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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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handle Path instances for Weights.file
#127
kaczmarj
closed
1 year ago
0
[BUG] slides can raise error on `cv2.findContours` if no contour is found
#126
kaczmarj
closed
1 year ago
1
[BUG] saving JSON with weights file of type pathlib.Path raises error
#125
kaczmarj
closed
1 year ago
1
make cli for running a single slide (not a directory of slides)
#124
kaczmarj
closed
1 year ago
1
fix bug in setting state dict from relative path
#123
kaczmarj
closed
1 year ago
0
replace prad label grade4+5 -> grade4or5
#122
kaczmarj
closed
1 year ago
0
[ENH] change PRAD model outputs from grade4+5 to grade4or5
#121
kaczmarj
closed
1 year ago
0
it is possible for one slide ID to have multiple slides with different extensions
#120
kaczmarj
closed
1 year ago
0
add --segmentation-dir option with pre-existing tissue masks
#119
kaczmarj
closed
1 year ago
0
qupath integration
#118
kaczmarj
closed
1 year ago
1
make a better figure for wsinfer
#117
kaczmarj
closed
1 year ago
0
[BUG] relative path to model in yaml config does not work
#116
kaczmarj
closed
1 year ago
0
[ENH] use pytorch 2.0.0 as base image
#115
kaczmarj
closed
1 year ago
0
[ENH] adds ability to run inference inside ROI
#114
kaczmarj
closed
1 year ago
0
[BUG] in sbu conversion, prediction- and color- calculate patches differently
#113
kaczmarj
opened
1 year ago
0
[ADD] vgg16 tils model
#112
kaczmarj
closed
1 year ago
0
use pytorch 2.0 docker image as base
#111
kaczmarj
closed
1 year ago
0
add TILs VGG16 model
#110
kaczmarj
closed
1 year ago
1
generate qupath project directly from wsinfer outputs
#109
kaczmarj
closed
1 year ago
1
accept a ROI as a geojson
#108
kaczmarj
closed
1 year ago
2
[DIST] release wsinfer in a cross-platform manner without users creating environment
#107
kaczmarj
closed
1 year ago
4
add strided patch predictions
#106
kaczmarj
closed
6 months ago
1
add multi-proc geojson conversion
#105
kaczmarj
closed
11 months ago
1
add more intro content to index.rst
#104
kaczmarj
closed
1 year ago
0
[ENH] add multi-gpu support
#103
kaczmarj
closed
1 year ago
0
[ENH] add ability to use multiple GPUs
#102
kaczmarj
closed
1 year ago
0
[DOCS] remove REF links that point to github repositories
#101
kaczmarj
closed
1 year ago
0
write one run_metadata.json file per run
#100
kaczmarj
closed
1 year ago
0
set cache_tilesource_maximum to 1
#99
kaczmarj
closed
1 year ago
0
[BUG] disable cache of tilesources in large_image
#98
kaczmarj
closed
1 year ago
1
[ENH] do not overwrite run_metadata.json
#97
kaczmarj
closed
1 year ago
0
[FIX] remove duplicate choices in 'wsinfer run' cli + clarify model-weight pairs
#96
kaczmarj
closed
1 year ago
0
[FIX] do not panic on unreadable files
#95
kaczmarj
closed
1 year ago
0
handle unknown images better
#94
kaczmarj
closed
1 year ago
0
duplicate models in click --model choices
#93
kaczmarj
closed
1 year ago
0
unknown model error is confusing
#92
kaczmarj
closed
1 year ago
0
version doesn't show in "running wsinfer version ___"
#91
kaczmarj
closed
1 year ago
1
handle 'git' not being installed
#90
kaczmarj
closed
1 year ago
0
[BUG] filenotfounderror if user does not have 'git' installed
#89
kaczmarj
closed
1 year ago
0
[CI] build docs + separate style/type tests
#88
kaczmarj
closed
1 year ago
0
[DOCS] fix readthedocs build by adding config
#87
kaczmarj
closed
1 year ago
0
use a default config for inception_v4 to prevent stderr message
#86
kaczmarj
closed
1 year ago
0
print slide ids that failed patching or inference
#85
kaczmarj
closed
1 year ago
0
allow pytest to fail in nightly
#84
kaczmarj
closed
1 year ago
0
divide by total time only if it is nonzero
#83
kaczmarj
closed
1 year ago
0
add cli docs with sphinx-click
#82
kaczmarj
closed
1 year ago
0
zero division error (sometimes) if patching is rerun on patched output
#81
kaczmarj
closed
1 year ago
0
place test_input on same device as model in jit_compile
#80
kaczmarj
closed
1 year ago
0
test_input and model can be on different devices
#79
kaczmarj
closed
1 year ago
0
fix undefined path + add test of valid yaml config
#78
kaczmarj
closed
1 year ago
0
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