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StabiTissue
Stabilizes in vivo intravital microscopy images that suffer from soft-tissue background movement. StabiTissue quantifies the coincidence between image pairs from randomly distributed image regions. The method stabilizes the full 3D stack, aligning images within and across stacks. It provides an easy to use interface for the specific problem of stabilization. The method is more immune to noise and provides better performance for datasets’ possessing nonlinear tissue deformations.
μManager / Micro-Manager
A software package for control of automated microscopes. Together with the image processing application ImageJ, μManager provides a comprehensive, freely available, imaging solution. μManager has a simple and clean user interface, through which it lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging.
PySight
New
Aims to embed photon counting into most existing multi-photon imaging systems. PySight is a program dedicated to perform planar and volumetric imaging. It can calculate the difference between photon arrival times and the respective synchronization signals from the laser beam steering element. It integrates features for solving distinct laminar dynamics simultaneously sampled by the variofocal lens, rather than merely extending the effective depth of field using Bessel beams.
YouScope
Allows automatization of complex microscopy protocols. YouScope is an open-source microscope control platform for implementing complex measurement protocols. The software enables users to perform single-cell imaging as well as microplate imaging on a motorized light-microscope. It also provides a set of tools and configurable measurement types. The platform offers a large set of plug-in interfaces, allowing existing protocols to be extended, and allowing creation of new protocols from parts of existing ones.
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