INDIVIDUAL RESEARCH PROJECT 15
Integration of spatiotemporal image analysis tools into Fractal, a scalable and FAIR (Findable, Accessible, Interoperable, Reproducible) analysis platform
Abstract
The two main challenges standing in the way of democratizing bioimage analysis in plant biology are 1) the availability of algorithms carrying out complex analysis tasks across spatial and temporal dimensions, and 2) the integration of these algorithms into frameworks making them accessible to all researchers, regardless of their computational expertise.
Recognizing the power of modern image analysis methods and the value of the next-generation image file format OME-Zarr as an open standard for microscopy, this project will focus on integrating cutting-edge image analysis algorithms for 3D segmentation and time-lapse tracking into the Fractal platform (https://fractal-analytics-platform.github.io/), which provides a no-code framework to process large-scale OME-Zarr datasets (https://doi.org/10.1007/s00418-023-02209-1). The interoperability of the developed analysis methods with other resources for image management (OMERO) and analysis (Imaris) will be ensured through secondments with partners within the AGILE consortium. The projet will also involve extensive benchmarking of the newly-developed analysis tools on images generated in the AGILE consortium to characterize their range of applicability and ultimately facilitate their broad adoption and reuse across the plat biology community.
More information
Training benefits
- Build advanced bioimage analysis expertise
- Develop novel open and FAIR computational tools
- Evolve at the forefront of next-generation file formats for microscopy data
- Work in an interdisciplinary project involving computational and experimental researchers
Requirements
Background knowledge and experience with microscopy image data analysis and Python programming is required. Basic notions of modern machine learning are desirable.
Environment
The University of Zurich (UZH) is Switzerland’s largest university with 28,000 enrolled students and one of the leading research institutions in Europe. The university excels in computational and data-driven research and offers an exceptional environment for interdisciplinary computational research. The BioVisionCenter, at UZH, is Switzerland’s first academic center fully dedicated to bioimage analysis. Its mission is to empower biologists to use state-of-the-art machine vision methods to analyze their bioimage data
