Visit https://quasar.codes to download and our Quasar page to get started!Primary packagesOrange 3.36.2orange-spectroscopy 0.6.12python 3.10.11numpy 1.24.4scipy 1.10.1scikit-learn 1.3.2Notable changes2D Correlation Spectroscopy widgetPreprocess Spectra: Unify Cut preprocessorPLS supports multiple targets and has scores + loadings outputsSpectra, Hyperspectra: DaskTable support (on experimental Dask version[1])ICYMIThere have been a few notable changes in the last few versions (1.9, 1.7):Spectra widget: waterfall plot (1.9)New visualization parameters dialog for Spectra and HyperSpectra for easy setting of captions / axis labels (1.9)Feature Constructor is now called Formula (1.9)Data Table now takes a single input, can send a subset input for visualizing subset rows in context (1.9)Tile File widget can now accept multiple Preprocessor inputs (1.7)See included example workflow for a demonstration combining Preprocess Spectra and Integrate widgets[1] Experimental Dask version: https://orangedatamining.com/blog/dask-spectroscopy/

Biochar is a form of charcoal - formed from pyrolysis of plant material. This carbon-rich material is a key player in soil health - benefiting both nutrient cycling and microorganisms. However, biochar breakdown processes - and its affinity to bind with environmental pollutants - make the long-term utilization of this fertilizer an environmental risk. Synchrotron FTIR analysis using the Bruker endstation analyzed surfaces of biochar, identifying functional group changes with typical uses of biochar and its interractions with pollutants. This study contributes to understanding the aging and contaminant distribution processes of biochar in the natural environment.Read the paper! Shen, Jian; Huang, Guohe; Yao, Yao; Zhang, Peng; Rosendahl, Scott. Surface Alteration on Biochar in Long-Term Application: Insights into Pyrolysis, Freeze-Thaw Aging, and Dissipation. Surf. Interfaces 2024, 104118. 10.1016/j.surfin.2024.104118.

Stroke is a large concern to the public health sector. This intricate review article advertises the use of infrared imaging conducted with the Agilent microscope at the Mid-IR beamline to identify key biomarkers of stroke within brain tissue. Researchers use FTIR imaging to analyze changes in brain tissue enabling a more holistic approach to characterizing pathophysiological responses - helping us understand the processes occuring in stroke incidence and identifying risk factors - in disease and disease models. A detailed description of machine learning with Orange/Quasar data analysis is presented to aid differentiation and characterization of tissue sections. Tissue preparation methods suitable for FTIR imaging analysis are also detailed.Read the paper!Boseley, R.E.; Sylvain, N.J.; Peeling, L.; Kelly, M.E.; Pushie, M.J. A review of concepts and methods for FTIR imaging of biomarker changes in the post-stroke brain. Biochim Biophys Acta Biomembr 2024, 1866 (3), 184287. https://doi.org/10.1016/j.bbamem.2024.184287

A new release of Quasar is available!Visit https://quasar.codes to download and our Quasar page to get started!Primary packagesOrange 3.36.1orange-spectroscopy 0.6.11python 3.9.12numpy 1.24.4scipy 1.10.1scikit-learn 1.1.3Notable changesTile File widget can now accept multiple Preprocessor inputsSee included example workflow for a demonstration combining Preprocess Spectra and Integrate widgetsASCII column reader supports files with ";" commentsSome fixes to new separate baselines peak integration methodICYMIThere have been a few notable changes in the last few versions (1.7, 1.6, 1.5):Tile File widget can now accept multiple Preprocessor inputsNew peak area integration method which allows separate definition of the baseline pointsSpectra widget can now display custom peak labelsAtmospheric gas correction preprocessorWidgets now show little data table previews of their inputs/outputsFile widget allows explicit specification of file formatNew "Transform" widget category to distinguish widgets which load/create/view/annotate data, and those which modify the data table

Synchrotron FTIR spectroscopy using the Bruker endstation at the Mid-IR beamline reveals changes in microalgal lipids and proteins indicating nanoplastic toxicity and risk assessment of emerging pollutants. Researchers conclude the mechanism of toxicity induced by nanoplastics to microalgae under multiple environmental conditions - contributing to emphasize the importance of ecological risk assessments and environmental management of nanoplastics.Read the paper!Sichen Gao, Gordon Huang, Peng Zhang, Xiaying Xin, Jianan Yin, Dengcheng Han, Scott Rosendahl, Stuart Read, Toxicity and mechanism of nanoplastics to phytoplankton in high-latitude aquatic ecosystems of Canadian prairie: Effects of multiple environmental factors. Sci. Total Environ 2023, 893, 164676. https://doi.org/10.1016/j.scitotenv.2023.164676.

