Department of Biomedical Informatics

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115 repositories

PathDB
Public
PHP
•
BSD 3-Clause "New" or "Revised" License
•5•2•1•11•Updated Feb 5, 2025Feb 5, 2025
SpinPath
Public
CLI tool to run specimen-level inference on whole slide images
digital-pathology whole-slide-imaging multiple-instance-learning histopathology
Python
•
Apache License 2.0
•0•2•0•1•Updated Jan 13, 2025Jan 13, 2025
hatch
Public
Java
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GNU General Public License v2.0
•2•1•0•0•Updated Nov 5, 2024Nov 5, 2024
wsinfer
Public
🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
deep-learning pytorch classification pathology whole-slide-imaging
Python
•
Apache License 2.0
•12•65•13•0•Updated Jul 11, 2024Jul 11, 2024
wsinfer-zoo
Public
Model zoo for WSInfer
Python
•
Apache License 2.0
•0•1•1•0•Updated Jul 9, 2024Jul 9, 2024
quip_distro
Public
visualization database analysis docker-image slide-tissue-images
JavaScript
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BSD 3-Clause "New" or "Revised" License
•16•32•6•3•Updated May 2, 2024May 2, 2024
MappingOHDSI2HDF5
Public
Build JSON mappings for mapping OHDSI tables to HDF5
Jupyter Notebook
•3•6•0•0•Updated Oct 23, 2023Oct 23, 2023
region-templates
Public
Region Templates development
C++
•5•4•0•1•Updated Oct 11, 2023Oct 11, 2023
til_align
Public
TIL Alignment
R
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Apache License 2.0
•1•0•1•0•Updated Aug 6, 2023Aug 6, 2023
champkit
Public
Benchmarking toolkit for patch-based histopathology image classification.
benchmarking benchmark deep-learning pytorch image-classification histopathology
Python
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Apache License 2.0
•4•38•3•0•Updated Jun 2, 2023Jun 2, 2023
uploadHeatmaps
Public
Shell
•4•0•1•0•Updated May 25, 2023May 25, 2023
SegmentationLoader
Public
Load WSI segmentations to mongodb instance
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated May 25, 2023May 25, 2023
tumor-til-survival-analysis
Public
Scripts to run analysis of tumor/TILs.
Shell
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Apache License 2.0
•0•2•6•0•Updated May 22, 2023May 22, 2023
quip_cnn_segmentation
Public
CNN based segmentation codes
Python
•
BSD 3-Clause "New" or "Revised" License
•17•47•4•3•Updated Jan 19, 2023Jan 19, 2023
QuIPImageFetch
Public
Python
•0•2•0•0•Updated Jan 12, 2023Jan 12, 2023
ImageLoader
Public
Dockerfile
•0•0•1•0•Updated Sep 20, 2022Sep 20, 2022
quip_paad_cancer_detection
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•8•8•2•2•Updated Aug 8, 2022Aug 8, 2022
quip_prad_cancer_detection
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•1•3•0•0•Updated Aug 8, 2022Aug 8, 2022
quip_lung_cancer_detection
Public
Python
•
GNU General Public License v3.0
•3•1•0•0•Updated Aug 8, 2022Aug 8, 2022
quip_cancer_segmentation
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•4•15•1•0•Updated Aug 8, 2022Aug 8, 2022
quip_classification
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•11•5•3•1•Updated Jul 17, 2022Jul 17, 2022
deep_survival_analysis
Public
Survival analysis with deep learning
Python
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BSD 3-Clause "New" or "Revised" License
•1•3•1•0•Updated May 18, 2022May 18, 2022
generate_heatmap_pannels
Public
2•0•0•0•Updated May 3, 2022May 3, 2022
til_classification
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•5•2•0•0•Updated Feb 19, 2022Feb 19, 2022
manifest_util
Public
manifest file generator
Python
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BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Nov 5, 2021Nov 5, 2021
quip_converter
Public
Convert vendor format to tiled, multires tiff format
Shell
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BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Aug 2, 2021Aug 2, 2021
nscale
Public
Libraries of high performance analysis methods
C++
•7•6•0•0•Updated Jun 16, 2021Jun 16, 2021
quip_reports
Public
Report generator
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 2, 2021Mar 2, 2021
u24_lymphocyte
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•20•30•5•0•Updated Jan 22, 2021Jan 22, 2021
featuremap_util
Public
Transform raw data to featuremaps
Python
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BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Jan 8, 2021Jan 8, 2021