Ecosyste.ms: Issues

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GitHub / TissueImageAnalytics/tiatoolbox issues and pull requests

#857 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#854 - Add `WSIReader` type annotation to `input_img` for `PatchExtrator`

Pull Request - State: open - Opened by Jiaqi-Lv 3 months ago - 1 comment
Labels: documentation

#853 - I can't download the pre-training model

Issue - State: closed - Opened by 24hourssss 3 months ago - 2 comments

#852 - FileNotFoundError When Running HoVer-Net on WSI

Issue - State: open - Opened by tjbencomo 3 months ago - 2 comments

#851 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#850 - 🐛 Fix Immutable Output from `WSIReader`

Pull Request - State: closed - Opened by mostafajahanifar 3 months ago - 1 comment
Labels: bug, enhancement

#849 - Documentation for `PatchExtractor` is inconsistent

Issue - State: open - Opened by Jiaqi-Lv 3 months ago
Labels: documentation

#848 - is there a way to turn off warning?

Issue - State: closed - Opened by ml-and-ml 3 months ago - 2 comments

#847 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#846 - Fix `mypy` type errors in `tiatoolbox/cli`

Pull Request - State: open - Opened by Jiaqi-Lv 4 months ago - 1 comment
Labels: bug, code readability, dev tools

#845 - :bug: Fix `test_dsl` for `pytest`>=8.3.0

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

#844 - Nucleus Detection gives error

Issue - State: closed - Opened by ankana999 4 months ago - 1 comment

#843 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#842 - 🧑‍💻 Fix `mypy` Type Error in `tiatoolbox/tools`

Pull Request - State: closed - Opened by Jiaqi-Lv 4 months ago - 1 comment
Labels: bug, code readability, dev tools

#841 - 🆕 Address `TIAViz` Review Comments

Pull Request - State: open - Opened by measty 4 months ago
Labels: enhancement

#839 - How to save images as TIFF files with metadata preserved

Issue - State: closed - Opened by ziyuanzhao2000 4 months ago - 1 comment

#838 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#837 - Image reader `read_region` returns read-only np.ndarray

Issue - State: closed - Opened by ziyuanzhao2000 4 months ago - 1 comment

#836 - :technologist: Add Coverage Context

Pull Request - State: closed - Opened by shaneahmed 5 months ago - 2 comments
Labels: dev tools

#835 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 1 comment

#834 - TIAToolbox cannot read all scenes of OME-TIFF that was originally a CZI

Issue - State: closed - Opened by KenAncheta 5 months ago - 2 comments
Labels: bug

#833 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 1 comment

#832 - 📌 Fix Compatibility with `bokeh` Version `3.5.0`

Pull Request - State: closed - Opened by measty 5 months ago - 1 comment
Labels: bug, dependencies

#831 - 🐛 Add `mypy` Type Check `tools/wsi_registration.py`

Pull Request - State: closed - Opened by Jiaqi-Lv 5 months ago - 1 comment
Labels: bug, code readability, dev tools

#830 - :pushpin: Pin `bokeh` to `<3.5.0` Due to Incompatibility.

Pull Request - State: closed - Opened by shaneahmed 5 months ago - 1 comment

#829 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 1 comment

#828 - [skip ci] :memo: Enhance Download Paths in `10-wsi-registration.ipynb`

Pull Request - State: closed - Opened by shaneahmed 5 months ago - 2 comments

#827 - :white_check_mark: Add Test to Reset `logger` Filters.

Pull Request - State: closed - Opened by shaneahmed 5 months ago - 1 comment

#826 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 1 comment

#825 - 🆕Multichannel Image Reading

Pull Request - State: open - Opened by measty 5 months ago - 1 comment
Labels: enhancement

#824 - 🐛 Fix Type Annotation for `annotation/storage.py`

Pull Request - State: closed - Opened by Jiaqi-Lv 5 months ago - 1 comment

#823 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago - 1 comment

#822 - 🆕 Use Annotations as a Filter for Patch Extraction

Pull Request - State: open - Opened by measty 6 months ago - 7 comments
Labels: enhancement

#821 - :pushpin: Update `ruff` version.

Pull Request - State: closed - Opened by shaneahmed 6 months ago - 1 comment
Labels: dependencies

#820 - Image Registration feature request

Issue - State: closed - Opened by sm-ak-r33 6 months ago - 3 comments
Labels: enhancement

#819 - Empty slide visualizer on a remote machine

Issue - State: closed - Opened by coolmule0 6 months ago - 1 comment

#818 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago - 1 comment

#817 - Difference in CoNSeP results

Issue - State: closed - Opened by FabianHoerst 7 months ago - 2 comments

#816 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#815 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#814 - 🐛 Fix Code Complexity in `wsireader`

Pull Request - State: closed - Opened by shaneahmed 7 months ago - 1 comment
Labels: bug

#813 - 🐛 Fix Rendering Annotations with Holes

Pull Request - State: closed - Opened by measty 7 months ago - 2 comments
Labels: bug

#812 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#811 - :bug: Fix `codecov` Reporting

Pull Request - State: closed - Opened by shaneahmed 7 months ago - 1 comment
Labels: bug, dev tools

#810 - Enhance download paths in the examples notebooks

Issue - State: closed - Opened by GeorgeBatch 7 months ago - 2 comments

#809 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago - 1 comment

#808 - PanNuke TCGA-Slide List

Issue - State: closed - Opened by FabianHoerst 8 months ago - 2 comments
Labels: question

#807 - Add support for `ignore_is_tiled_tiff` in `WSIReader.open()`

Pull Request - State: closed - Opened by GeorgeBatch 8 months ago - 21 comments
Labels: bug, enhancement

#806 - Add `mypy` type check to `annotation/`

Pull Request - State: closed - Opened by Jiaqi-Lv 8 months ago - 1 comment
Labels: code readability

#805 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#803 - Tiatoolbox stopped working after generating yml file. SSL problem with openslide?

