuwen about 2 months ago
Labels: enhancement

#252 - Implement WsiAnnotations in C++

Pull Request - State: closed - Opened by jonasteuwen about 2 months ago - 2 comments

#251 - Extend dunder methods and code simplification for annotations

Pull Request - State: closed - Opened by BPdeRooij about 2 months ago - 1 comment

#250 - Feature/c++ tiffwriter

Pull Request - State: closed - Opened by jonasteuwen about 2 months ago

#249 - Feature/c tiffwriter

Pull Request - State: closed - Opened by jonasteuwen about 2 months ago - 1 comment

#248 - Multiple annotation output (serialization) formats

Issue - State: open - Opened by jonasteuwen 2 months ago
Labels: enhancement

#247 - Be more graceful when libvips or openslide is not available

Issue - State: open - Opened by jonasteuwen 2 months ago
Labels: enhancement

#246 - Annotation filter bugfix

Pull Request - State: closed - Opened by EricMarcus-ai 2 months ago - 1 comment

#245 - Allow annotation files with raster type (yet not supported)

Pull Request - State: closed - Opened by jonasteuwen 2 months ago - 1 comment

#244 - v0.7 tracking

Issue - State: open - Opened by jonasteuwen 2 months ago - 1 comment
Labels: enhancement, Stale

#243 - Feature/v0.7

Pull Request - State: open - Opened by jonasteuwen 2 months ago - 1 comment

#242 - Feature/speedup masking

Pull Request - State: closed - Opened by jonasteuwen 2 months ago - 1 comment

#241 - Fix annotations not being cropped

Pull Request - State: closed - Opened by jonasteuwen 3 months ago
Labels: bug

#240 - z-index is not imported or exported with GeoJSONs

Issue - State: open - Opened by BPdeRooij 3 months ago - 2 comments
Labels: bug

#238 - Properly close open file handlers with PYVIPS image backend

Pull Request - State: closed - Opened by AjeyPaiK 3 months ago - 3 comments

#237 - SlideImage doesn't close file handlers with PYVIPS backend

Issue - State: closed - Opened by AjeyPaiK 3 months ago
Labels: bug

#235 - Pickling of `dlup.annotation.Polygon` doesn't work

Issue - State: closed - Opened by AjeyPaiK 3 months ago
Labels: bug

#234 - Bugfix/multiclass flag

Pull Request - State: closed - Opened by AjeyPaiK 3 months ago

#233 - `ConvertAnnotationsToMask` breaks

Issue - State: closed - Opened by AjeyPaiK 3 months ago
Labels: bug

#232 - Feature/multiclass annotations

Pull Request - State: closed - Opened by jonasteuwen 3 months ago - 1 comment

#231 - v0.5 tracking

Issue - State: closed - Opened by jonasteuwen 3 months ago
Labels: enhancement

#230 - Add grid_local_index to output sample of TiledWsiDataset

Issue - State: closed - Opened by VanessaBotha 3 months ago - 1 comment
Labels: enhancement, Stale

#229 - Incorrect grid order of grid_local_coordinates in TiledWsiDataset

Issue - State: open - Opened by VanessaBotha 3 months ago - 1 comment
Labels: bug

#228 - Add color and z-index to annotations, support multiclass output

Pull Request - State: closed - Opened by jonasteuwen 4 months ago - 1 comment
Labels: bug, enhancement

#227 - version 1.0 tracking

Issue - State: open - Opened by jonasteuwen 4 months ago - 1 comment
Labels: enhancement

#226 - Use vips.Image rather than PIL.Image.Image

Pull Request - State: closed - Opened by jonasteuwen 5 months ago

#225 - Enlarge scope backends

Pull Request - State: closed - Opened by jonasteuwen 5 months ago

#224 - Fixes reading of multiple holes in annotations

Pull Request - State: closed - Opened by moerlemans 5 months ago - 1 comment
Labels: bug

#223 - Multiple holes in annotations are not read correctly

Issue - State: closed - Opened by moerlemans 5 months ago - 3 comments
Labels: Stale

