Nadeem Lab @ Memorial Sloan Kettering Cancer Center

All

12 repositories

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
•82•219•0•0•Updated Oct 30, 2025Oct 30, 2025
smprofiler
Public
Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)
python spatial-analysis spatial-data image-analysis spatial-proteomics biomarker-discovery deeplearning-ai single-cell-analysis spatial-transcriptomics tumor-microenvironment
Python
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Other
•2•22•7•0•Updated Oct 29, 2025Oct 29, 2025
ImPartial
Public
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
deep-learning interactive pytorch segmentation cell-segmentation denoising instance-segmentation cell-biology
Jupyter Notebook
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Other
•3•40•0•0•Updated Aug 31, 2025Aug 31, 2025
adi-semantic-highlights
Public
VSCode extension to show tooltips and completions for definitions and fields of a relational database schema/ontology.
TypeScript
•0•0•0•0•Updated Aug 15, 2025Aug 15, 2025
CEP
Public
Computational Endoscopy Platform (advanced deep learning toolset for analyzing endoscopy videos) [MICCAI'25, MICCAI'22, MICCAI'21, ISBI'21, CVPR'20]
tracking computer-vision deep-learning pytorch gan videos segmentation unsupervised-learning domain-adaptation endoscopy
Python
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Other
•11•80•0•0•Updated Jun 29, 2025Jun 29, 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
•10•48•0•1•Updated Jun 19, 2025Jun 19, 2025
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•20•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
•35•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•68•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
•7•37•0•0•Updated Feb 9, 2023Feb 9, 2023
coincidencetest
Public
Exact test for significant feature combination
Python
•0•6•0•0•Updated Jun 22, 2022Jun 22, 2022