{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"SPT","owner":"nadeemlab","isFork":false,"description":"Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images","topicNames":["python","spatial-analysis","image-analysis","biomarker-discovery","single-cell-analysis","tumor-microenvironment","clinical-workflow"],"topicsNotShown":0,"allTopics":["python","spatial-analysis","image-analysis","biomarker-discovery","single-cell-analysis","tumor-microenvironment","clinical-workflow"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":12,"starsCount":22,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-21T23:54:16.341Z"}},{"type":"Public","name":"ImPartial","owner":"nadeemlab","isFork":false,"description":"Interactive deep learning whole-cell segmentation and thresholding using partial annotations","topicNames":["interactive","cell-segmentation","denoising","instance-segmentation","cell-biology","deep-learning","pytorch","segmentation"],"topicsNotShown":0,"allTopics":["interactive","cell-segmentation","denoising","instance-segmentation","cell-biology","deep-learning","pytorch","segmentation"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":29,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-15T20:08:22.327Z"}},{"type":"Public","name":"DeepLIIF","owner":"nadeemlab","isFork":false,"description":"Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (<a href=\"https://deepliif.org\" rel=\"nofollow\">https://deepliif.org</a>) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]","topicNames":["deep-learning","pytorch","stitching","segmentation","datasets","image-segmentation","multiplex","super-resolution","immunohistochemical-images","cell-segmentation"],"topicsNotShown":10,"allTopics":["deep-learning","pytorch","stitching","segmentation","datasets","image-segmentation","multiplex","super-resolution","immunohistochemical-images","cell-segmentation","digital-pathology","pathology","whole-slide-imaging","cell-biology","cloud-native-applications","multitask-learning","pathology-image","pathology-gan","immunohistochemistry","ai-ready"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":144,"forksCount":55,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-15T15:56:27.521Z"}},{"type":"Public","name":"DoseRTX","owner":"nadeemlab","isFork":false,"description":"Domain knowledge driven 3D radiation dose prediction [PMB'22]","topicNames":["deep-learning","pytorch","radiotherapy","radiation-dose","domain-knowledge-integration","3d-dose-prediction"],"topicsNotShown":0,"allTopics":["deep-learning","pytorch","radiotherapy","radiation-dose","domain-knowledge-integration","3d-dose-prediction"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":34,"forksCount":8,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-23T00:56:54.784Z"}},{"type":"Public","name":"SeqX2Y","owner":"nadeemlab","isFork":false,"description":"Sequence-to-sequence image and contour prediction library for longitudinal datasets [PMB'23]","topicNames":["deep-learning","lung-cancer","segmentation","longitudinal-data","radiotherapy","motion-estimation","lung-segmentation","image-prediction","pytorch-implementation"],"topicsNotShown":0,"allTopics":["deep-learning","lung-cancer","segmentation","longitudinal-data","radiotherapy","motion-estimation","lung-segmentation","image-prediction","pytorch-implementation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":15,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-08T07:39:07.060Z"}},{"type":"Public","name":"spt-cg-gnn","owner":"nadeemlab","isFork":false,"description":"SPT plugin providing default graph deep learning functionality","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-31T16:25:46.334Z"}},{"type":"Public","name":"tmi2022","owner":"nadeemlab","isFork":true,"description":"A graph-transformer for whole slide image classification","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":35,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-25T18:58:00.568Z"}},{"type":"Public","name":"spt-plugin","owner":"nadeemlab","isFork":false,"description":"Template for SPT plugin development","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-20T22:23:29.159Z"}},{"type":"Public","name":"cg-gnn","owner":"nadeemlab","isFork":false,"description":"Create cell graphs from pathology slide data and train a graph neural network to predict patient outcomes for SPT.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-18T22:39:17.770Z"}},{"type":"Public","name":"Physics-ArX","owner":"nadeemlab","isFork":false,"description":"Physics-based data augmentation library for quantifying CT and CBCT images in radiotherapy [PMB'23, PMB'21, Medical Physics'21, AAPM'21]","topicNames":["deep-learning","physics-simulation","radiology","data-augmentation","radiotherapy","computed-tomography","cone-beam-ct","motion-simulation","artifacts-generation"],"topicsNotShown":0,"allTopics":["deep-learning","physics-simulation","radiology","data-augmentation","radiotherapy","computed-tomography","cone-beam-ct","motion-simulation","artifacts-generation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":50,"forksCount":14,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-10T15:39:48.611Z"}},{"type":"Public","name":"CIR","owner":"nadeemlab","isFork":false,"description":"Clinically-Interpretable Radiomics [MICCAI'22, CMPB'21]","topicNames":["python","deep-learning","medical-imaging","feature-extraction","cancer-imaging-research","computational-imaging","radiomics","interpretability","radiomics-features","interpretable-deep-learning"],"topicsNotShown":4,"allTopics":["python","deep-learning","medical-imaging","feature-extraction","cancer-imaging-research","computational-imaging","radiomics","interpretability","radiomics-features","interpretable-deep-learning","pytorch-implementation","radiomics-feature-extraction","medical-imaging-datasets","clinical-interpretation-algorithm"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":24,"forksCount":6,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-09T18:13:13.355Z"}},{"type":"Public","name":"CEP","owner":"nadeemlab","isFork":false,"description":"Computational Endoscopy Platform (advanced deep learning toolset for analyzing endoscopy videos) [MICCAI'22, MICCAI'21, ISBI'21, CVPR'20]","topicNames":["tracking","videos","segmentation","unsupervised-learning","domain-adaptation","endoscopy","sim2real","colonoscopy","real2sim","area-coverage"],"topicsNotShown":4,"allTopics":["tracking","videos","segmentation","unsupervised-learning","domain-adaptation","endoscopy","sim2real","colonoscopy","real2sim","area-coverage","computer-vision","deep-learning","pytorch","gan"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":64,"forksCount":10,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-15T21:46:11.481Z"}},{"type":"Public","name":"coincidencetest","owner":"nadeemlab","isFork":false,"description":"Exact test for significant feature combination","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-22T20:58:08.443Z"}}],"repositoryCount":13,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}