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SBU-BMI
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wsinfer
🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
https://wsinfer.readthedocs.io
Apache License 2.0
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path is undefined when loading model from file in config
#77
kaczmarj
closed
1 year ago
0
add documentation for command line interface
#76
kaczmarj
closed
1 year ago
0
ENH: add a --speedup option and tests
#75
kaczmarj
closed
1 year ago
0
validate brca model to test effect of resizing super patches
#74
kaczmarj
closed
1 year ago
1
inception_v4nobn shows message to stderr
#73
kaczmarj
closed
1 year ago
0
ENH: pytorch 2.0
#72
kaczmarj
closed
1 year ago
1
validate tcga brca against original outputs
#71
kaczmarj
closed
1 year ago
3
ENH: consider using frozen torchscript models for speed
#70
kaczmarj
closed
1 year ago
0
FIX: use inceptionv4 from timm
#69
kaczmarj
closed
1 year ago
0
[ENH] look into bioimage spec
#68
kaczmarj
opened
1 year ago
5
release torchscript versions of the current models
#67
kaczmarj
closed
1 year ago
1
OSError: libopenslide.so.0: cannot open shared object file: No such file or directory
#66
Yuw-zhang
closed
1 year ago
0
ENH: print errored slides at the end of `wsinfer run`
#65
kaczmarj
closed
1 year ago
0
DOCS: add info on how to download models in singularity image
#64
kaczmarj
closed
1 year ago
0
Dockerfiles: use wsinfer version 0.3.3
#63
kaczmarj
closed
1 year ago
0
BUG: slides that cannot be read by openslide / large-image exit the entire script
#62
kaczmarj
closed
1 year ago
1
TST: run tests in docker image + fix setup.cfg regression
#61
kaczmarj
closed
1 year ago
0
CI: add tests on docker image
#60
kaczmarj
closed
1 year ago
0
FIX: add geojson validation in tests + update copyright year
#59
kaczmarj
closed
1 year ago
0
use geojson module to validate geojson output
#58
kaczmarj
closed
1 year ago
0
update copyright on website
#57
kaczmarj
closed
1 year ago
0
REF: make modellib private + support numpy docstring style in sphinx docs
#56
kaczmarj
closed
1 year ago
0
ENH: add more sphinx documentation + update docker versions
#55
kaczmarj
closed
1 year ago
0
DOCS: add usage examples and dedicated installation page
#54
kaczmarj
closed
1 year ago
0
ADD: sphinx docs
#53
kaczmarj
closed
1 year ago
0
FIX: use updated run_metadata.json keys in `wsinfer tosbu`
#52
kaczmarj
closed
1 year ago
0
ENH: update app dockerfiles + add mypy/flake8 to github ci + support weights from timm
#51
kaczmarj
closed
1 year ago
0
ENH: update dockerfiles and add version to config spec
#50
kaczmarj
closed
1 year ago
0
ADD: tests of patching and of run_metadata.json
#49
kaczmarj
closed
1 year ago
0
ENH: use yaml config files to define models
#48
kaczmarj
closed
1 year ago
0
add regression tests for all models
#47
kaczmarj
closed
1 year ago
1
Minor fixes
#46
kaczmarj
closed
1 year ago
0
ADD: pytest tests and run in CI
#45
kaczmarj
closed
1 year ago
0
ADD: 'wsinfer list' command
#44
kaczmarj
closed
1 year ago
0
do not use underscores in command line options
#43
kaczmarj
closed
1 year ago
1
ENH: rename the cli to wsinfer
#42
kaczmarj
closed
1 year ago
0
use large_image for patching instead of openslide
#41
kaczmarj
closed
1 year ago
0
update model-specific docker image versions + fix _in_container + make --model required
#40
kaczmarj
closed
1 year ago
0
in_container does not detect when in singularity 3.6 container
#39
kaczmarj
closed
1 year ago
0
add support for python 3.11
#38
kaczmarj
closed
1 year ago
2
FIX: conversion script to make SBU BMI output format
#37
kaczmarj
closed
1 year ago
0
fix sbu format outputs
#36
kaczmarj
closed
1 year ago
0
add table of available models to readme
#35
kaczmarj
closed
1 year ago
0
ENH: add center patch prediction
#34
kaczmarj
closed
1 year ago
1
verify TIL model implementation
#33
kaczmarj
closed
1 year ago
2
Fix error in sbubmi output json lines
#32
kaczmarj
closed
1 year ago
0
FIX: make downloaded models readable by all users
#31
kaczmarj
closed
1 year ago
0
ADD: docker apps
#30
kaczmarj
closed
1 year ago
0
ADD: paad model
#29
kaczmarj
closed
1 year ago
0
FIX: disable tilesource tile cache
#28
kaczmarj
closed
1 year ago
0
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