HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression.

Area of Science:

• Cell biology
• Bioimaging
• Computational biology

Background:

• High-throughput imaging (HTI) generates vast datasets, but current software limits customization and integration of novel algorithms.
• Existing open-source platforms offer modules but struggle with seamless integration of new analysis techniques.

Approach:

• Introduced High-Throughput Image Processing Software (HiTIPS), an open-source platform for customizable HTI analysis.
• HiTIPS integrates advanced image processing and machine learning for automated segmentation, detection, tracking, and quantification.
• Features a GUI supporting integration of new algorithms and pipelines via plugins.

Key Points:

• Automated cell and nuclei segmentation.
• Nucleus and spot tracking capabilities.
• Quantification of spot signal intensity.

Conclusions:

• HiTIPS provides a user-friendly, flexible, and extensible platform for diverse cell biology applications.
• Enables custom analysis workflows for high-throughput DNA FISH, immunofluorescence, and live-cell imaging.
• Facilitates the adoption of novel algorithms in HTI analysis pipelines.