{"id":13717236,"url":"https://github.com/adalca/neurite","last_synced_at":"2025-05-07T07:30:35.861Z","repository":{"id":38298016,"uuid":"84505424","full_name":"adalca/neurite","owner":"adalca","description":"Neural networks toolbox focused on medical image analysis","archived":false,"fork":false,"pushed_at":"2024-09-20T01:17:27.000Z","size":775,"stargazers_count":338,"open_issues_count":20,"forks_count":66,"subscribers_count":21,"default_branch":"dev","last_synced_at":"2024-10-30T11:27:26.873Z","etag":null,"topics":["brain","convolutional-neural-networks","keras","medical-image-computing","medical-imaging","python","tensorflow"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/adalca.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citations.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-03-10T01:25:06.000Z","updated_at":"2024-10-18T03:25:51.000Z","dependencies_parsed_at":"2023-12-26T06:33:59.279Z","dependency_job_id":"c85e3d0b-9984-4e6f-8749-bb1c1bd28406","html_url":"https://github.com/adalca/neurite","commit_stats":{"total_commits":670,"total_committers":27,"mean_commits":"24.814814814814813","dds":0.3985074626865671,"last_synced_commit":"95b2b568b124cbc654467177ddcdb2cb3526788c"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adalca%2Fneurite","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adalca%2Fneurite/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adalca%2Fneurite/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adalca%2Fneurite/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/adalca","download_url":"https://codeload.github.com/adalca/neurite/tar.gz/refs/heads/dev","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224573331,"owners_count":17333802,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["brain","convolutional-neural-networks","keras","medical-image-computing","medical-imaging","python","tensorflow"],"created_at":"2024-08-03T00:01:19.666Z","updated_at":"2024-11-14T05:31:08.311Z","avatar_url":"https://github.com/adalca.png","language":"Python","readme":"# Neurite\n\nA neural networks toolbox with a focus on medical image analysis in tensorflow/keras for now.\n\n\n## Install\n\nTo use the Neurite library, either clone this repository and install the requirements listed in `setup.py` or install directly with pip.\n\n```\npip install neurite\n```\n\n## Main tools\n- [layers](neurite/tf/layers.py): various network layers, sparse operations (e.g. `SpatiallySparse_Dense`), and `LocallyConnected3D` currently not included in `keras`  \n- [utils](neurite/tf/utils/utils.py): various utilities, including `interpn`: N-D gridded interpolation, and several nonlinearities  \n  - [model](neurite/tf/utils/model.py): `stack_models`: keras model stacking  \n  - [vae](neurite/tf/utils/vae.py): tools for analyzing (V)AE style models  \n  - [seg](neurite/tf/utils/seg.py): segmentation tools  \n- [models](neurite/tf/models.py): flexible models (many parameters to play with) particularly useful in medical image analysis, such as UNet/hourglass model, convolutional encoders and decoders   \n- [generators](neurite/tf/generators.py): generators for medical image volumes and various combinations of volumes, segmentation, categorical and other output  \n- [callbacks](neurite/tf/callbacks.py): a set of callbacks for `keras` training to help with understanding your fit, such as Dice measurements and volume-segmentation overlaps  \n- [dataproc](neurite/py/dataproc.py): a set of tools for processing medical imaging data for preparation for training/testing  \n- [metrics](neurite/tf/metrics.py): metrics (most of which can be used as loss functions), such as Dice or weighted categorical crossentropy  \n- [plot](neurite/py/plot.py): plotting tools, mostly for debugging models  \n\n\n## Papers:\nIf you use this code, please cite:\n\n**Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation**  \n[Adrian V. Dalca](http://adalca.mit.edu), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/)  \nCVPR 2018.  \n[ [PDF](http://www.mit.edu/~adalca/files/papers/cvpr2018_priors.pdf) | [arxiv](http://arxiv.org/abs/1903.03148) | [bibtex](citations.bib) ]\n\nIf you are using any of the sparse/imputation functions, please cite:  \n\n**Unsupervised Data Imputation via Variational Inference of Deep Subspaces**  \n[Adrian V. Dalca](http://adalca.mit.edu), [John Guttag](https://people.csail.mit.edu/guttag/), [Mert R. Sabuncu](http://sabuncu.engineering.cornell.edu/)  \nArxiv preprint 2019  \n[ [arxiv](https://arxiv.org/abs/1903.03503) | [bibtex](citations.bib) ]\n\n\n## Development:\nWe welcome contributions; please make sure your code respects `pep8`, except for `E731,W291,W503,W504`, by running:  \n```pycodestyle --ignore E731,W291,W503,W504 --max-line-length 100 /path/to/neurite```  \nPlease open an [issue](https://github.com/adalca/neurite/issues) [preferred] or contact Adrian Dalca at adalca@csail.mit.edu for question related to `neurite`.\n\n\n## Use/demos:\nParts of `neurite` were used in [VoxelMorph](http://voxelmorph.mit.edu) and [brainstorm](https://github.com/xamyzhao/brainstorm/), which we encourage you to check out!\n","funding_links":[],"categories":["Python","Other"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadalca%2Fneurite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadalca%2Fneurite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadalca%2Fneurite/lists"}