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Christoph C. H. Langer and Daniel W. Gerlich (Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.)
Phenotypic image analysis is the task of translating cell properties (e.g. morphological or biochemical features) into meaningful biological information. Adoptive feedback microscopy allows for a reproducible acquisition of relevant data by using online image analysis to automatically acquire structures of interest. Visual data analysis helps a domain scientist to reason about the data by providing him interactive visual interfaces. For these three tasks a multitude of tools exist with unique strengths and weaknesses. No satisfactory out of the box solution exists to combine these tasks into an interactive work-flow. Our tool allows a domain scientist to set up, perform and analyze his/her experiments in a fast, independent manner with little previous computer science knowledge. CellCognition 2.0 is a lightweight and easily extendable framework that provides a unified graphical interface to interact with existing phenomics software and provide exploration and brushing operations on the final data. It now delegates previous core functionality to powerful python libraries and uses them to interact with the “ZEN blue” interface to control ZEISS laser-based 3D imaging systems.https://www.imba.oeaw.ac.at/research/daniel-gerlich/our-approach/