#221 - Feature/remote backends

Pull Request - State: open - Opened by jonasteuwen 6 months ago - 2 comments

#220 - pyhaloxml and actions update

Pull Request - State: closed - Opened by rharkes 6 months ago

#219 - Enlarge scope of possible backends

Pull Request - State: closed - Opened by jonasteuwen 7 months ago
Labels: python

#218 - Extend `ConvertAnnotationsToMask` features

Issue - State: closed - Opened by BPdeRooij 8 months ago - 1 comment
Labels: enhancement, Stale

#217 - Custom properties for bounding boxes in GeoJSON

Issue - State: closed - Opened by BPdeRooij 8 months ago - 4 comments
Labels: enhancement, Stale

#216 - When using read_region on an MRXS file the none tissue stuff becomes black

Issue - State: closed - Opened by moerlemans 8 months ago - 1 comment
Labels: bug

#215 - Fix annotation order of WsiAnnotations when sorting is None

Pull Request - State: closed - Opened by BPdeRooij 9 months ago - 2 comments
Labels: python

#214 - Unwanted label sorting in `WsiAnnotations`.

Issue - State: closed - Opened by BPdeRooij 9 months ago
Labels: bug

#213 - Add an optional `colormap` parameter while writing tiff files.

Pull Request - State: closed - Opened by AjeyPaiK 10 months ago
Labels: python

#212 - Add `colormap` to TiffWriter

Issue - State: closed - Opened by AjeyPaiK 10 months ago - 1 comment
Labels: enhancement

#211 - Remove multiscale dataset

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python

#210 - Design new multiscale dataset

Issue - State: closed - Opened by jonasteuwen 10 months ago - 2 comments
Labels: enhancement, Stale

#209 - Remove mask utility

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: documentation, python

#208 - Tiff Backend should support ICC profiles

Issue - State: closed - Opened by jonasteuwen 10 months ago - 1 comment
Labels: enhancement, Stale

#207 - Implement mode in backends

Pull Request - State: closed - Opened by jonasteuwen 10 months ago - 2 comments
Labels: python

#206 - Implement ICC profile in the pyvips backend

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python

#205 - Improve HaloXML parsing

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python, Stale

#204 - Implement offset for HaloXML

Pull Request - State: closed - Opened by jonasteuwen 10 months ago - 2 comments
Labels: python

#203 - Bug/fix annotation sorting

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python

#202 - Docs should be improved

Issue - State: closed - Opened by moerlemans 10 months ago - 6 comments
Labels: enhancement, Stale

#201 - Improve logic of `limit_bounds` together with `rois`

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python

#200 - v1 tracking and discussion

Issue - State: closed - Opened by jonasteuwen 10 months ago - 1 comment

#199 - Added complete tests for convert_annotations

Pull Request - State: closed - Opened by jonasteuwen 10 months ago
Labels: python

#198 - 197 convertannotationstomask doesnt give an empty mask when there are no annotations

Pull Request - State: closed - Opened by moerlemans 11 months ago - 1 comment
Labels: python

#196 - Bug/fix slide bounds in TiffFile

Pull Request - State: closed - Opened by jonasteuwen 11 months ago - 4 comments
Labels: bug, python

#195 - Allow selection of annotation sorting

Issue - State: closed - Opened by jonasteuwen 11 months ago
Labels: enhancement

#194 - Fix sorting

Pull Request - State: closed - Opened by jonasteuwen 11 months ago
Labels: python

#193 - Add `output_tile_size` parameter to BaseWsiDataset

Pull Request - State: closed - Opened by AjeyPaiK 11 months ago
Labels: python

#192 - Fixes{#191}

Pull Request - State: closed - Opened by AjeyPaiK 11 months ago
Labels: python

#190 - Fix invalid polygons

Pull Request - State: closed - Opened by AjeyPaiK 11 months ago - 1 comment
Labels: python, Stale

#189 - `mask_to_polygon()` utility in `dlup.utils.mask` returns empty or invalid polygons

Issue - State: closed - Opened by AjeyPaiK 11 months ago - 1 comment
Labels: bug, Stale

#188 - Add colors and maybe index map to `WsiAnnotations`

Issue - State: closed - Opened by jonasteuwen 11 months ago - 1 comment
Labels: enhancement

