Ecosyste.ms: Issues

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

GitHub / SBU-BMI/wsinfer issues and pull requests

#228 - MPS support [minor]

Issue - State: open - Opened by Michael-L-Miller 5 months ago

#227 - only use specified backend (or tifffile) to read mpp

Pull Request - State: closed - Opened by kaczmarj 7 months ago

#226 - fix backend setting

Pull Request - State: closed - Opened by kaczmarj 7 months ago

#225 - Backend set to tiffslide, but openslide is used

Issue - State: open - Opened by vthorsson 8 months ago - 7 comments

#223 - CTransPath

Issue - State: closed - Opened by masudalynn0704 8 months ago - 1 comment

#222 - results not ideal

Issue - State: open - Opened by TingTingShao 9 months ago - 6 comments

#221 - Use your own model

Issue - State: open - Opened by Nazim0001 11 months ago - 8 comments

#219 - [STYLE] use ruff in lieu of black/flake8/isort + add pre-commit

Pull Request - State: closed - Opened by kaczmarj 12 months ago

#218 - Cleanup + add strided patches

Pull Request - State: closed - Opened by kaczmarj 12 months ago

#217 - Add segmentation options to wsinfer run

Pull Request - State: closed - Opened by kaczmarj 12 months ago

#216 - [FEAT] check that thumbnail is an RGB image

Issue - State: closed - Opened by kaczmarj 12 months ago

#215 - [STYLE] format with black

Pull Request - State: closed - Opened by kaczmarj about 1 year ago

#214 - [bug] symlinked file names can cause problems

Issue - State: closed - Opened by kaczmarj about 1 year ago

#213 - wsinfer.errors.CannotReadSpacing

Issue - State: closed - Opened by jeginderof about 1 year ago - 8 comments

#211 - fix types when using cv2

Pull Request - State: closed - Opened by kaczmarj about 1 year ago

#210 - types for opencv causing errors

Issue - State: closed - Opened by kaczmarj about 1 year ago

#209 - Feat/qupath

Pull Request - State: closed - Opened by swaradgat19 about 1 year ago - 19 comments

#208 - Fix/recursion limit

Pull Request - State: closed - Opened by swaradgat19 about 1 year ago - 5 comments

#207 - Handle recursionlimit error dynamically

Pull Request - State: closed - Opened by swaradgat19 about 1 year ago - 2 comments

#206 - backwards compatibility of output directory

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

#205 - results directory not found if patching fails on all slides

Issue - State: closed - Opened by kaczmarj about 1 year ago

#204 - set chunksize to some value greater than 1 in geojson conversion

Issue - State: closed - Opened by kaczmarj about 1 year ago - 5 comments

#203 - [TEST] test that openslide/tiffslide pad tiles on slide edges

Issue - State: closed - Opened by kaczmarj over 1 year ago
Labels: help wanted, test

#202 - [ENH] add strided tiles

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

#201 - [DOCS] add video walkthrough to user guide + update version switcher

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

#200 - clarify docs on gpu install + explain model output directory

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

#199 - test that openslide.OpenSlide is available

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

#198 - improve docs on how to install GPU dependencies for PyTorch

Issue - State: closed - Opened by kaczmarj over 1 year ago
Labels: documentation

#197 - add python 3.12 to ci

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

#196 - test openslide import more strictly

Issue - State: closed - Opened by kaczmarj over 1 year ago

#194 - add CITATION.cff

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

#193 - test python 3.12 when it is released

Issue - State: closed - Opened by kaczmarj over 1 year ago
Labels: test

#192 - RecursionError: maximum recursion depth exceeded in comparison

Issue - State: closed - Opened by jecaJeca over 1 year ago - 9 comments
Labels: bug

#191 - Fix/geojson command

Pull Request - State: closed - Opened by swaradgat19 over 1 year ago - 10 comments

#189 - MIRAX (.mrxs) support

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

#188 - check that page0 is TiffPage inst

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

#187 - add favicon to docs

Issue - State: closed - Opened by kaczmarj over 1 year ago

#186 - conversion to SBU format is broken

Issue - State: closed - Opened by kaczmarj over 1 year ago - 8 comments
Labels: bug

#185 - some arguments in data class are unused

Issue - State: closed - Opened by kaczmarj over 1 year ago

#184 - Generating geojson files on run command

Pull Request - State: open - Opened by swaradgat19 over 1 year ago - 13 comments

#183 - consider making releases automatically with intuit's 'auto'

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

#182 - clone batch_coords tensor to prevent Too many open files error

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

#181 - always create geojson outputs with 'wsinfer run'

Issue - State: closed - Opened by kaczmarj over 1 year ago - 18 comments

#180 - skip openslide/tiffslide tests if those backends not available

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

#179 - changed GeoJSON format

Pull Request - State: closed - Opened by swaradgat19 over 1 year ago - 22 comments

