![]() Although many image analysis problems can be well solved with one or the other. Even though in the CellProfiler wiki page for installation on Ubuntu 20.04 is. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. Its not a command that you run by itself. Basic Protocol 1: Studying cell morphology and cell migration in time-lapse datasets using TrackMate (Fiji) and CellProfiler Basic Protocol 2: Creating whole plate montages to easily assess adaptability of segmentation parameters.ĬellProfiler ImageJ cell tracking image stitching segmentation. ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. CellProfiler output files in MATLAB (.mat) and HDF5 (.h5) can be opened by CellProfiler's data tools. In addition to performing image analysis to generate measurements, CellProfiler has built-in tools in the Data Tools menu to generate a few types of plots. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other. Software for analyzing CellProfiler-produced data. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. No single platform can provide all the key and most efficient functionality needed for all studies. 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. 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. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. ![]() ![]() ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ![]()
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