#187 - Axes swapped when using Image backend TIFFfile

Issue - State: closed - Opened by sinberlin2 11 months ago - 2 comments
Labels: bug

#186 - Too many parameters get passed to the dataset classes

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: enhancement, Stale

#185 - Bug fixes, initial work to support OpenSlide 4.0.0, improve type checking

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: python

#184 - Support OpenSlide 4.0

Issue - State: closed - Opened by jonasteuwen 12 months ago - 2 comments
Labels: enhancement, Stale

#183 - mpp issues and requirements

Pull Request - State: closed - Opened by martvanrijthoven 12 months ago - 2 comments

#182 - OpenSlide attaches ICC profiles

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: bug

#181 - Improve exceptions

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: documentation, python

#180 - More informative errors for : Requested region is outside level boundaries

Issue - State: closed - Opened by manyids2 12 months ago - 2 comments
Labels: enhancement

#179 - Implement enhancement requested in {#175}

Pull Request - State: closed - Opened by AjeyPaiK 12 months ago - 2 comments
Labels: python, Stale

#178 - Update pyvips_backend.py

Pull Request - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: python

#177 - HaloXML parser does not parse annotation types

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: bug, Stale

#176 - Implement functional interface for RenameLabels

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: python

#175 - Can we have `WsiAnnotations.get_scaled_view(scaling)`?

Issue - State: closed - Opened by AjeyPaiK 12 months ago - 6 comments
Labels: enhancement

#174 - Swap mpp_x, mpp_y in pyvips backend

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: python

#173 - Fixed __iter__ and added .pre-commit-config.yaml

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: documentation, python, ci

#172 - Improvement/mypy strict

Pull Request - State: closed - Opened by jonasteuwen 12 months ago
Labels: python, ci

#171 - Inconsistent MPP in output of get_mask function

Issue - State: closed - Opened by BPdeRooij 12 months ago - 4 comments
Labels: bug, Stale

#170 - v1 feature tracking

Issue - State: closed - Opened by jonasteuwen 12 months ago
Labels: documentation, enhancement, help wanted

#169 - mypy should pass strictly.

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: enhancement

#168 - Improve test coverage to >90%

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: enhancement, Stale

#167 - Do not use resampling when requested mpp is close to value in pyramid

Issue - State: closed - Opened by jonasteuwen 12 months ago - 1 comment
Labels: enhancement, Stale

#166 - Improve mypy

Pull Request - State: closed - Opened by jonasteuwen about 1 year ago - 1 comment
Labels: python

#165 - Increase test coverage

Pull Request - State: closed - Opened by jonasteuwen about 1 year ago
Labels: python

#164 - Fix rename labels

Pull Request - State: closed - Opened by jonasteuwen about 1 year ago
Labels: python

#163 - Multiple file handlers are created for the same file while opening WSIs.

Issue - State: closed - Opened by AjeyPaiK about 1 year ago - 1 comment
Labels: bug, Stale

#162 - Implement Darwin v7 reader and improve annotation class

Pull Request - State: closed - Opened by jonasteuwen about 1 year ago - 1 comment
Labels: documentation, python, ci

#161 - added new parameter and according changes so that limit bounds or oth…

Pull Request - State: closed - Opened by moerlemans about 1 year ago - 9 comments
Labels: documentation, python, ci

#160 - Annotations made by HALO for mrxs slide are not read correctly due to limit bounds

Issue - State: closed - Opened by moerlemans about 1 year ago - 7 comments
Labels: bug, Stale

#159 - add CITATION.cff file with main contributors

Pull Request - State: closed - Opened by YoniSchirris over 1 year ago
Labels: documentation

#158 - Add citation file

Issue - State: closed - Opened by YoniSchirris over 1 year ago - 1 comment
Labels: enhancement, Stale

#157 - Use context manager for pyhaloxml

Pull Request - State: closed - Opened by rharkes over 1 year ago - 1 comment

#156 - Libvips throws an error on some incomplete header information for a .svs file

Issue - State: closed - Opened by moerlemans over 1 year ago - 1 comment
Labels: enhancement, Stale