Light-sheet microscopy

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

An ImageJ/Fiji macro which measures quality through two stacks of images assumed to be acquired from two opposite angle of views using gray-level standard deviation.

Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

See more CSBDeep in Knime.

Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.