Microscopy Pipeline Constructor (MyPiC) allows intuitive set-up of complex time-lapse experiments for Zeiss confocal microscopes (ZEN black). Different modules can be combined to an experiment-tailored workflow: Hardware-(reflection), object-based autofocus (cell tracking), grid scanning, tile images, and adaptive feedback microscopy for rare event detection, automated FRAP and FCS. MyPiC replaces the AutofocusScreen (AFS3.1.3) macro. Previous versions of AFS can be downloaded from EMBLEM website. AFS compatible with LSM software can be found at the Zeiss website Zeiss website. Follow the Wiki instructions to install the software. A packaged version can be found here.
FCSRunner is a VBA macro for Zeiss confocals (ZEN black) to acquire multi-position FCS measurements. FCSRunner acquires a reference image, fluorescence (cross)correlation spectroscopy (F(C)CS) measurements, and save FCS positions to a xml file. Points need to be specified manually. The tool can be used to create data for FCS-calibrated imaging. Refer to the Wiki on how to install and use this tool. A packaged version can be found here.
ImageJ/FiJi tools to be used with the Zeiss VBA macro Microscopy Pipeline Constructor to perform adaptive feedback microscopy experiments. The user can specify segmentation parameters and commands to be sent to the microscope for initiating a different imaging, FRAP or FC(C)S pipeline. A packaged version can be found here.
Quantitative microscopy relies on imaging of large cell numbers but is often hampered by time-consuming manual selection of specific cells. The 'Micropilot' software automatically detects cells of interest and launches complex imaging experiments including three-dimensional multicolor time-lapse or fluorescence recovery after photobleaching in live cells. In three independent experimental setups this allowed us to statistically analyze biological processes in detail and is thus a powerful tool for systems biology.