elephant server
v0.6.0
| 开发商 | 菅原浩 |
| 论坛 | 图像.sc 论坛 请将反馈和问题发布到论坛。 将 elephant标签添加到您的帖子中非常重要，以便我们能够快速联系到您。 |
| 源代码 | GitHub |
| 发布 | Sukawara, K.、Çevrim, C. 和 Averof, M。通过增量深度学习跟踪 3D 细胞谱系。 eLife 2022.doi:10.7554/eLife.69380 |
ELEPHANT 是一个基于增量和交互式深度学习的 3D 细胞跟踪平台。
它适用于客户端-服务器架构。该服务器被构建为一个 Web 应用程序，为基于深度学习的算法提供服务。
该存储库提供了 ELEPHANT 服务器的实现。 ELEPHANT 客户端可以在这里找到。
详细信息请参阅文档。
设置 ELEPHANT 服务器有三个选项。
使用 Docker 设置
如果您拥有一台功能强大且能够满足具有 root 权限的服务器要求 (Docker) 的计算机，建议使用此选项。
设置奇点
如果您可以作为非 root 用户（例如 HPC 集群）访问满足服务器要求（Singularity）的功能强大的计算机，则建议使用此选项。
使用 Google Colab 设置
或者，您可以使用 Google Colab 设置 ELEPHANT 服务器，Google Colab 是 Google Research 提供的免费产品。在此选项中，您不需要拥有高端 GPU 或 Linux 机器即可开始使用 ELEPHANT 的深度学习功能。
每个选项的详细说明可以在文档中找到。
请引用我们在 eLife 上的论文。
@article { Sugawara2022 ,
author = { Sugawara, Ko and {c{C}}evrim, {c{C}}a?r? and Averof, Michalis } ,
title = { Tracking cell lineages in 3D by incremental deep learning } ,
year = { 2022 } ,
doi = { 10.7554/eLife.69380 } ,
abstract = {Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software's performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 time-points). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort.},
URL = { https://doi.org/10.7554/eLife.69380 } ,
journal = { eLife }
}BSD-2 条款
