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

#155 - Documentation: `dlup.data.dataset.SlideImageDatasetBase` has incorrect docstring for `regions`

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 1 comment
Labels: Stale

#154 - Add colors to annotations

Issue - State: closed - Opened by jonasteuwen almost 2 years ago - 2 comments
Labels: enhancement, Stale

#153 - Support halo annotations

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago
Labels: documentation, python, ci

#152 - Entropy masker

Pull Request - State: closed - Opened by siemdejong almost 2 years ago - 2 comments
Labels: wontfix

#151 - `ImageBackend.AUTODETECT` does not close file handlers

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 5 comments
Labels: bug, Stale

#150 - Bounding box property WSIAnnotations class errors when loading multipoint.

Issue - State: closed - Opened by Dafidofff almost 2 years ago - 2 comments
Labels: bug, Stale

#149 - Improving typing

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago
Labels: python, ci

#148 - Support multipoint

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago
Labels: python

#147 - Implement anti-aliasing in tiff writer

Issue - State: closed - Opened by jonasteuwen almost 2 years ago - 2 comments
Labels: enhancement, Stale

#146 - Limit bounds

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago - 3 comments
Labels: python

#145 - Added imagecodecs as a dependency

Pull Request - State: closed - Opened by AjeyPaiK almost 2 years ago - 2 comments
Labels: python

#144 - Allow to select a different interpolator in TiffWriter

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago - 1 comment
Labels: python

#143 - Strict parsing of mypy

Issue - State: closed - Opened by jonasteuwen almost 2 years ago - 1 comment
Labels: enhancement, Stale

#142 - Have a .toml file for mask-to-polygon

Issue - State: closed - Opened by rharkes almost 2 years ago - 1 comment
Labels: enhancement, Stale

#141 - resampling is only implemented for RGB images, not for segmentation masks

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 6 comments
Labels: bug

#140 - Add message or progress bar when writing tiff

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 1 comment
Labels: enhancement, Stale

#139 - Allow `mpp` argument for `SlideImage.get_thumbnail`

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 3 comments
Labels: enhancement, Stale

#138 - Wsi to polygon

Pull Request - State: closed - Opened by jonasteuwen almost 2 years ago - 6 comments
Labels: python, ci

#137 - incorrect docstring of `SlideImage.get_thumbnail`

Issue - State: closed - Opened by YoniSchirris almost 2 years ago - 1 comment
Labels: documentation

#136 - WsiAnnotations does not support MultiPoint

Issue - State: closed - Opened by manyids2 about 2 years ago
Labels: bug

#135 - Feat: use `openslide.bounds-{}` if available

Issue - State: closed - Opened by YoniSchirris about 2 years ago - 3 comments
Labels: enhancement, Stale

#134 - Allow mask threshold of None

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#133 - Extend concatdataset

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#132 - Add property to compute the bounding box of `WsiAnnotations`

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#131 - Come up with a way to use `SlideImage` as an input to the dataset

Issue - State: closed - Opened by jonasteuwen about 2 years ago - 1 comment
Labels: enhancement, Stale

#130 - dlup CLI: mask_colors argument missing & thumbnail and mask sizes not matching

Issue - State: closed - Opened by VanessaBotha about 2 years ago - 1 comment
Labels: bug, Stale

#129 - Allow setting of mpp, modernize typing

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#128 - Allow to overwrite mpp

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python, ci

#127 - Different tile size in the grid

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#126 - `SlideImage.read_region` fails because the box overflows the region in `PIL.Image.resize`

Issue - State: closed - Opened by YoniSchirris about 2 years ago - 3 comments
Labels: bug

#125 - Different grids for TiledROIsSlideImageDataset

Issue - State: closed - Opened by manyids2 about 2 years ago - 2 comments
Labels: enhancement, Stale

#124 - Feat: Add warning about `multiprocessing` context when using `TifffileImageWriter.from_tiles_iterator`

Issue - State: closed - Opened by YoniSchirris about 2 years ago - 3 comments
Labels: enhancement, Stale

#123 - Allow mpp to differ by 1.5%

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#122 - Allow setting a default value for the mask

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago
Labels: python

#121 - Update shapely

Pull Request - State: closed - Opened by jonasteuwen about 2 years ago - 1 comment
Labels: documentation, python, ci

#120 - Add number of workers as a parameter for tiffwriters.

Issue - State: closed - Opened by Tkootstra over 2 years ago - 2 comments
Labels: enhancement, Stale

#119 - Remap labels differently

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#118 - Add py.typed

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago

#117 - Allow to overwrite mpp

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#116 - The conversion augmentation always returns an roi.

Issue - State: closed - Opened by AjeyPaiK over 2 years ago - 1 comment
Labels: wontfix

#115 - Fix multiplier

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#114 - Bug in `ConvertAnnotationsToMask` transform

Issue - State: closed - Opened by AjeyPaiK over 2 years ago - 1 comment
Labels: bug

#113 - points annotation conversion hotfix

Pull Request - State: closed - Opened by Tkootstra over 2 years ago
Labels: python

#112 - converting annotiations does not return point annotations

Issue - State: closed - Opened by Tkootstra over 2 years ago
Labels: bug

#111 - Cannot read some images from the TCGA dataset

Issue - State: closed - Opened by AjeyPaiK over 2 years ago - 1 comment
Labels: wontfix

#110 - AttributeError: module 'shapely' has no attribute 'affinity'

Issue - State: closed - Opened by TangTangFei over 2 years ago - 2 comments
Labels: bug

#109 - Extending functionality of `WsiAnnotations` and allow polygons as mask

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: documentation, python, ci

#108 - Tifffile Image backend makes a mistake while reading mpp values of images.