Issue - State: closed - Opened by KenAncheta 8 months ago - 4 comments
Labels: dependencies

#802 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#801 - Add `mypy` Type Check to `wsi_registration.py`

Pull Request - State: closed - Opened by Jiaqi-Lv 8 months ago - 1 comment
Labels: code readability

#800 - ⚡️Refine `torch.compile` and Add to WSI Registration

Pull Request - State: closed - Opened by Abdol 8 months ago - 3 comments
Labels: enhancement

#799 - :pushpin: Fix `docs/requirements.txt` for `sphinx-design`

Pull Request - State: closed - Opened by shaneahmed 9 months ago - 1 comment
Labels: dependencies

#798 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago - 1 comment

#797 - 🧑‍💻 Replace `black` with `ruff` Formatter

Pull Request - State: closed - Opened by shaneahmed 9 months ago - 2 comments
Labels: dev tools, dependencies

#796 - :alien: Change `size` to `radius` for `bokeh 3.4` Compatibility

Pull Request - State: closed - Opened by measty 9 months ago - 1 comment
Labels: bug, dependencies

#795 - :children_crossing: Refactor `cli.visualize` to Improve `cli` Response

Pull Request - State: open - Opened by shaneahmed 9 months ago - 1 comment
Labels: enhancement

#794 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago - 1 comment

#793 - Reading CZI files

Issue - State: closed - Opened by KenAncheta 9 months ago - 2 comments

#792 - 📝 Fix a Typo in `examples/README.md`

Pull Request - State: closed - Opened by moodyhunter 9 months ago - 1 comment

#791 - Kernel keeps dying while trying to create image masks

Issue - State: closed - Opened by ShataDg 9 months ago - 2 comments

#790 - Runtime of UNet Breast Cancer Segmenter

Issue - State: closed - Opened by rictoo 9 months ago - 4 comments

#789 - 🆕 Add Reading Slide-level info & Simple Plugins for Visualization Tool

Pull Request - State: open - Opened by measty 9 months ago - 1 comment
Labels: enhancement

#788 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#787 - :hammer: Add `mypy` Type Check to `stainnorm`, `stainaugment`, `patchextraction`

Pull Request - State: closed - Opened by Jiaqi-Lv 10 months ago - 2 comments

#786 - :pushpin: Update minimum Python version to `3.9`

Pull Request - State: closed - Opened by shaneahmed 10 months ago - 2 comments
Labels: dependencies

#785 - 📌 Update `wsidicom` dependency

Pull Request - State: closed - Opened by shaneahmed 10 months ago - 3 comments
Labels: dependencies

#784 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#783 - 🧑‍💻 Define `PatchPredictor`

Pull Request - State: open - Opened by shaneahmed 10 months ago - 5 comments
Labels: enhancement

#782 - :hammer: `mypy` type check `tools/`

Pull Request - State: closed - Opened by Jiaqi-Lv 10 months ago - 2 comments
Labels: refactoring

#781 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#780 - NucleusInstanceSegmentor.predict() has no "patch" mode

Issue - State: open - Opened by alevangel 10 months ago - 2 comments
Labels: bug, enhancement

#779 - 🐛Fix `test` in `test_annotation_stores.py`

Pull Request - State: closed - Opened by measty 10 months ago - 1 comment
Labels: bug

#778 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#777 - 🐛 Fix `TIFFWSIReader` `read_bound`

Pull Request - State: closed - Opened by vqdang 10 months ago - 9 comments
Labels: bug, help wanted

#776 - ⚡️ Add `torch.compile` to `PatchPredictor`

Pull Request - State: closed - Opened by Abdol 10 months ago - 6 comments
Labels: enhancement

#775 - Misspelling the "Classifier" layer in pretrained model files

Issue - State: closed - Opened by mostafajahanifar 10 months ago - 1 comment
Labels: bug

#774 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#773 - AttributeError: 'IOSegmentorConfig' object has no attribute 'margin'

Issue - State: closed - Opened by alevangel 10 months ago - 2 comments

#772 - 🐛 Fix `json_extract` Construction

Pull Request - State: closed - Opened by measty 11 months ago - 1 comment
Labels: bug

#771 - Unexpected behaviour in annotation store when property key has a . in it

Issue - State: closed - Opened by measty 11 months ago
Labels: help wanted

#770 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago - 1 comment

#769 - ♻️ Remove `POWER` from sqlite-dist Calculations

Pull Request - State: closed - Opened by measty 11 months ago - 2 comments
Labels: bug

#768 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#767 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago - 1 comment

#766 - 🚑 Release 1.5.1

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment
Labels: release

#765 - Error importing modules in tiatoolbox.models using Google Colab

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

#764 - 🚑 Release 1.5.1

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment
Labels: release

#763 - Conda feedstock build fails

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

#762 - :pushpin: Specify Python versions

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment

#761 - 🔖 Release 1.5.0

Pull Request - State: closed - Opened by shaneahmed 12 months ago
Labels: release

#760 - [skip ci] :bug: Fix `idars` example notebook

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment

#759 - [skip ci] :bug: Fix Example Notebook 09

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment

#758 - [skip ci] :bug: Fix Error in `06-semantic-segmentation`

Pull Request - State: closed - Opened by shaneahmed 12 months ago - 1 comment