scholarly journals Selecting XFEL single-particle snapshots by geometric machine learning

2021 ◽  
Vol 8 (1) ◽  
pp. 014701
Author(s):  
Eduardo R. Cruz-Chú ◽  
Ahmad Hosseinizadeh ◽  
Ghoncheh Mashayekhi ◽  
Russell Fung ◽  
Abbas Ourmazd ◽  
...  
2021 ◽  
Author(s):  
Koji Yonekura ◽  
Saori Maki-Yonekura ◽  
Hisashi Naitow ◽  
Tasuku Hamaguchi ◽  
Kiyofumi Takaba

In cryo-electron microscopy (cryo-EM) data collection, locating a target object is the most error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation showed its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and for locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection.


Author(s):  
Timothy R. Holbrook ◽  
Doriane Gallot-Duval ◽  
Thorsten Reemtsma ◽  
Stephan Wagner

Using the multi-element capabilities of single-particle inductively coupled plasma time-of-flight mass spectrometry (spICP-ToF-MS) in combination with a laser ablation introduction system, complex environmentally relevant road runoff samples from three different...


2019 ◽  
Vol 12 (7) ◽  
pp. 3885-3906 ◽  
Author(s):  
Kara D. Lamb

Abstract. Single particle soot photometers (SP2) use laser-induced incandescence to detect aerosols on a single particle basis. SP2s that have been modified to provide greater spectral contrast between their narrow and broad-band incandescent detectors have previously been used to characterize both refractory black carbon (rBC) and light-absorbing metallic aerosols, including iron oxides (FeOx). However, single particles cannot be unambiguously identified from their incandescent peak height (a function of particle mass) and color ratio (a measure of blackbody temperature) alone. Machine learning offers a promising approach for improving the classification of these aerosols. Here we explore the advantages and limitations of classifying single particle signals obtained with a modified SP2 using a supervised machine learning algorithm. Laboratory samples of different aerosols that incandesce in the SP2 (fullerene soot, mineral dust, volcanic ash, coal fly ash, Fe2O3, and Fe3O4) were used to train a random forest algorithm. The trained algorithm was then applied to test data sets of laboratory samples and atmospheric aerosols. This method provides a systematic approach for classifying incandescent aerosols by providing a score, or conditional probability, that a particle is likely to belong to a particular aerosol class (rBC, FeOx, etc.) given its observed single particle features. We consider two alternative approaches for identifying aerosols in mixed populations based on their single particle SP2 response: one with specific class labels for each species sampled, and one with three broader classes (rBC, anthropogenic FeOx, and dust-like) for particles with similar SP2 responses. Predictions of the most likely particle class (the one with the highest mean probability) based on applying the trained random forest algorithm to the single particle features for test data sets comprising examples of each class are compared with the true class for those particles to estimate generalization performance. While the specific class approach performed well for rBC and Fe3O4 (≥99 % of these aerosols are correctly identified), its classification of other aerosol types is significantly worse (only 47 %–66 % of other particles are correctly identified). Using the broader class approach, we find a classification accuracy of 99 % for FeOx samples measured in the laboratory. The method allows for classification of FeOx as anthropogenic or dust-like for aerosols with effective spherical diameters from 170 to >1200 nm. The misidentification of both dust-like aerosols and rBC as anthropogenic FeOx is small, with <3 % of the dust-like aerosols and <0.1 % of rBC misidentified as FeOx for the broader class case. When applying this method to atmospheric observations taken in Boulder, CO, a clear mode consistent with FeOx was observed, distinct from dust-like aerosols.


2017 ◽  
Author(s):  
Elliott D. SoRelle ◽  
Orly Liba ◽  
Jos L. Campbell ◽  
Roopa Dalal ◽  
Cristina L. Zavaleta ◽  
...  

2021 ◽  
Author(s):  
Mette Malle ◽  
Philipp Loffler ◽  
Soeren Bohr ◽  
Magnus Sletfjerding ◽  
Nikolaj Risgaard ◽  
...  

