ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis

Area of Science:

• Bioimage analysis
• Cell biology
• Image processing

Background:

• ImageJ and CellProfiler are leading open-source bioimage analysis platforms.
• ImageJ excels in single-image analysis, while CellProfiler is suited for large-scale pipelines.
• Integrating these platforms can leverage their complementary strengths.

Purpose of the Study:

• To demonstrate productive integration of ImageJ and CellProfiler in bioimage analysis workflows.
• To showcase pipelines for cell morphology and migration studies using tracking.
• To present advanced stitching techniques for large, tiled image sets to enhance segmentation.

Main Methods:

• Developed and shared two integrated pipelines combining ImageJ (Fiji/TrackMate) and CellProfiler.
• Pipeline 1: Cell morphology and migration tracking in time-lapse datasets.
• Pipeline 2: Advanced stitching for whole plate montages to assess segmentation.

Main Results:

• Demonstrated effective integration of ImageJ and CellProfiler for specific bioimage analysis tasks.
• Showcased improved cell tracking and morphology analysis through combined platform use.
• Validated advanced stitching techniques for handling large image datasets and enhancing segmentation.

Conclusions:

• Combining ImageJ and CellProfiler in a single workflow offers powerful advantages over using them separately.
• Integrated pipelines can address complex bioimage analysis challenges, including cell tracking and segmentation.
• Ongoing interoperability development between ImageJ and CellProfiler promises further advancements in bioimage analysis.