Automated image acquisition and analysis in light microscopy

Abstract

We develop and maintain a number of workflows for automated acquisition and analysis of light microscopy imaging data. Large number of images acquired by high-throughput commercial microscopes requires automation of all steps in analysis protocols. By combining and customizing open-source software tools for image and data processing we create and support robust workflows consisting of data preprocessing, image analysis, quality control and statistical post-processing. Complex acquisitions of images, in which microscope settings need to be changed during the experiment, are automated using Adaptive Feedback Microscopy technology. We developed the AutoMicTools package for Fiji which can be used with several commercial microscope brands. The package combines tools to configure robust protocols for Automated Feedback Microscopy and post-acquisition data analysis for microscopy-driven studies of various biological systems