Plant-based meat alternatives are increasingly in demand. Innovative strategies are required to provide consumers with appropriately textured and nutrient-dense protein sources. This study aims to increase the nutritional value of the food, reduce production costs, and improve the environmental footprint of plant-based meat analogues. Infrared imaging using the Agilent microscope at the Mid-IR beamline was used to analyze plant protein secondary structures. Orange/Quasar data analysis using K-means clustering was used to identify unique patterns in the data.This publication represents cross-beamline collaboration. The FTIR results complement synchrotron-based micro-computed tomography collected at BMIT.Read the paper!Dobson, S.; Stobbs, J.; Laredo, T.; Marangoni, A.G. A facile strategy for plant protein fiber formation without extrusion or shear processing. Innov Food Sci Emerg Technol 2023, 86, 103385. https://doi.org/10.1016/j.ifset.2023.103385

Learned representations of hyperspectral infrared images obtained at the Mid-IR beamline are used to extract physicochemical spectral markers of aging and cracking in cross-linked polyethylene pipes. Indicators of degredation were identified and learned by the model and applied to identify both unused and damaged pipes.These results will help pipe manufacturers optimize fabrication methods and improve stress-testing protocols, extending the use of their pipes into ever more vigorous and challenging operating environments. The study also highlights the use of representation learning via deep generative modeling to provide interpretable information from complicated data sets - unlocking new capabilities for hyperspectral IR imaging using the Agilent microscope at the Mid-IR beamline to solve complex problems across global sectors.Read the paper!Grossutti, M.; D’Amico, J.; Quintal, J.; MacFarlane, H.W.; Wareham, C.; Quirk, A.; Dutcher, J.R. ACS Appl Mater Interfaces 2023, 15 (18), 22532-22542. https://doi.org/10.1021/acsami.3c02564

Pulse production is an integral pillar of the Canadian agricultural economy. Changes to the nutritional properties and protein structure of green lentil and yellow pea flour post-seed milling and processing are determined. The authors used the Agilent endstation at the Mid-IR beamline to examine pulse flours - reporting changes to protein structure and an improvement in starch digestibility with tempering and IR heating. Sample preparation used KBr pellets / flour mixtures.Read the paper!Laing, E.; Stone, A.K.; Shi, D.; Pickard, M.; House, J.D.; Wang, N.; Nickerson, M.T. Effect of infrared heating on the nutritional properties of yellow pea and green lentil flours. Cereal Chem 2023, 100, 614-627. https://doi.org/10.1002/cche.10653

This is primarily a bugfix release with some small performance improvements.Visit https://quasar.codes to download and our Quasar to get started!Primary packagesOrange 3.34.0orange-spectroscopy 0.6.8python 3.9.15numpy 1.23.5scipy 1.9.3scikit-learn 1.1.3Important notesThis release bumps the included Python major version to 3.9. As a result, some installations (especially on Windows) will require a full uninstallation before installing the new version.Notable changesTile File widget can now accept multiple Preprocessor inputsSee included example workflow for a demonstration combining Preprocess Spectra and Integrate widgetsASCII column reader supports files with ";" commentsSome fixes to new separate baselines peak integration methodICYMIThere have been a few notable changes in the last few versions (1.6, 1.5):New peak area integration method which allows separate definition of the baseline pointsSpectra widget can now display custom peak labelsAtmospheric gas correction preprocessorWidgets now show little data table previews of their inputs/outputsFile widget allows explicit specification of file formatNew "Transform" widget category to distinguish widgets which load/create/view/annotate data, and those which modify the data table

The millisecond to microsecond time regime spans many dynamic processes such as reaction kinetics, molecular dynamics and complex system evolution. Accessing this time regime in the mid-infrared can be challenging and different existing approaches have inherent trade-offs such as requiring rapidly repeatable processes, sacrificing broadband spectral context or unacceptably low signal-to-noise.In this talk, a new laser-based instrument at the Mid-IR beamline capable of accessing these fast timescales with reasonable spectral bandwidth will be introduced. This spectrometer is an excellent complement to broadband FT-IR measurements where information about the dynamics of the system of interest is limited by the useful time resolution of rapid-scan measurements or by the reproducibility requirements of step-scan measurements. Examples of applications and practical sampling considerations will be presented.When: January 20, 2:00 pm CST (Saskatoon time)Where: The webinar will be on Webex. Please email us for connection details.

