ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data

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Title: ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data
Author(s): Reynolds, SC
Abrahamsson, T
Schuck, R
Sjöström, PJ
Schultz, SR
Dragotti, PL
Item Type: Journal Article
Abstract: We present an algorithm for detecting the location of cells from two-photon calcium imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and exterior, in which all pixels have maximally ‘similar’ time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cell’s morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mouse in vitro dataset, containing synchronously spiking cells, and a manually labelled mouse in vivo dataset, on which ABLE achieves a 67.5% success rate.
Publication Date: 16-Oct-2017
Date of Acceptance: 15-Sep-2017
URI: http://hdl.handle.net/10044/1/50835
DOI: https://dx.doi.org/10.1523/ENEURO.0012-17.2017
ISSN: 2373-2822
Publisher: Society for Neuroscience
Journal / Book Title: Eneuro
Volume: 4
Issue: 5
Copyright Statement: Copyright © 2017 Reynolds et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
Sponsor/Funder: Commission of the European Communities
The Royal Society
Biotechnology and Biological Sciences Research Council (BBSRC)
Commission of the European Communities
Funder's Grant Number: 277800
IF110059
BB/K001817/1
289146
Keywords: active contour
calcium imaging
fluorescence microscopy
level set method
segmentation
Publication Status: Published online
Article Number: ENEURO.0012-17.2017
Appears in Collections:Faculty of Engineering
Bioengineering
Electrical and Electronic Engineering



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