Research Snapshot: Researchers develop open-source software program to facilitate automatic imaging

A team of researchers led by UF Health Cancer Center members Xin Tang, Ph.D., and Dietmar Siemann, Ph.D., has developed an open-source software program to help researchers with user-programmable, multifunctional and automatic time-lapse live cell/tissue imaging.

Cells

Such imaging is essential for studying active, multifaceted, long-term biological events, but it often requires researchers to buy additional software programs and hardware that rely on the manufacturers’ specifications.

The team developed a Java-based, hardware-independent system, called Automatic Multi-functional Integration Program (AMFIP), to meet this need in a cost-effective manner. AMFIP enables syncing of the μManager software platform, the Nikon NIS-Elements platform and other third-party software to enable automatic operations of most commercially available microscopy systems, including Nikon.

The AMFIP software has a user-friendly and programmable graphical user interface, which will allow researchers to customize it for particular experiments and environments. These methodologies open the door to expanding the customizability for myriad hardware and software systems from different companies according to user-specific experimental requirements and environments. The software programs and algorithms are available upon request to Tang, the corresponding author (xin.tang@ufl.edu).

The team validated the software by conducting a series of experiments using a CRISPR/Cas9-engineered human epithelial Beas2B (B2B) cell line that expresses the mNeonGreen2-tagged mechanosensitive Yes-associated protein (YAP). AMFIP enabled the discovery of a previously unknown cellular behavior: Single B2B cells are able to sense, distinguish and respond to mechanical cues from the substrates before the establishment of mature focal adhesion sites and full cell spreading.

The findings were published recently in the journal PLOS One.

Tang is assistant professor in the department of mechanical & aerospace engineering and affiliate faculty in the J. Clayton Pruitt Family department of biomedical engineering and Siemann is professor and associate chair for research in the department of radiation oncology and associate director for education and training at the Cancer Center. Another Cancer Center member who contributed was Juan Guan, Ph.D., assistant professor in the department of physics.

The study was funded by a UF Health Cancer Center Pilot Award (to Tang and Siemann) and the UF Gatorade Award Start-up Package (to Tang). The authors also thanked the following Cancer Center leaders for their invaluable support: Jonathan Licht, M.D., director of the Cancer Center; Rolf Renne, Ph.D., professor and associate director for basic sciences at the Cancer Center; Christopher Vulpe, M.D., Ph.D., the team’s gene editing collaborator and professor and director of the CRISPR Functional Screening Shared Resource; Lizi Wu, Ph.D., the team’s biochemistry collaborator at the Cancer Center and professor in the department of molecular genetics & microbiology; and Shu Wang, Ph.D., assistant professor in the department of biostatistics.

READ MORE IN PLOS ONE.