Open Science / Pipelines
Analysis pipelines
Code the lab uses to analyse MuLTEE data.
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Cell Segmentation and shape measurement (ImageJ + Cellpose)
Segments individual cells in images of snowflake yeast clusters crushed into a single cell layer, then measures each cell’s size and shape (area, major/minor axis, aspect ratio, circularity, solidity) and, optionally, fluorescence intensity. Used for the cell aspect ratio and cell volume protocols.
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Cluster segmentation and measurement (ImageJ)
Segments snowflake yeast clusters in brightfield images, single fields of view or stitched whole wells, with optional manual correction, then measures cluster size and other features. Needs Fiji with the BioVoxxel and IJPB-plugins update sites
Other code is available on request: see who to write to.