Issue - State: closed - Opened by AjeyPaiK over 2 years ago - 3 comments
Labels: bug

#107 - Fixed transformation bug

Pull Request - State: closed - Opened by Dafidofff over 2 years ago - 1 comment
Labels: python

#106 - Empty annotation bug in transforms.

Issue - State: closed - Opened by Dafidofff over 2 years ago - 3 comments
Labels: bug

#105 - Ensure multipolygon is always valid

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#104 - Extend annotations, improve errors

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python, ci

#103 - Bug in MajorityClassToLabel transformation.

Issue - State: closed - Opened by Dafidofff over 2 years ago - 1 comment
Labels: bug

#102 - Transforms should only be applied on the used class

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#101 - Simplifications

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: documentation, python

#100 - Adding a few transforms

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#99 - Add tests for annotations

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#98 - Allow simplification of polygons

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#97 - Fix SlideImage as annotation

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#96 - Fix tiff size order

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: documentation, python

#95 - Allow L regions

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#94 - Made `self.transform` a private member in the base classes.

Pull Request - State: closed - Opened by AjeyPaiK over 2 years ago
Labels: python

#92 - Fixes for ROI in datasets

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#91 - Remap labels

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#90 - Remap labels

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#89 - TypeError: 'WsiSingleLabelAnnotation' object is not iterable

Issue - State: closed - Opened by Dafidofff over 2 years ago - 1 comment
Labels: bug

#88 - Remap labels

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#87 - Export GeoJSON and support scaling

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: documentation, python

#86 - Read GeoJSON and annotation class fixes

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#85 - Extend annotations (#83)

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#84 - Implement tiff writer

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#83 - Extend annotations

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#82 - Fix some TIGER tiffs

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#81 - fix unit_dict in _read_as_tiff

Pull Request - State: closed - Opened by Tkootstra over 2 years ago - 1 comment
Labels: python

#80 - Bug in reading TIGER slides with new experimental image backends

Issue - State: closed - Opened by Tkootstra over 2 years ago
Labels: bug

#79 - Shapely fix

Pull Request - State: closed - Opened by Tkootstra over 2 years ago
Labels: bug, python

#78 - Shapely upstream change in srtree breaks annotations read_region()

Issue - State: closed - Opened by Tkootstra over 2 years ago - 2 comments
Labels: bug

#77 - Allow SlideImage as input to mask parameter of dataset classes

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago - 1 comment
Labels: python

#76 - Openslide will not read slide image files that don't adhere to assumptions about mpp properties

Issue - State: closed - Opened by Tkootstra over 2 years ago - 3 comments
Labels: bug

#75 - Backends dataset

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago - 2 comments
Labels: documentation, python

#74 - Implement backends

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: documentation, python, ci

#73 - Use max dimension to compute scaling for background

Pull Request - State: closed - Opened by lromor over 2 years ago - 1 comment
Labels: python

#72 - Read TIFF mpp values

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago
Labels: python

#71 - Named tuple output for dataset classes

Issue - State: closed - Opened by jonasteuwen over 2 years ago - 1 comment
Labels: enhancement, Stale

#70 - Experimental annotations class

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago - 10 comments
Labels: python, ci

#69 - Multiscale dataset

Pull Request - State: closed - Opened by jonasteuwen over 2 years ago - 3 comments
Labels: python

#68 - Numpy bug in Cashing-branch

Issue - State: closed - Opened by Dafidofff over 2 years ago - 4 comments
Labels: bug, Stale

#67 - First commit on caching SlideImage

Pull Request - State: closed - Opened by jonasteuwen about 3 years ago - 1 comment
Labels: python, ci, docker

#66 - Experimental implementation of caching mechanism

Pull Request - State: closed - Opened by jonasteuwen about 3 years ago
Labels: python

#65 - fixing bug of over-writting the bbox variable if colour is given and …

Pull Request - State: closed - Opened by Baggsy about 3 years ago
Labels: Stale

#61 - Documentation out of date

Issue - State: closed - Opened by jonasteuwen about 3 years ago - 1 comment
Labels: bug, Stale

#58 - Added TiffMaskWriter class

Pull Request - State: closed - Opened by AjeyPaiK about 3 years ago - 1 comment
Labels: python

#57 - A utility to save slidescore annotations as multi-resolution masks in .tiff file format.

Issue - State: closed - Opened by AjeyPaiK about 3 years ago - 3 comments
Labels: enhancement, Stale

#56 - I want a feature to tile the whole WSI by disabling the FESI, improved FESI algorithms.

Issue - State: closed - Opened by AjeyPaiK about 3 years ago - 2 comments
Labels: enhancement, Stale

#55 - Plotting bboxes with colors

Issue - State: closed - Opened by manyids2 about 3 years ago - 1 comment
Labels: Stale

#47 - draw location and size of used tiles on thumbnail during wsi tiling cli

Pull Request - State: closed - Opened by YoniSchirris over 3 years ago - 1 comment
Labels: python

#44 - Add dry run to wsi tiling CLI

Pull Request - State: closed - Opened by YoniSchirris over 3 years ago - 4 comments
Labels: python

#40 - OpenSlide image.magnification attribute not found for CAMELYON16 scanners (.tif)

Issue - State: closed - Opened by DennisHaijma over 3 years ago - 4 comments
Labels: bug, Stale

#39 - dlup wsi tile - unstackable tensors due to irregular tile sizes

Issue - State: closed - Opened by DennisHaijma over 3 years ago - 2 comments
Labels: bug, Stale