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CalciumCV: Computer Vision Software for Calcium Signaling in Astrocytes

  • Valentina Kustikova
  • Mikhail Krivonosov
  • Alexey Pimashkin
  • Pavel Denisov
  • Alexey Zaikin
  • Mikhail Ivanchenko
  • Iosif MeyerovEmail author
  • Alexey SemyanovEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11179)

Abstract

Developing computational analysis of time-lapse imaging of calcium events in astrocytes is a challenging task in neuroscience. Here we report the implementation of an algorithm that solves this task. After noise reduction with the block-matching and 3D filtering (BM3D) algorithm, calcium activity is identified as fluorescence elevation above the baseline level. Individual events are detected by sliding window approach applied to the variation of pixel intensity relative to the baseline level. The maximal projection and duration of astrocytic calcium events are then assessed. The novelty of the proposed method is an adaptive construction of the baseline level. The statistical results generated by our program are consistent with the previous algorithm reported and used by us for the reference. The software is publicly available.

Keywords

Bioinformatics Calcium signaling in astrocytes Computer vision Image analysis Statistical analysis 

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Valentina Kustikova
    • 1
  • Mikhail Krivonosov
    • 1
  • Alexey Pimashkin
    • 1
  • Pavel Denisov
    • 1
  • Alexey Zaikin
    • 1
    • 2
  • Mikhail Ivanchenko
    • 1
  • Iosif Meyerov
    • 1
    Email author
  • Alexey Semyanov
    • 1
    • 3
    Email author
  1. 1.Lobachevsky State University of Nizhni NovgorodNizhni NovgorodRussian Federation
  2. 2.Department of Mathematics and Institute for Women’s HealthUniversity College LondonLondonUK
  3. 3.Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation

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