ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.
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DOI：
10.1002/cpz1.89
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发表时间：
2021-05
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影响因子：
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通讯作者：
Eliceiri KW
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文献类型：
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作者：
Dobson ETA;Cimini B;Klemm AH;Wählby C;Carpenter AE;Eliceiri KW
ImageJ和CellProfiler长期以来一直是生物图像分析领域的领先开源平台。ImageJ的传统优势在于单一图像处理和调查，而CellProfiler则旨在构建大规模的模块化分析管道。虽然许多图像分析问题可以很好地解决一个或另一个，使用这两个平台在一个单一的工作流程可以是强大的。在这里，我们分享了两个流水线，展示了高效方便地集成ImageJ和CellProfiler的机制，用于1）通过跟踪研究细胞形态和迁移，2）用于处理大型平铺图像集以改善分割的高级拼接技术。没有一个单一的平台可以提供所有研究所需的所有关键和最有效的功能。虽然这两个程序可以并且经常单独使用，但这些管道展示了将它们一起用于图像分析工作流程的好处。ImageJ和CellProfiler都致力于其平台之间的互操作性，并正在进行开发，以改善两者之间的相互利用。使用TrackMate（Fiji）和CellProfiler在Timelapse数据集中研究细胞形态和细胞迁移创建全板蒙太奇以轻松评估分割参数的适应性
ImageJ and CellProfiler have long been leading open source platforms in the field of bioimage analysis. ImageJ’s traditional strength is in single image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. Although many image analysis problems can be well-solved with one or the other, using these two platforms together in a single workflow can be powerful. Here we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for 1) studying cell morphology and migration via tracking and 2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. No single platform can provide all the key and most efficient functionality needed for all studies. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. ImageJ and CellProfiler are both committed to interoperability between their platforms with ongoing development to improve how both are leveraged from the other. Studying Cell Morphology and Cell Migration in Timelapse Datasets using TrackMate (Fiji) and CellProfiler Creating Whole Plate Montages to Easily Assess Adaptability of Segmentation Parameters