A dual infrared frequency comb spectrometer with heterodyne detection has been used to perform time-resolved electrochemical attenuated total reflectance surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS). In collaboration with the Canadian Light Source and IRsweep, the desorption of a monolayer of a pyridine derivative with 10 μs time resolution and a detection limit of 5% of a monolayer was demonstrated. The applications of the method are potentially immense for the study of short lived adsorbed species during electrocatalysis. You can access the pre-print (https://harvest.usask.ca/handle/10388/12909) in the UofS open access repository.Analytical Chemistry.(https://pubs.acs.org/doi/10.1021/acs.analchem.0c00260).

Fourier transform infrared (FTIR) spectromicroscopy was used to study individual living cells of three closely-related species of the green algal genus Chlamydomonas. Three types of spectral variation were observed between individual cells within a single culture, as well as between different cultures: variation around a mean, individual outliers, and the presence of subpopulations. By understanding and controlling this variation, we were able to spectroscopically differentiate between the three closely-related species. Spectral differences were confirmed using principal component analysis, leading to an understanding of the biochemical differences between species. This work highlights the additional information obtained by studying individual cells, and has implications for more traditional bulk measurements.Analyst, (https://doi.org/10.1039/D0AN01386B )

Mid-IR is hosting a workshop!When: October 15-16, 2020Presenter: Christophe Sandt, Beamline Scientist, SOLEIL synchrotronTopics: Theory, Preprocessing Data, Data Exploration, Imaging, Classification and PredictionLocation: webinar, information sent with registrationWho can attend: Anyone who is interested! Please register:RegistrationHaving trouble with registration? Please send us an email with the subject Mid-IR workshop.AgendaOctober 14, 2020 - 12:00 (CST) → 14:00 (CST) Technical Help SessionProvide online technical support for the installation of Quasar to workshop attendees.October 15, 2020 - 08:00 (CST) → 10:00 (CST) First Session - Theory and Preprocessing DataTheoryData Collection StrategyNeed for Multivariate Analysis and ClusteringExample Applications (Bio-Spectroscopy)Preprocessing TheoryPreprocessing DataHands on training with QuasarQuality controlBaseline correction, normalization, derivationSmoothing/denoisingEMSC - Extended Multiplicative Scatter CorrectionAdvanced preprocessing that exist but not demonstrated (ATR, atmospheric suppression, interference fringes, KK, KM)October 15, 2020 - 12:00 (CST) → 14:00 (CST) Second Session - Data Exploration and ImagingData Exploration: PCAHands OnTheory and InterpretationPCA Classification (SIMCA)ImagingGenerate Images in QuasarManipulate Images: Graphical and "Intelligent" selection of DataOctober 16, 2020 - 08:00 (CST) → 10:00 (CST) Third Session - Classification and PredictionClassification and PredictionUnsupervised Clustering (K-Means, HCA)Supervised Clustering (KNN, CART, RFC, ANN, logit)Theory: Calibration and ValidationTest and ScorePredictionChristophe Sandt - BiographyChristophe Sandt was trained as a biochemist and is currently beamline scientist at the SOLEIL synchrotron near Paris, France. He earned a PhD in Biospectroscopy from the Pharmacy University of Reims Champagne-Ardenne under the guidance of Prof. Manfait and Sockalingum. He has a 20 year long experience in the field of vibrational microspectroscopy of biological materials, cells and tissues including two post-doctoral fellowships in Canada, at the Chemistry Department of Université de Montréal working with Prof. Lafleur, and at the Chemistry Department of St Francis Xavier University with Prof. Pink and Smith-Palmer. His first research interests focused on the early identification of pathogenic microorganisms by infrared spectroscopy, the study of biocide penetration in bacterial biofilms with ATR-FTIR, and pioneering the analysis of bacterial biofilms by Raman microspectroscopy. He joined the French national synchrotron light source, SOLEIL, in 2008 and has since been helping scientists perform experiment in various fields of science such as cultural heritage, plant biology, cell chemistry, catalysis, astrophysics... He has used the bright IR synchrotron light to conduct various studies in biochemistry: to profile induced pluripotent and embryonic stem cells, to monitor tyrosine kinase activity in multiresistant hematopietic progenitor cells, to study the chemical changes associated with tumor hypoxia, to follow the penetration of IR probes in living cells and tissues, to study abnormal protein conformation in diverse neurodegenerative diseases.

Yay data! Publishing research articles? Submitting a thesis? Attending conferences? Send us an email! Include a figure and summary of the work and we'll highlight it in our research news. Make sure you report your published works to the CLS, too!

Mid-IR is open for beamtime.Have an active project? Interested in starting a new project?Please contact beamline staff to discuss how to implement your experiments.Information on shipping and sample in the user guideADD + CHANGE