Bioimage Analysis 3: Segmentation (Anne Carpenter)

https://www.ibiology.org/techniques/b... In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data. Speaker Biographies: First Speaker: Anne Carpenter (Broad Institute) Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images. Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison) Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.