DeepSinse: deep learning based detection of single molecules.

Bioinformatics
John S H DanialAna J Garcia Saez

Abstract

Imaging single molecules has emerged as a powerful characterization tool in the biological sciences. The detection of these under various noise conditions requires the use of algorithms that are dependent on the end-user inputting several parameters, the choice of which can be challenging and subjective. In this work, we propose DeepSinse, an easily-trainable and useable deep neural network that can detect single molecules with little human input and across a wide range of signal-to-noise ratios. We validate the neural network on the detection of single bursts in simulated and experimental data and compare its performance with the best-in-class, domain-specific algorithms. Ground truth ROI simulating code, neural network training, validation code, classification code, ROI picker, GUI for simulating, training and validating DeepSinse as well as pre-trained networks are all released under the MIT License on www.github.com/jdanial/DeepSinse.The dSTORM dataset processing code is released under the MIT License on www.github.com/jdanial/StormProcessor. Supplementary data are available at Bioinformatics online.

References

Sep 18, 2001·Methods : a Companion to Methods in Enzymology·T Ha
Jul 21, 2005·Accounts of Chemical Research·Achillefs N KapanidisShimon Weiss
Aug 10, 2006·Nature Methods·Michael J RustXiaowei Zhuang
Aug 12, 2006·Science·Eric BetzigHarald F Hess
Sep 19, 2006·Biophysical Journal·Samuel T HessMichael D Mason
Mar 21, 2007·Nature Methods·Maximilian H Ulbrich, Ehud Y Isacoff
May 16, 2007·Chembiochem : a European Journal of Chemical Biology·Somes K DasHagan Bayley
Jul 23, 2008·Angewandte Chemie·Mike HeilemannMarkus Sauer
Feb 15, 2012·Optics Express·I IzeddinJ B Sibarita
Apr 6, 2019·Journal of the American Chemical Society·Jiachao XuXiaohong Fang
Sep 29, 2019·Nature Methods·Jervis Vermal ThevathasanJonas Ries
Dec 25, 2019·Proceedings of the National Academy of Sciences of the United States of America·Leonhard MöcklW E Moerner
Jun 17, 2020·Nature Methods·Elias NehmeYoav Shechtman

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Pamela H RussellNichole E Carlson
Data in Brief
Ben GelmanDavid Slater
BioRxiv : the Preprint Server for Biology
Andrew L Jones
© 2021 Meta ULC. All rights reserved