Ecosyste.ms: Issues

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GitHub / DIAGNijmegen/pathology-whole-slide-data issues and pull requests

#65 - Update imagewriter.py with tile and coordinate checks and corrections

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

#64 - Update `DetectionPatchLabelSampler`

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

#63 - Add comment about simplify to convert_mask_to_xml_or_json.py

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

#62 - Implement check for "partial" tiles in combine.py

Pull Request - State: closed - Opened by rolandnemeth000 3 months ago - 1 comment

#61 - Allow PointAnnotation sampling in RandomPointSampler

Pull Request - State: closed - Opened by rolandnemeth000 3 months ago - 2 comments

#60 - Exemplary JSON Annotation File

Issue - State: closed - Opened by FraukeWilm 5 months ago - 2 comments

#59 - Patch iterator compatibility with .geojson annotation files

Issue - State: open - Opened by mdeleeuw1 6 months ago - 8 comments

#58 - fix: cucim backend

Pull Request - State: closed - Opened by siemdejong 8 months ago - 1 comment

#57 - cuCIM backend not fully supported

Issue - State: closed - Opened by polejowska 8 months ago - 1 comment

#56 - fix: remove metaclass class argument

Pull Request - State: closed - Opened by siemdejong 8 months ago - 3 comments

#55 - Cucim backend not available

Issue - State: closed - Opened by siemdejong 8 months ago

#54 - Added executable main with argparse

Pull Request - State: closed - Opened by JoeySpronck 10 months ago

#53 - add conda recipe

Issue - State: open - Opened by sarthakpati 10 months ago - 5 comments

#50 - Overhauled convert_mask_to_xml fixing #48

Pull Request - State: closed - Opened by JoeySpronck 11 months ago

#49 - Mask to xml/json overhaul #48

Pull Request - State: closed - Opened by JoeySpronck 11 months ago

#48 - mask to xml/json overhaul

Issue - State: closed - Opened by JoeySpronck 11 months ago - 1 comment

#47 - Support qptiff?

Issue - State: closed - Opened by yuling-luo 11 months ago - 4 comments

#46 - fix #45

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

#45 - Patch label sampler fails with point annotation

Issue - State: closed - Opened by JoeySpronck 12 months ago - 3 comments

#44 - Implement annotation offset for offset bounds in mrxs files

Issue - State: closed - Opened by martvanrijthoven 12 months ago - 1 comment

#43 - Plot holes if any within annotations

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

#42 - Implementation of qupath annotation parser ('.geojson')

Pull Request - State: closed - Opened by tsikup about 1 year ago - 4 comments

#41 - QuPath annotations (.geojson) format not readable by parser

Issue - State: closed - Opened by tsikup about 1 year ago - 1 comment

#40 - from wholeslidedata.source.configuration.config import insert_paths_into_config

Issue - State: closed - Opened by ZhangRan24 about 1 year ago - 2 comments

#39 - create_batch_iterator fails when copy_path != None and number_of_batches > 0

Issue - State: closed - Opened by robinlomans about 1 year ago - 2 comments

#38 - Advantage of ConcurrentBuffer against standard pytorch data loader

Issue - State: closed - Opened by CharlieCheckpt over 1 year ago - 2 comments

#36 - Add class for indexed masks

Pull Request - State: closed - Opened by daangeijs over 1 year ago - 3 comments

#35 - Installing package on local machine

Issue - State: closed - Opened by PierpaoloV over 1 year ago - 3 comments

#34 - I got confused between branch 'main' and '0.0.16'

Issue - State: closed - Opened by BestVIncent over 1 year ago - 1 comment

#33 - V0.1.0

Pull Request - State: closed - Opened by martvanrijthoven almost 2 years ago

#32 - ASAP compatibility in imagewriter

Pull Request - State: closed - Opened by leandervaneekelen almost 2 years ago

#30 - Sliding Window configuration

Issue - State: closed - Opened by michelbotros about 2 years ago - 6 comments
Labels: question

#29 - AsapAnnotationParser label colors from group

Issue - State: closed - Opened by robinlomans about 2 years ago - 1 comment
Labels: enhancement

#28 - read images from s3 bucket

Pull Request - State: closed - Opened by rj678 over 2 years ago - 9 comments

#27 - plot_annotations plots everything flipped

Issue - State: closed - Opened by michelbotros over 2 years ago - 1 comment

#26 - Tissue masking

Issue - State: closed - Opened by michelbotros over 2 years ago - 7 comments
Labels: question

#25 - Iterating over classes in WholeSlideAnnotation objects

Issue - State: closed - Opened by leandervaneekelen over 2 years ago - 2 comments
Labels: enhancement

#24 - read images and annotation directly from s3 bucket

Issue - State: closed - Opened by rj678 over 2 years ago - 9 comments
Labels: enhancement, question

#23 - Sliding window with Segmentation Mask Sampling

Issue - State: closed - Opened by Vishwesh4 over 2 years ago - 9 comments
Labels: question

#22 - Extracting randomly rotated patches from the WSI.

Issue - State: closed - Opened by michelbotros over 2 years ago - 4 comments
Labels: question

#21 - changing image backend to pyvips

Issue - State: closed - Opened by 99snowleopards over 2 years ago - 4 comments
Labels: question

#20 - write docs

Issue - State: open - Opened by martvanrijthoven over 2 years ago - 1 comment
Labels: documentation

#19 - create_batch_iterator that associates files with exact matching

Issue - State: closed - Opened by michelbotros over 2 years ago - 3 comments
Labels: question

#18 - Artifacts from batch iterator

Issue - State: closed - Opened by sumeetgadagkar over 2 years ago - 4 comments
Labels: bug

#16 - use github url as package website

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

#15 - Feature/inst norm albu

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

#14 - RegistrantNotRegisteredError in Tiger-Hooknet Example

Issue - State: closed - Opened by AmartyaCSB over 2 years ago - 2 comments
Labels: question

#13 - Feature/inst norm albu

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

#12 - Refactor/parsing

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

#11 - enhance shape and spacing error messages

Pull Request - State: closed - Opened by kaczmarj over 2 years ago - 1 comment

#10 - how to calculate number of samples in one full pass of BatchIterator

Issue - State: closed - Opened by kaczmarj over 2 years ago - 1 comment
Labels: question

#9 - Feature/create yaml from folders

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

#8 - Feature/albumentation callback

Pull Request - State: closed - Opened by thijsgelton over 2 years ago - 4 comments

#7 - Added colors to both the parsing and converting (groups and annotation)

Pull Request - State: closed - Opened by thijsgelton over 2 years ago - 3 comments

#6 - weighted sampling of patches based on different labels for segmentation

Issue - State: closed - Opened by Vishwesh4 over 2 years ago - 2 comments
Labels: question

#5 - write tests

Issue - State: open - Opened by martvanrijthoven almost 3 years ago
Labels: enhancement

#4 - improve writing checks in write_mask

Issue - State: closed - Opened by martvanrijthoven almost 3 years ago
Labels: enhancement

#3 - Feature writing

Pull Request - State: closed - Opened by martvanrijthoven about 3 years ago

#2 - Copy_data_path freezes upon first trial

Issue - State: closed - Opened by CyrilRJK about 3 years ago - 1 comment
Labels: bug

#1 - create deterministic pause/restart functionality iterator

Issue - State: closed - Opened by martvanrijthoven about 3 years ago
Labels: enhancement