PMID- 37963228
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231201
IS  - 1520-6882 (Electronic)
IS  - 0003-2700 (Print)
IS  - 0003-2700 (Linking)
VI  - 95
IP  - 47
DP  - 2023 Nov 28
TI  - Comparison of Tiling Artifact Removal Methods in Secondary Ion Mass Spectrometry 
      Images.
PG  - 17384-17391
LID - 10.1021/acs.analchem.3c03887 [doi]
AB  - Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging is used across 
      many fields for the atomic and molecular characterization of surfaces, with both 
      high sensitivity and high spatial resolution. When large analysis areas are 
      required, standard ToF-SIMS instruments allow for the acquisition of adjoining 
      tiles, which are acquired by rastering the primary ion beam. For such large area 
      scans, tiling artifacts are a ubiquitous challenge, manifesting as intensity 
      gradients across each tile and/or sudden changes in intensity between tiles. Such 
      artifacts are thought to be related to a combination of sample charging, local 
      detector sensitivity issues, and misalignment of the primary ion gun, among other 
      instrumental factors. In this work, we investigated six different computational 
      tiling artifact removal methods: tensor decomposition, multiplicative linear 
      correction, linear discriminant analysis, seamless stitching, simple averaging, 
      and simple interpolating. To ensure robustness in the study, we applied these 
      methods to three hyperspectral ToF-SIMS data sets and one OrbiTrapSIMS data set. 
      Our study includes a carefully designed statistical analysis and a quantitative 
      survey that subjectively assessed the quality of the various methods employed. 
      Our results demonstrate that while certain methods are useful and preferred more 
      often, no one particular approach can be considered universally acceptable and 
      that the effectiveness of the artifact removal method is strongly dependent on 
      the particulars of the data set analyzed. As examples, the multiplicative linear 
      correction and seamless stitching methods tended to score more highly on the 
      subjective survey; however, for some data sets, this led to the introduction of 
      new artifacts. In contrast, simple averaging and interpolation methods scored 
      subjectively poorly on the biological data set, but more highly on the microarray 
      data sets. We discuss and explore these findings in depth and present general 
      recommendations given our findings to conclude the work.
FAU - Kandanaarachchi, Sevvandi
AU  - Kandanaarachchi S
AUID- ORCID: 0000-0002-0337-0395
AD  - CSIRO's Data61, Research Way, Clayton, Victoria 3168, Australia.
FAU - Gardner, Wil
AU  - Gardner W
AUID- ORCID: 0000-0002-6903-1978
AD  - Centre for Materials and Surface Science and Department of Mathematical and 
      Physical Sciences, La Trobe University, Melbourne, Victoria 3086, Australia.
FAU - Alexander, David L J
AU  - Alexander DLJ
AUID- ORCID: 0000-0001-5028-9189
AD  - CSIRO's Data61, Research Way, Clayton, Victoria 3168, Australia.
FAU - Muir, Benjamin W
AU  - Muir BW
AUID- ORCID: 0000-0002-8858-3217
AD  - CSIRO Manufacturing, Clayton, Victoria, 3168, Australia.
FAU - Chouinard, Philippe A
AU  - Chouinard PA
AD  - School of Psychology and Public Health, La Trobe University, Melbourne, Victoria 
      3086, Australia.
FAU - Crewther, Sheila G
AU  - Crewther SG
AD  - School of Psychology and Public Health, La Trobe University, Melbourne, Victoria 
      3086, Australia.
FAU - Scurr, David J
AU  - Scurr DJ
AUID- ORCID: 0000-0003-0859-3886
AD  - School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 
      2RD, United Kingdom.
FAU - Halliday, Mark
AU  - Halliday M
AD  - Altos Laboratories, Cambridge Institute of Science, The Portway Building, Granta 
      Park, Great Abington CB21 6GP, United Kingdom.
FAU - Pigram, Paul J
AU  - Pigram PJ
AUID- ORCID: 0000-0002-7972-492X
AD  - Centre for Materials and Surface Science and Department of Mathematical and 
      Physical Sciences, La Trobe University, Melbourne, Victoria 3086, Australia.
LA  - eng
PT  - Journal Article
DEP - 20231114
PL  - United States
TA  - Anal Chem
JT  - Analytical chemistry
JID - 0370536
SB  - IM
PMC - PMC10688221
COIS- The authors declare no competing financial interest.
EDAT- 2023/11/14 18:42
MHDA- 2023/11/14 18:43
PMCR- 2023/11/30
CRDT- 2023/11/14 14:33
PHST- 2023/11/14 18:43 [medline]
PHST- 2023/11/14 18:42 [pubmed]
PHST- 2023/11/14 14:33 [entrez]
PHST- 2023/11/30 00:00 [pmc-release]
AID - 10.1021/acs.analchem.3c03887 [doi]
PST - ppublish
SO  - Anal Chem. 2023 Nov 28;95(47):17384-17391. doi: 10.1021/acs.analchem.3c03887. 
      Epub 2023 Nov 14.