Image registration of low signal-to-noise cryo-STEM data

Ultramicroscopy
Benjamin H SavitzkyLena F Kourkoutis

Abstract

Combining multiple fast image acquisitions to mitigate scan noise and drift artifacts has proven essential for picometer precision, quantitative analysis of atomic resolution scanning transmission electron microscopy (STEM) data. For very low signal-to-noise ratio (SNR) image stacks - frequently required for undistorted imaging at liquid nitrogen temperatures - image registration is particularly delicate, and standard approaches may either fail, or produce subtly specious reconstructed lattice images. We present an approach which effectively registers and averages image stacks which are challenging due to their low-SNR and propensity for unit cell misalignments. Registering all possible image pairs in a multi-image stack leads to significant information surplus. In combination with a simple physical picture of stage drift, this enables identification of incorrect image registrations, and determination of the optimal image shifts from the complete set of relative shifts. We demonstrate the effectiveness of our approach on experimental, cryogenic STEM datasets, highlighting subtle artifacts endemic to low-SNR lattice images and how they can be avoided. High-SNR average images with information transfer out to 0.72 Å are achieved a...Continue Reading

References

Jul 26, 2002·Ultramicroscopy·Laurent Joyeux, Pawel A Penczek
Sep 6, 2002·Ultramicroscopy·K WatanabeM Shiojiri
Sep 29, 2004·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Dirk Robinson, Peyman Milanfar
Jan 28, 2006·Journal of Microscopy·A M SanchezP J Goodhew
Jul 29, 2006·Ultramicroscopy·David A MullerMatthew Weyland
Aug 18, 2006·Nature·W EerensteinJ F Scott
Feb 5, 2008·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Hassan ForooshMarc Berthod
Jan 27, 2009·Journal of Structural Biology·Maxim ShatskyRobert M Glaeser
Jun 26, 2012·Ultramicroscopy·Nadi BraidyChristian Ricolleau
May 16, 2013·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Lewys Jones, Peter D Nellist
Feb 11, 2014·Ultramicroscopy·Benjamin BerkelsThomas Vogt
Feb 18, 2014·Nature Methods·Sharon Grayer WolfMichael Elbaum
Aug 25, 2015·Journal of Structural Biology·John L Rubinstein, Marcus A Brubaker
Dec 2, 2015·Ultramicroscopy·Xiahan Sang, James M LeBeau
Sep 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·Robert HovdenLena F Kourkoutis
Nov 22, 2016·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Michael J ZachmanLena F Kourkoutis
Dec 2, 2017·Nature Communications·Benjamin H SavitzkyLena F Kourkoutis
Feb 1, 2018·Proceedings of the National Academy of Sciences of the United States of America·Ismail El BaggariLena F Kourkoutis

❮ Previous
Next ❯

Citations

May 14, 2019·Angewandte Chemie·Michael J ZachmanMiaofang Chi
Jun 6, 2020·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Berit H GoodgeLena F Kourkoutis
Jul 7, 2020·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Magnus NordGary W Paterson
Nov 24, 2020·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Chenyu ZhangPaul M Voyles
Oct 31, 2020·Physical Review Letters·Ismail El BaggariLena F Kourkoutis
May 22, 2021·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Benjamin H SavitzkyColin Ophus
Jul 31, 2019·ACS Nano·Troels Lindahl ChristiansenKirsten M Ø Jensen
Aug 21, 2021·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Jingyue Jimmy Liu
Aug 21, 2021·Accounts of Chemical Research·Elisabeth Bianco, Lena F Kourkoutis

❮ 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

Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
Lewys Jones, Peter D Nellist
IEEE Transactions on Medical Imaging
Emine U SaritasDwight G Nishimura
Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
Jong Seok Jeong, K Andre Mkhoyan
© 2022 Meta ULC. All rights reserved