A computationally efficient filter for reducing shot noise in low S/N data

Mami Okada, Tomoe Ishikawa, Yuji Ikegaya

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Functional multineuron calcium imaging (fMCI) provides a useful experimental platform to simultaneously capture the spatiotemporal patterns of neuronal activity from a large cell population in situ. However, fMCI often suffers from low signal-to-noise ratios (S/N). The main factor that causes the low S/N is shot noise that arises from photon detectors. Here, we propose a new denoising procedure, termed the Okada filter, which is designed to reduce shot noise under low S/N conditions, such as fMCI. The core idea of the Okada filter is to replace the fluorescence intensity value of a given frame time with the average of two values at the preceding and following frames unless the focused value is the median among these three values. This process is iterated serially throughout a time-series vector. In fMCI data of hippocampal neurons, the Okada filter rapidly reduces background noise and significantly improves the S/N. The Okada filter is also applicable for reducing shot noise in electrophysiological data and photographs. Finally, the Okada filter can be described using a single continuous differentiable equation based on the logistic function and is thus mathematically tractable.

Original languageEnglish
Article numbere0157595
JournalPLoS One
Volume11
Issue number6
DOIs
Publication statusPublished - 2016 Jun 1
Externally publishedYes

Fingerprint

Shot noise
Calcium
Imaging techniques
image analysis
calcium
Signal-To-Noise Ratio
Photons
Neurons
Noise
Logistics
Time series
Signal to noise ratio
Fluorescence
Cells
photographs
detectors
time series analysis
Detectors
neurons
fluorescence

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

A computationally efficient filter for reducing shot noise in low S/N data. / Okada, Mami; Ishikawa, Tomoe; Ikegaya, Yuji.

In: PLoS One, Vol. 11, No. 6, e0157595, 01.06.2016.

Research output: Contribution to journalArticle

@article{45d1f4cda4434596902b55b36b14a45f,
title = "A computationally efficient filter for reducing shot noise in low S/N data",
abstract = "Functional multineuron calcium imaging (fMCI) provides a useful experimental platform to simultaneously capture the spatiotemporal patterns of neuronal activity from a large cell population in situ. However, fMCI often suffers from low signal-to-noise ratios (S/N). The main factor that causes the low S/N is shot noise that arises from photon detectors. Here, we propose a new denoising procedure, termed the Okada filter, which is designed to reduce shot noise under low S/N conditions, such as fMCI. The core idea of the Okada filter is to replace the fluorescence intensity value of a given frame time with the average of two values at the preceding and following frames unless the focused value is the median among these three values. This process is iterated serially throughout a time-series vector. In fMCI data of hippocampal neurons, the Okada filter rapidly reduces background noise and significantly improves the S/N. The Okada filter is also applicable for reducing shot noise in electrophysiological data and photographs. Finally, the Okada filter can be described using a single continuous differentiable equation based on the logistic function and is thus mathematically tractable.",
author = "Mami Okada and Tomoe Ishikawa and Yuji Ikegaya",
year = "2016",
month = "6",
day = "1",
doi = "10.1371/journal.pone.0157595",
language = "English",
volume = "11",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "6",

}

TY - JOUR

T1 - A computationally efficient filter for reducing shot noise in low S/N data

AU - Okada, Mami

AU - Ishikawa, Tomoe

AU - Ikegaya, Yuji

PY - 2016/6/1

Y1 - 2016/6/1

N2 - Functional multineuron calcium imaging (fMCI) provides a useful experimental platform to simultaneously capture the spatiotemporal patterns of neuronal activity from a large cell population in situ. However, fMCI often suffers from low signal-to-noise ratios (S/N). The main factor that causes the low S/N is shot noise that arises from photon detectors. Here, we propose a new denoising procedure, termed the Okada filter, which is designed to reduce shot noise under low S/N conditions, such as fMCI. The core idea of the Okada filter is to replace the fluorescence intensity value of a given frame time with the average of two values at the preceding and following frames unless the focused value is the median among these three values. This process is iterated serially throughout a time-series vector. In fMCI data of hippocampal neurons, the Okada filter rapidly reduces background noise and significantly improves the S/N. The Okada filter is also applicable for reducing shot noise in electrophysiological data and photographs. Finally, the Okada filter can be described using a single continuous differentiable equation based on the logistic function and is thus mathematically tractable.

AB - Functional multineuron calcium imaging (fMCI) provides a useful experimental platform to simultaneously capture the spatiotemporal patterns of neuronal activity from a large cell population in situ. However, fMCI often suffers from low signal-to-noise ratios (S/N). The main factor that causes the low S/N is shot noise that arises from photon detectors. Here, we propose a new denoising procedure, termed the Okada filter, which is designed to reduce shot noise under low S/N conditions, such as fMCI. The core idea of the Okada filter is to replace the fluorescence intensity value of a given frame time with the average of two values at the preceding and following frames unless the focused value is the median among these three values. This process is iterated serially throughout a time-series vector. In fMCI data of hippocampal neurons, the Okada filter rapidly reduces background noise and significantly improves the S/N. The Okada filter is also applicable for reducing shot noise in electrophysiological data and photographs. Finally, the Okada filter can be described using a single continuous differentiable equation based on the logistic function and is thus mathematically tractable.

UR - http://www.scopus.com/inward/record.url?scp=84975893897&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84975893897&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0157595

DO - 10.1371/journal.pone.0157595

M3 - Article

C2 - 27304217

AN - SCOPUS:84975893897

VL - 11

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 6

M1 - e0157595

ER -