Despite external symmetry, the human body displays numerous asymmetrical characteristics - including at the cellular level. This so-called cell polarity provides important information on physiological and pathological processes. However, analysing them remains challenging, as common microscopic tools are often incompatible.
In a study led by Dr. Wolfgang Giese in the Integrative Vascular Biology lab of Professor Holger Gerhardt at the Max Delbrück Center and Jan Philip Albrecht, a computer scientist working with Deborah Schmidt (Image Data Analysis platform) at Helmholtz Imaging, researchers introduce Polarity-JaM – an open-source, freely available and user-friendly tool to analyze cell polarity data from fluorescence microscopy images. The study was published in “Nature Communications.” Wolfgang Giese is a member of the Young DZHK network, Holger Gerhardt is a member of the DZHK Executive Board.
“We wanted to create a tool that enables scientists, including those with minimal programming experience, to explore and analyze cell polarity data in a straightforward and reproducible way,” says Giese. “By integrating circular statistics and user-friendly visualization, Polarity-JaM helps researchers uncover patterns in cell behavior that were previously difficult to analyze quantitatively.”
Addressing a challenge in cell image analysis
Researchers study cell polarity to better understand processes such as tissue repair, organ development and immune responses. But despite advances in fluorescence microscopy that have made it easy to capture detailed images of cell polarity, tools to analyze the data remain fragmented, time-consuming, or require specialized coding skills. This makes large-scale, reproducible research nearly impossible.
Polarity-JaM combines analyses of cell polarity, morphology, and cell-cell contact formation among other features into a single, holistic software package that takes advantage of deep learning.
The tool quantifies and helps to visualize multiple aspects of cell polarity, including the position of Golgi organelles with respect to cell nuclei, cell shape and orientation, and the location of cellular organelles, to name just a few examples. To demonstrate the tool’s capabilities, the researchers showed that they could study how endothelial cells alter their shape, orientation, and signaling responses when exposed to different shear stresses – conditions that mimic blood flow.
Understanding cell polarity can help to explain how the body maintains healthy organs and tissues and what goes wrong in diseases like cancer, cardiovascular disorders, and inflammation, says Gerhardt. “The ability of machine learning-based segmentation tools to accurately identify and outline cells within a microscopic image almost as well as a human expert exceeded our expectations,” he adds. “It demonstrates the potential for further automation in biological research and beyond, freeing up scientists to focus on higher-level analysis and discovery.”
An open-source solution
The researchers have made Polarity-JaM documentation and tutorials available at https://polarityjam.readthedocs.io. The site includes a how-to video, ensuring that users can easily learn and apply the tool to their research. In addition, a web-based application hosted at www.polarityjam.com enables researchers to perform circular statistical analyses – which involves analyzing data that is circular in nature such as angles or the orientation of cellular structures in 3D space – and visualize their data without requiring users to install software, making the tool accessible to a broader audience.
“The open-source nature of Polarity-JaM allows researchers, developers, and the wider scientific community to contribute, improve, and expand its capabilities, ensuring continuous development and adaptation to new research challenges,” says Albrecht. The team is now looking to expand the capabilities of PolarityJaM to be able to analyze 3D tissue and organoid models, for example. They also hope to include analyses of other subcellular structures, time lapse imaging and dynamic tracking to study how cell polarity evolves over time, and to add other features as well.
Original Publication: Wolfgang Giese, Jan Philipp Albrecht, Olya Oppenheim et.al. (2025): „Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification.“ Nature Communications
Scientific Contact:
Prof. Holger Gerhardt
Head of the ‘Integrative Vascular Biology’ working group
Max Delbrück Center
Holger.Gerhardt(at)mdc-berlin.de
Dr. Wolfgang Giese
Scientist in the ‘Integrative Vascular Biology’ working group
Max Delbrück Center
Wolfgang.Giese(at)mdc-berlin.de
