Improving microscopy experience with optimized software: Leibniz IPHT receives Chan Zuckerberg Initiative Award
The Leibniz Institute of Photonic Technology (Leibniz IPHT) was awarded $20,000 from the Chan Zuckerberg Initiative for the napari Plugin Foundations Grant. The financial support is intended to be used to develop and optimize software tools for imaging. In this way, the Jena researchers want to contribute to further advances in the field of modern microscopy for research and industry.
In the search for new knowledge, scientists – from biomedicine to materials science – rely on reliable and efficient tools for microscopic observation and detailed analysis of samples. Software solutions for image processing, such as the open-source software napari, support the control of microscopy workstations as well as the development of scientific data.
In order to unleash the full potential of such software tools for microscopy and imaging, Leibniz IPHT researchers are working on a new plugin. This is intended to bridge the gap between microscopy setups, the used acquisition devices of these setups and the napari multi-dimensional image viewer software. „Our new plugin to be developed for napari will provide an interface to further optimize microscopy image acquisition and processing. Almost every camera can be integrated into existing setups thanks to the plugin. The image data can then be recorded directly with the microscope acquisition device, viewed immediately in the imaging software, processed in real-time and the data analyzed while experiments are still in progress. Researchers thus gain complete control over the imaging parameters as well as their data at any time,“ explains Jacopo Abramo, PhD student in the Biophysical Imaging Department at Leibniz IPHT, who together with his scientific colleague, Dr. Francesco Reina, was able to secure the CZI grant.
With the development of the software-based add-on module for napari, the Jena scientists want to contribute to further improving the performance of modern imaging software through additional functionalities and to better solve microscopic tasks – from cell observation to particle tracking. „This will give researchers the opportunity to generate and analyze complex image data even faster and more intuitively. The open-source concept of the software as well as the plugins also makes microscopy accessible to everyone and enables advances in bioanalytical diagnostics to be achieved even without high-end software solutions,“ says Jacopo Abramo.
Prof. Dr. Christian Eggeling, Head of the Biophysical Imaging Department, adds: “With CZI, we share the common goal of not only deciphering the development and treatment of diseases, but also being able to prevent them in the future and thus contribute to a better quality of life for patients. By exploring new effective observation methods and procedures at Leibniz IPHT to uncover a deeper understanding of cell biological relationships and processes, we can – in combination with smart software solutions – achieve important steps in this direction.”
About the Chan Zuckerberg Initiative (CZI)
The Chan Zuckerberg Initiative was founded in 2015 to help solve some of society’s toughest challenges — from eradicating disease and improving education, to addressing the needs of our communities. Through collaboration, providing resources and building technology, our mission is to help build a more inclusive, just and healthy future for everyone. For more information, please visit chanzuckerberg.com
The napari Plugin Foundation Grant is part of CZI’s Imaging Program, which seeks to develop conditions to better understand diseases. The collaboration between CZI and napari aims to give researchers access to the latest developments in advanced imaging using software-based analysis tools.
In the picture (from left to right.):
CZI Grantees: Dr. Francesco Reina and Jacopo Abramo from the Biophysical Imaging Department at Leibniz IPHT with a custom-built interferometric scattering microscope (iSCAT). This microscope was used to prototype the napari plugin first version, in order to control acquisition from a high-speed camera device mounted within the setup.
Open source: Bioinformatics tools from Jena facilitate phage detection and PCR design
In two scientific publications, InfectoGnostics researchers with participation of Leibniz IPHT recently presented new bioinformatics tools whose open source code can now be used and further developed free of charge. The software What the Phage enables the detection of phages, while ConsensusPrime can be used for the development of various molecular tests. The tools were developed by researchers at Jena University Hospital, Leibniz IPHT and the startup nanozoo.
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