#177 - Gracefully handle missing backends

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

#176 - fixed togeojson and tosbu commands

Pull Request - State: closed - Opened by swaradgat19 over 1 year ago

#175 - Incorrect command to convert model outputs to GeoJson in documentation

Issue - State: closed - Opened by swaradgat19 over 1 year ago - 4 comments

#174 - add link to github repo in navbar

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

#173 - [DOCS] add a link to the source code on readthedocs page

Issue - State: closed - Opened by kaczmarj over 1 year ago

#172 - make model output names align with QuPath

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

#171 - make TILs column name lymphocytes

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

#169 - remove vgg16 and inception breast models

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

#168 - [PKG] add wsinfer to conda-forge channel for conda installation

Issue - State: closed - Opened by kaczmarj over 1 year ago - 4 comments

#167 - [TEST] add tests for the various mpp calculation functions we have

Issue - State: open - Opened by kaczmarj over 1 year ago
Labels: help wanted, test

#166 - ADD: calcuate mpp with openslide tiff tags

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

#165 - add mpp calculation in openslide using tiff resolution tags

Issue - State: closed - Opened by kaczmarj over 1 year ago

#164 - [ENH] rm pyyaml dep

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

#163 - [ENH] consider adding test time augmentation

Issue - State: open - Opened by kaczmarj over 1 year ago - 4 comments
Labels: enhancement, help wanted

#162 - create a qupath project from the model inference results

Issue - State: closed - Opened by kaczmarj over 1 year ago - 51 comments
Labels: enhancement

#161 - [DOCS] add version dropdown and code block copy button

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

#160 - DOCS: update website, docstrings, and types for upcoming 0.4.0 release

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

#159 - wsinfer run --help needs updating

Issue - State: closed - Opened by ebremer over 1 year ago

#158 - added pyproject.toml file

Pull Request - State: closed - Opened by swaradgat19 over 1 year ago - 13 comments

#157 - Fix/setup.cfg

Pull Request - State: closed - Opened by swaradgat19 over 1 year ago - 8 comments

#156 - Fix: use pep 604 type annotations

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

#155 - Remove model-specific dockerfiles + Remove ROI functionality

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

#154 - pin tifffile dependency to something greater than version 2023.*

Issue - State: closed - Opened by kaczmarj over 1 year ago - 7 comments

#153 - [REF] use custom patching implementation and use Apache 2.0 license

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

#152 - remove env var prefix for CLI

Issue - State: closed - Opened by kaczmarj over 1 year ago

#151 - [TEST] add test for WholeSlideImagePatches class

Issue - State: open - Opened by kaczmarj over 1 year ago
Labels: help wanted, test

#150 - [TEST] add tests for the function _read_patch_coords

Issue - State: open - Opened by kaczmarj over 1 year ago
Labels: help wanted, test

#149 - [TEST] ensure that wsinfer functions without openslide or without tiffslide

Issue - State: open - Opened by kaczmarj over 1 year ago - 1 comment
Labels: help wanted, test

#148 - use Apache 2.0 license

Issue - State: closed - Opened by kaczmarj over 1 year ago

#147 - remove inference within ROIs

Issue - State: closed - Opened by kaczmarj over 1 year ago

#146 - add tests on macos and windows

Issue - State: closed - Opened by kaczmarj over 1 year ago

#145 - deprecate python 3.7

Issue - State: closed - Opened by kaczmarj over 1 year ago

#144 - REF: use torchscript models from huggingface hub

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

#143 - TST: update tests for dev branch

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

#142 - [TEST] add devices to tests

Issue - State: open - Opened by kaczmarj over 1 year ago
Labels: help wanted, test

#141 - differences in padding between large_image and openslide/tiffslide

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

#140 - remove timm dependency

Issue - State: closed - Opened by kaczmarj over 1 year ago

#139 - ADD choice of backends (tiffslide or openslide)

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

#138 - deprecate the dense patch grid creation

Issue - State: closed - Opened by kaczmarj over 1 year ago

#137 - handle multi-workers data loaders more gracefully

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

#136 - add a choice of slide backend: openslide and tiffslide

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

#135 - stride length is not scaled by slide spacing

Issue - State: closed - Opened by kaczmarj over 1 year ago

#134 - use pyproject.toml instead of setup.cfg

Issue - State: closed - Opened by kaczmarj over 1 year ago - 7 comments

#133 - Fix/issue 131

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

#132 - Support MPS on Apple Silicon

Pull Request - State: closed - Opened by petebankhead over 1 year ago - 2 comments

#131 - remove large_image dependency

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

#130 - fix auto-skip bug and gracefully handle failed patching

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

#129 - patching empty slides throws an error

Issue - State: closed - Opened by kaczmarj over 1 year ago

#128 - bug in argument to patching auto skip

Issue - State: closed - Opened by kaczmarj over 1 year ago