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

High-throughput imaging (HTI) generates complex imaging datasets from a large number of
experimental perturbations. Commercial HTI software for image analysis workflows does not
allow full customization and adoption of new image processing algorithms in the analysis modules.
While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei
segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis
modules or algorithms. Here, we introduce the High-Throughput Image Processing Software
(HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS
incorporates advanced image processing and machine learning algorithms for automated cell and
nuclei segmentation, spot signal detection, nucleus tracking, spot tracking, and quantification of
spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to
integration of new algorithms for existing analysis pipelines and to adding new analysis pipelines
through separate plugins. To demonstrate the utility of HiTIPS, we present three examples of
image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-
cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-
friendly, flexible, and open-source HTI analysis platform for a variety of cell biology applications