Nadeem Lab @ Memorial Sloan Kettering Cancer Center

All

11 repositories

SPT
Public
Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
python spatial-analysis image-analysis biomarker-discovery single-cell-analysis tumor-microenvironment clinical-workflow
Python
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Other
•2•21•8•0•Updated Jan 11, 2025Jan 11, 2025
DeepLIIF
Public
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
deep-learning pytorch stitching segmentation datasets image-segmentation multiplex super-resolution immunohistochemical-images cell-segmentation
Python
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Other
•67•186•0•0•Updated Jan 7, 2025Jan 7, 2025
ImPartial
Public
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
interactive cell-segmentation denoising instance-segmentation cell-biology deep-learning pytorch segmentation
Jupyter Notebook
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Other
•3•35•0•0•Updated Jan 7, 2025Jan 7, 2025
DoseRTX
Public
Domain knowledge driven 3D radiation dose prediction [PMB'22]
deep-learning pytorch radiotherapy radiation-dose domain-knowledge-integration 3d-dose-prediction
Python
•8•39•0•0•Updated Nov 24, 2024Nov 24, 2024
SeqX2Y
Public
Sequence-to-sequence image and contour prediction library for longitudinal datasets [PMB'23]
deep-learning lung-cancer segmentation longitudinal-data radiotherapy motion-estimation lung-segmentation image-prediction pytorch-implementation
Python
•7•17•0•0•Updated Apr 8, 2024Apr 8, 2024
tmi2022
Public
A graph-transformer for whole slide image classification
Python
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MIT License
•36•0•0•0•Updated Jan 25, 2024Jan 25, 2024
cg-gnn
Public
Create cell graphs from pathology slide data and train a graph neural network to predict patient outcomes for SPT.
Python
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GNU Affero General Public License v3.0
•0•4•0•0•Updated Jan 18, 2024Jan 18, 2024
Physics-ArX
Public
Physics-based data augmentation library for quantifying CT and CBCT images in radiotherapy [PMB'23, PMB'21, Medical Physics'21, AAPM'21]
deep-learning physics-simulation radiology data-augmentation radiotherapy computed-tomography cone-beam-ct motion-simulation artifacts-generation
Python
•16•59•0•0•Updated May 10, 2023May 10, 2023
CIR
Public
Clinically-Interpretable Radiomics [MICCAI'22, CMPB'21]
python deep-learning medical-imaging feature-extraction cancer-imaging-research computational-imaging radiomics interpretability radiomics-features interpretable-deep-learning
Python
•6•31•0•0•Updated Feb 9, 2023Feb 9, 2023
CEP
Public
Computational Endoscopy Platform (advanced deep learning toolset for analyzing endoscopy videos) [MICCAI'22, MICCAI'21, ISBI'21, CVPR'20]
tracking videos segmentation unsupervised-learning domain-adaptation endoscopy sim2real colonoscopy real2sim area-coverage
Python
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Other
•11•69•0•0•Updated Nov 15, 2022Nov 15, 2022
coincidencetest
Public
Exact test for significant feature combination
Python
•0•6•0•0•Updated Jun 22, 2022Jun 22, 2022