Glossary

segmentation

The general process of dividing an image based on the contents of that image, in our case, based on neuron location.

source-extraction

Umbrella term for all of the individual processes that produce a segmented image.

deconvolution

The process performed after segmentation to the resulting traces to infer spike times from flourescence values.

CNMF

The name for a set of algorithms within the flatironinstitute’s CaImAn Pipeline that initialize parameters and run source extraction.

Rigid-registration

The object retains shape and size.

Non-rigid-registration

The object is moved and transforms shape or size.

pixel-resolution

The length of each pixel, in micron (px/um).