Miscellaneous
This episode is brought to you by Visiopharm.In this third and last episode of the multiplex mini-series with Regan Baird from Visiopharm we look at the considerations when choosing an image analysis software for phenotyping.The two main points to consider when choosing phenotyping image analysis software are segmentation assistance and data visualization. Segmentation assistance:Before different markers are attributed to different cells in the tissue and cell phenotypes are determined, cell boundaries need to be delineated. The automatic delineation of these boundaries by image analysis software is called cell segmentation. Cells in tissue slides can have different shapes and sizes, which depend on the plane of sectioning, heterogeneity of the investigated tissue, and the disease stage. This makes the task of segmentation challenging. Unlike in single-cell confocal microscopy images, where the cell borders are very well-demarcated, in tissue they often need to be estimated. A separate segmentation (e.g., membrane) marker can help significantly, but a perfect cell segmentation is not attainable.To best estimate the cell boundaries, rule-based classical computer vision approaches or artificial intelligence (AI) – powered approaches can be used. In rule-based approaches, we are working with well-defined features on which the segmentation is based, but we need to make concessions. The AI-powered models are only as good as the examples we train the models on. To combine the advantages of both, Visiopharm offers an AI-based nuclear segmentation as the starting point and a rule-based and marker-based second step to obtain the most reliable cell segmentation for phenotyping. Data visualization:The adequate visualization and handling of the obtained data depend on the software used. To understand and interpret the multidimensional multiplex and phenotyping data we need to interpret graphs, plots, two-dimensional reduction plots, and other data visualizations for all the images in multiplex studies. In order to evaluate how well the phenotyping has performed and to export meaningful results, the correct visualization tools need to be used.If you need assistance or have questions about multiplexing and phenotyping visit the Visiopharm’s website and contact the Visiopharm team. This episode’s resources:Multiplexing mini-series Part 1: Introduction to multiplex for tissue image analysis (part 1) w/ Regan Baird, VisiopharmMultiplexing mini-series Part 2: How to make sense of multiplex data with phenotyping? (part 2) w/ Regan Baird