HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies.Calcium imaging is a key method in neuroscience for investigating patterns of neuronal activity in vivo.  We introduce the HNCcorr algorithm for cell identification in calcium-imaging datasets that addresses these shortcomings.  HNCcorr relies on the combinatorial clustering problem HNC (Hochbaum's Normalized Cut), which is similar to the Normalized Cut problem of Shi and Malik, a well known problem in image segmentation.  HNCcorr guarantees a globally optimal solution to the underlying optimization problem as well as minimal dependence on initialization techniques.  HNCcorr also uses a new method, called "similarity squared", for measuring similarity between pixels in calcium-imaging movies.  The effectiveness of HNCcorr is demonstrated by its top performance on the Neurofinder cell identification benchmark.  We believe HNCcorr is an important addition to the toolbox for analysis of calcium-imaging movies.
HNCcorr
HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies.Calcium imaging is a key method in neuroscience for investigating patterns of neuronal activity in vivo.  We introduce the HNCcorr algorithm for cell identification in calcium-imaging datasets that addresses these shortcomings.  HNCcorr relies on the combinatorial clustering problem HNC (Hochbaum's Normalized Cut), which is similar to the Normalized Cut problem of Shi and Malik, a well known problem in image segmentation.  HNCcorr guarantees a globally optimal solution to the underlying optimization problem as well as minimal dependence on initialization techniques.  HNCcorr also uses a new method, called "similarity squared", for measuring similarity between pixels in calcium-imaging movies.  The effectiveness of HNCcorr is demonstrated by its top performance on the Neurofinder cell identification benchmark.  We believe HNCcorr is an important addition to the toolbox for analysis of calcium-imaging movies.
HNCcorr