{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"model-seg-human-brain-cars","owner":"axondeepseg","isFork":false,"description":"Axon and myelin segmentation model in histology images to quantify myelination in the human brain. Training data was acquired in the uncinate fasciculus using CARS microscopy.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-25T12:47:15.599Z"}},{"type":"Public","name":"axon-detection","owner":"axondeepseg","isFork":false,"description":"Exploration of object detection applied to the AxonDeepSeg project ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-18T22:18:10.183Z"}},{"type":"Public","name":"axondeepseg","owner":"axondeepseg","isFork":false,"description":"Axon/Myelin segmentation using Deep Learning","allTopics":["machine-learning","segmentation","electron-microscopy","microscopy","myelin","spinalcord","histology","neuropoly","deep-learning","convolutional-neural-networks","axon"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":8,"issueCount":156,"starsCount":114,"forksCount":32,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-17T17:10:34.707Z"}},{"type":"Public","name":"data-testing","owner":"axondeepseg","isFork":false,"description":"Images and files used for software testing (unit and integration tests).","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-15T20:15:06.537Z"}},{"type":"Public","name":"model_seg_unmyelinated_tem","owner":"axondeepseg","isFork":false,"description":"Model for unmyelinated axon segmentation in TEM images, based on nnUNet","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-08T21:33:10.313Z"}},{"type":"Public","name":"AxonDeepSynth","owner":"axondeepseg","isFork":true,"description":"Official PyTorch implementation of SynDiff described in the paper (https://arxiv.org/abs/2207.08208).","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":38,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-24T19:04:12.806Z"}},{"type":"Public","name":"seg_ci","owner":"axondeepseg","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-26T14:00:52.045Z"}},{"type":"Public","name":"nn-axondeepseg","owner":"axondeepseg","isFork":false,"description":"1-class and 2-class segmentation of axon/myelin using nnunetv2 ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-01T21:21:31.951Z"}},{"type":"Public","name":"model_seg_generalist","owner":"axondeepseg","isFork":false,"description":"Axon and myelin segmentation model trained on all ADS datasets. Works across contrasts and resolutions.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-30T02:19:50.048Z"}},{"type":"Public","name":"model_seg_nerve","owner":"axondeepseg","isFork":false,"description":"Nerve area segmentation for axon density estimation in BF images","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-18T17:36:43.653Z"}},{"type":"Public","name":"awesome-histology-segmentation","owner":"axondeepseg","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":"Creative Commons Zero v1.0 Universal","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-17T17:40:58.387Z"}},{"type":"Public","name":"default-wakehealth-model","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg default Wakehealth model and testing image","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-08T15:54:45.393Z"}},{"type":"Public","name":"default-BF-model","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg default BF model","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-05T18:43:13.976Z"}},{"type":"Public","name":"model_seg_rabbit_axon-myelin_bf","owner":"axondeepseg","isFork":false,"description":"Standard 2-class segmentation model for ADS trained on rabbit samples (Virginia Commonwealth University)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-05T17:18:28.692Z"}},{"type":"Public","name":"default-TEM-model","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg default TEM model and testing image","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T17:18:35.175Z"}},{"type":"Public","name":"default-CARS-model","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg default CARS model","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T16:51:19.008Z"}},{"type":"Public","name":"default-SEM-model","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg default SEM model and testing image","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-03T15:45:15.029Z"}},{"type":"Public","name":"model_postprocess_touching_myelin","owner":"axondeepseg","isFork":false,"description":"Training nnUNet v2 for Detecting Boundaries Between Touching Myelinated Axon","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-13T16:16:56.992Z"}},{"type":"Public","name":"model_seg_human_axon-myelin_bf","owner":"axondeepseg","isFork":false,"description":"AxonDeepSeg model trained on Toluidine Blue stained BF optical microscopy samples","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-13T22:04:07.609Z"}},{"type":"Public","name":"sam_myelin_seg_TEM","owner":"axondeepseg","isFork":false,"description":"Axon and Myelin segmentation using FAIR's Segment-Anything-Model (SAM)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":6,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-16T21:35:37.562Z"}},{"type":"Public","name":"synthetic_image_gen_model","owner":"axondeepseg","isFork":false,"description":"This repository is following the internship idea to generate synthetic data using GANS. ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-18T15:01:45.818Z"}},{"type":"Public","name":"doc-figures","owner":"axondeepseg","isFork":false,"description":"Repository that contains most figures for axondeepseg documentation.","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-24T00:25:00.397Z"}},{"type":"Public archive","name":"napari-plugin","owner":"axondeepseg","isFork":false,"description":"A (work in progress) plugin for napari that implements the AxonDeepSeg tools","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-02T06:34:10.370Z"}},{"type":"Public","name":"ometiff-tests","owner":"axondeepseg","isFork":false,"description":"Files used to test OME-TIFF images for BIDS-microscopy","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-06T04:56:58.775Z"}},{"type":"Public","name":"data_axondeepseg_sem","owner":"axondeepseg","isFork":false,"description":"SEM dataset for AxonDeepSeg. Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-11-30T14:36:52.454Z"}},{"type":"Public","name":"model_seg_rat_axon-myelin_sem","owner":"axondeepseg","isFork":false,"description":"[For Development] Early SEM IVADOMED model.","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-06T14:27:48.165Z"}},{"type":"Public","name":"data-example","owner":"axondeepseg","isFork":false,"description":"Example dataset used in documentation","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-21T16:17:14.259Z"}},{"type":"Public","name":"model-seg-pns-bf","owner":"axondeepseg","isFork":false,"description":"OM model that works at a resolution of 0.1 micrometer per pixel","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-15T18:43:56.643Z"}}],"repositoryCount":28,"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":"axondeepseg repositories"}