BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data.
Localization microscopy (LM) captures nanoscale detail with fluorescence imaging. As large-area cameras and multiplex imaging become standard, chromatic errors are growing more complex, challenging precise analysis. BeadBuddy is an open-source, user-friendly software that uses images of fluorescent beads to model and correct 3D, spatially varying chromatic errors. BeadBuddy achieves sub-voxel resolution in DNA Fluorescence In Situ Hybridization (FISH) and is applicable across LM modalities.
RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry et al Nature Methods 2022
Radial Symmetry-FISH (RS-FISH) is an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. RS-FISH offers interactive parameter tuning and readily scales to large datasets using distributed processing on workstations, clusters, or the cloud (collaboration with Stephan Preibsich and Kyle Harrington).
available as a FIJI plugin
AirLocalize: A Software to Localize Single Molecules in 2D and 3D Images.
Lionnet et al Nature Methods 2011
Airlocalize combines a Gaussian Kernel with a local affine background subtraction to calculate the position and brightness of each particle in the image. Can process individual images, series of images, movies.
Airlocalize is the basis of the EASI-FISH pipeline (Biorxiv / Github)