Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform

Advanced Structural and Chemical Imaging
R KannanSergei V Kalinin

Abstract

Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositi...Continue Reading

References

Dec 26, 2001·Chemical Reviews·M L Pacholski, N Winograd
Dec 5, 2002·Analytical Chemistry·Mark C BiesingerNils O Petersen
Aug 6, 2005·Advances in Biochemical Engineering/biotechnology·Timo Zimmermann
May 2, 2007·Mass Spectrometry Reviews·Liam A McDonnell, Ron M A Heeren
Jan 23, 2009·Journal of Electron Microscopy·Stephen J PennycookMatthew F Chisholm
Dec 17, 2010·Nature·Kazu Suenaga, Masanori Koshino
Dec 22, 2010·IEEE Transactions on Pattern Analysis and Machine Intelligence·Deng CaiThomas S Huang
Aug 3, 2011·Journal of Biomedical Optics·José M MedinaSergio M C Nascimento
Dec 7, 2011·Science·Gene E IceJudy W L Pang
Dec 12, 2012·Physical Review Letters·Wu ZhouJuan-Carlos Idrobo
Dec 22, 2012·The Journal of Physical Chemistry. B·Dan FuXiaoliang Sunney Xie
Mar 29, 2014·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Jean-Sebastien G BouillardAnatoly V Zayats
Apr 15, 2014·Advanced Materials·Jan SeidelRamamoorthy Ramesh
Oct 25, 2014·Journal of Synchrotron Radiation·Nouamane LaanaitPaul Fenter
Nov 28, 2014·Nature·Stephen J Pennycook, Sergei V Kalinin
Aug 10, 2016·Nanotechnology·Nouamane LaanaitChristian M Schlepütz
Nov 3, 2016·ACS Applied Materials & Interfaces·Anton V IevlevOlga S Ovchinnikova
Jan 10, 2017·Pattern Recognition·Meng LuXiaoning Qian
Apr 25, 2017·IEEE Transactions on Neural Networks and Learning Systems·Kailing GuoDong Xu

❮ Previous
Next ❯

Citations

Oct 13, 2020·Advanced Science·Yongtao LiuOlga S Ovchinnikova
Jun 26, 2021·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Frances I AllenAndrew M Minor

❮ Previous
Next ❯

Methods Mentioned

BETA
PCA
X-ray
transmission
transmission electron microscopy
scanning tunneling microscopy
imaging
imaging techniques

Software Mentioned

mlrmbo
hyperopt
XDM

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

Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry
Hemanth NoothalapatiTatsuyuki Yamamoto
IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Cedric Fevotte, Nicolas Dobigeon
IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Rita AmmanouilDavid Mary
Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Yehao MaGuangxin Zhang
© 2022 Meta ULC. All rights reserved