Integrative Biomedical
Data Analysis

Acccompanying DeepLIIF cloud-native platform CVPR'22 paper available here. DeepLIIF can be run locally (GPU required) by pip installing the package and using the deepliif CLI command. DeepLIIF can be used remotely (no GPU required) through the https://deepliif.org website, the ImageJ plgin, or via the Cloud-API (details here).

DeepLIIF IHC quantification paper published in Nature Machine Intelligence. DeepLIIF cloud-native platform with user-friendly web interface is now available here for users to upload input images, visualize, and download results. Multi-GPU training and highly-optimized inference implementations are now available via our GitHub.

GitHub for a new higher-order exact statistical significance test, Coincidence Test, is now public. Explore the limitless applications across radiology, pathology and molecular data. Preprint is available here.

ImPartial interactive deep learning whole-cell segmentation GitHub library is now public. Preprint available here. Integration with MONAI Label, ImageJ, QuPath, and napari coming soon!

Physics-ArX library is now public on our GitHub. It provides (smart) physics-based data augmentation tools for robust quantification of CT and CBCT images during radiotherapy, as shown in  our PMB'21 (generalizable cross-modality esophagus segmentation) and Medical Physics'21 (multitask CBCT-to-CT translation and OAR segmentation) papers.

Joseph Marino
(senior data scientist)
joins the lab.

Computational Endoscopy Platform (CEP) GitHub is now public with implementations of our MICCAI'21 (haustral fold detection), ISBI'21 (missing surface visualization), and CVPR'20 (scale-consistent depth inference) papers.

DeepLIIF IHC quantification preprint and code released. First AI model to be deployed in the MSK slide viewer.

James Mathews (senior data scientist), Rami Vanguri (senior data scientist), Gunjan Shrivastava (data scientist), and Eliram Nof (postdoc) join the lab.

Awarded $4.2M MSKCC DigITs funding for research and development of "institutional multiplex image analysis pipelines for biomarker quantification".

Invited MSK Hospital Research Forum talk on "Spatial Profiling for Quantitative and Predictive Biomarkers".