The Annals of Applied Statistics

SCALPEL: Extracting neurons from calcium imaging data

Ashley Petersen, Noah Simon, and Daniela Witten

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In the past few years, new technologies in the field of neuroscience have made it possible to simultaneously image activity in large populations of neurons at cellular resolution in behaving animals. In mid-2016, a huge repository of this so-called “calcium imaging” data was made publicly available. The availability of this large-scale data resource opens the door to a host of scientific questions for which new statistical methods must be developed.

In this paper we consider the first step in the analysis of calcium imaging data—namely, identifying the neurons in a calcium imaging video. We propose a dictionary learning approach for this task. First, we perform image segmentation to develop a dictionary containing a huge number of candidate neurons. Next, we refine the dictionary using clustering. Finally, we apply the dictionary to select neurons and estimate their corresponding activity over time, using a sparse group lasso optimization problem. We assess performance on simulated calcium imaging data and apply our proposal to three calcium imaging data sets.

Our proposed approach is implemented in the R package scalpel, which is available on CRAN.

Article information

Ann. Appl. Stat., Volume 12, Number 4 (2018), 2430-2456.

Received: March 2017
Revised: December 2017
First available in Project Euclid: 13 November 2018

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Calcium imaging cell sorting dictionary learning neuron identification segmentation clustering sparse group lasso


Petersen, Ashley; Simon, Noah; Witten, Daniela. SCALPEL: Extracting neurons from calcium imaging data. Ann. Appl. Stat. 12 (2018), no. 4, 2430--2456. doi:10.1214/18-AOAS1159.

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Supplemental materials

  • Supplementary Materials for “SCALPEL: Extracting neurons from calcium imaging data”. We provide additional results including the technical details of SCALPEL’s Step 3 and analyses illustrating the sensitivity of results to changes in SCALPEL’s tuning parameters.