FISSA: A neuropil decontamination toolbox for calcium imaging signals

Keemink, Sander W. and Lowe, Scott C. and Pakan, Janelle M.P. and Dylda, Evelyn and van Rossum, Mark C.W. and Rochefort, Nathalie L. (2018) FISSA: A neuropil decontamination toolbox for calcium imaging

Electromembrane Processes, a Toolbox for Advanced Separations

Spectral imaging toolbox

Background: Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a conve...

An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics

The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interacti...

Robust Estimation of Neural Signals in Calcium Imaging

Calcium imaging is a prominent technology in neuroscience research which allows for simultaneous recording of large numbers of neurons in awake animals. Automated extraction of neurons and their temporal activity in imaging datasets is an important step in the path to producing neuroscience results. However, nearly all imaging datasets contain gross contaminating sources which could be due to t...