Abstract Combinatorial high throughput methodologies are central for both screening and discovery in synthetic biochemistry and biomedical sciences. They are, however, often reliant on large scale analyses and thus limited by long running time and excessive materials cost. We herein present Single PARticle Combinatorial multiplexed Liposome fusion mediated by DNA (SPARCLD), for the parallelized, multi-step and non-deterministic fusion of individual zeptoliter nanocontainers. We observed directly the efficient (>93%), and leakage free stochastic fusion sequences for arrays of surface tethered target liposomes with six freely diffusing populations of cargo liposomes, each functionalized with individual lipidated ssDNA (LiNA) and fluorescent barcoded by distinct ratio of chromophores. The stochastic fusion results in distinct permutation of fusion sequences for each autonomous nanocontainer. Real-time TIRF imaging allowed the direct observation of >16000 fusions and 566 distinct fusion sequences accurately classified using machine learning. The high-density arrays of surface tethered target nanocontainers ~42,000 containers per mm2 offers entire combinatorial multiplex screens using only picograms of material.


2018 ◽  
Author(s):  
Costa D. Christopoulos ◽  
Sarvesh Garimella ◽  
Maria A. Zawadowicz ◽  
Ottmar Möhler ◽  
Daniel J. Cziczo

Abstract. Compositional analysis of atmospheric and laboratory aerosols is often conducted via single-particle mass spectrometry (SPMS), an in situ and real-time analytical technique that produces mass spectra on a single particle basis. In this study, machine learning classifiers are created using a dataset of SPMS spectra to automatically differentiate particles on the basis of chemistry and size. Machine learning algorithms build a predictive model from a training set for which the aerosol type associated with each mass spectrum is known a priori. Classification models were also created to differentiate aerosol within four broad categories: fertile soils, mineral/metallic particles, biological, and all other aerosols. Differentiation was accomplished using ~ 40 positive and negative spectral features. For the broad categorization, machine learning resulted in a classification accuracy of ~ 93 %. Classification of aerosols by specific type resulted in a classification accuracy of ~ 87 %. The ‘trained’ model was then applied to a ‘blind’ mixture of aerosols which was known to to be a subset of the training set. Model agreement was found on the presence of secondary organic aerosol, coated and uncoated mineral dust and fertile soil.


2020 ◽  
Author(s):  
Lucas Pereira ◽  
Max Frenzel ◽  
Duong Hoang ◽  
Raimon Tolosana-Delgado ◽  
Martin Rudolph ◽  
...  

2018 ◽  
Vol 11 (10) ◽  
pp. 5687-5699 ◽  
Author(s):  
Costa D. Christopoulos ◽  
Sarvesh Garimella ◽  
Maria A. Zawadowicz ◽  
Ottmar Möhler ◽  
Daniel J. Cziczo

Abstract. Compositional analysis of atmospheric and laboratory aerosols is often conducted via single-particle mass spectrometry (SPMS), an in situ and real-time analytical technique that produces mass spectra on a single-particle basis. In this study, classifiers are created using a data set of SPMS spectra to automatically differentiate particles on the basis of chemistry and size. Machine learning algorithms build a predictive model from a training set for which the aerosol type associated with each mass spectrum is known a priori. Our primary focus surrounds the growing of random forests using feature selection to reduce dimensionality and the evaluation of trained models with confusion matrices. In addition to classifying ∼20 unique, but chemically similar, aerosol types, models were also created to differentiate aerosol within four broader categories: fertile soils, mineral/metallic particles, biological particles, and all other aerosols. Differentiation was accomplished using ∼40 positive and negative spectral features. For the broad categorization, machine learning resulted in a classification accuracy of ∼93 %. Classification of aerosols by specific type resulted in a classification accuracy of ∼87 %. The “trained” model was then applied to a “blind” mixture of aerosols which was known to be a subset of the training set. Model agreement was found on the presence of secondary organic aerosol, coated and uncoated mineral dust, and fertile soil.


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