CellProfiler plugins – An easy image analysis platform integration for containers and Python tools

IF 1.5 4区工程技术 Q3 MICROSCOPY

Journal of microscopy Pub Date : 2023-09-10 DOI:10.1111/jmi.13223

Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R. Stirling, Fernanda Garcia-Fossa, Rebecca A. Senft, Mark C. Hiner, Marcelo B. de Jesus, Kevin W. Eliceiri, Beth A. Cimini

引用次数: 0

Abstract

CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or tools that are packaged in software containers. The CellProfiler-plugins repository contains a number of these CellProfiler modules, especially modules that are experimental and/or dependency-heavy. Here, we present an upgraded CellProfiler-plugins repository, an example of accessing containerised tools, improved documentation and added citation/reference tools to facilitate the use and contribution of the community.

查看原文本刊更多论文

CellProfiler插件-容器和Python工具的简单图像分析平台集成。

CellProfiler是一款广泛使用的软件，用于创建可重复使用的图像分析工作流程，而无需编码。除了构成CellProfiler主程序的>90个模块外，CellProfiler还有一个插件系统，允许创建与其他Python工具或封装在软件容器中的工具集成的新模块。CellProfiler插件库包含许多这样的CellProfiler模块，尤其是实验性和/或依赖性很强的模块。在这里，我们展示了一个升级的CellProfiler插件库，一个访问容器化工具的示例，改进了文档，并添加了引用/参考工具，以促进社区的使用和贡献。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Journal of microscopy 工程技术-显微镜技术

CiteScore

4.30

自引率

5.00%

发文量

审稿时长

1 months

期刊介绍： The Journal of Microscopy is the oldest journal dedicated to the science of microscopy and the only peer-reviewed publication of the Royal Microscopical Society. It publishes papers that report on the very latest developments in microscopy such as advances in microscopy techniques or novel areas of application. The Journal does not seek to publish routine applications of microscopy or specimen preparation even though the submission may otherwise have a high scientific merit. The scope covers research in the physical and biological sciences and covers imaging methods using light, electrons, X-rays and other radiations as well as atomic force and near field techniques. Interdisciplinary research is welcome. Papers pertaining to microscopy are also welcomed on optical theory, spectroscopy, novel specimen preparation and manipulation methods and image recording, processing and analysis including dynamic analysis of living specimens. Publication types include full papers, hot topic fast tracked communications and review articles. Authors considering submitting a review article should contact the editorial office first.