scholarly journals ISTDECO: In Situ Transcriptomics Decoding by Deconvolution

2021 ◽  
Author(s):  
Axel Andersson ◽  
Ferran Diego ◽  
Fred A. Hamprecht ◽  
Carolina Wählby
Keyword(s):  
Gene Expression ◽  
State Of The Art ◽  
Signal To Noise Ratio ◽  
Simulated Data ◽  
Signal To Noise ◽  
Tissue Samples ◽  
Image Series ◽  
Link Type ◽  
Efficient Decoding

In Situ Transcriptomics (IST) is a set of image-based transcriptomics approaches that enables localisation of gene expression directly in tissue samples. IST techniques produce multiplexed image series in which fluorescent spots are either present or absent across imaging rounds and colour channels. A spot’s presence and absence form a type of barcoded pattern that labels a particular type of mRNA. Therefore, the expression of a gene can be determined by localising the fluorescent spots and decode the barcode that they form. Existing IST algorithms usually do this in two separate steps: spot localisation and barcode decoding. Although these algorithms are efficient, they are limited by strictly separating the localisation and decoding steps. This limitation becomes apparent in regions with low signal-to-noise ratio or high spot densities. We argue that an improved gene expression decoding can be obtained by combining these two steps into a single algorithm. This allows for an efficient decoding that is less sensitive to noise and optical crowding.We present IST Decoding by Deconvolution (ISTDECO), a principled decoding approach combining spectral and spatial deconvolution into a single algorithm. We evaluate ISTDECO on simulated data, as well as on two real IST datasets, and compare with state-of-the-art. ISTDECO achieves state-of-the-art performance despite high spot densities and low signal-to-noise ratios. It is easily implemented and runs efficiently using a GPU.ISTDECO implementation, datasets and demos are available online at:github.com/axanderssonuu/istdeco

Multilag Correlation Estimators for Polarimetric Radar Measurements in the Presence of Noise

2012 ◽  
Vol 29 (6) ◽  
pp. 772-795 ◽  
Author(s):  
Lei Lei ◽  
Guifu Zhang ◽  
Richard J. Doviak ◽  
Robert Palmer ◽  
Boon Leng Cheong ◽  
...  
Keyword(s):  
Theoretical Analysis ◽  
Data Quality ◽  
Signal To Noise Ratio ◽  
Simulated Data ◽  
Radar Data ◽  
Polarimetric Radar ◽  
Signal To Noise ◽  
Spectral Moments ◽  
Radar Measurements

Abstract The quality of polarimetric radar data degrades as the signal-to-noise ratio (SNR) decreases. This substantially limits the usage of collected polarimetric radar data to high SNR regions. To improve data quality at low SNRs, multilag correlation estimators are introduced. The performance of the multilag estimators for spectral moments and polarimetric parameters is examined through a theoretical analysis and by the use of simulated data. The biases and standard deviations of the estimates are calculated and compared with those estimates obtained using the conventional method.

scholarly journals Discovery of allenyl acetylene, H2CCCHCCH, in TMC-1

2021 ◽  
Vol 647 ◽  
pp. L3 ◽  
Author(s):  
J. Cernicharo ◽  
C. Cabezas ◽  
M. Agúndez ◽  
B. Tercero ◽  
N. Marcelino ◽  
...  
Keyword(s):  
Column Density ◽  
State Of The Art ◽  
Rotational Temperature ◽  
Signal To Noise Ratio ◽  
Laboratory Data ◽  
The Other ◽  
Signal To Noise ◽  
Chemical Models ◽  
Upper Limit

We present the discovery in TMC-1 of allenyl acetylene, H2CCCHCCH, through the observation of nineteen lines with a signal-to-noise ratio ∼4–15. For this species, we derived a rotational temperature of 7 ± 1 K and a column density of 1.2 ± 0.2 × 1013 cm−2. The other well known isomer of this molecule, methyl diacetylene (CH3C4H), has also been observed and we derived a similar rotational temperature, Tr = 7.0 ± 0.3 K, and a column density for its two states (A and E) of 6.5 ± 0.3 × 1012 cm−2. Hence, allenyl acetylene and methyl diacetylene have a similar abundance. Remarkably, their abundances are close to that of vinyl acetylene (CH2CHCCH). We also searched for the other isomer of C5H4, HCCCH2CCH (1.4-Pentadiyne), but only a 3σ upper limit of 2.5 × 1012 cm−2 to the column density can be established. These results have been compared to state-of-the-art chemical models for TMC-1, indicating the important role of these hydrocarbons in its chemistry. The rotational parameters of allenyl acetylene have been improved by fitting the existing laboratory data together with the frequencies of the transitions observed in TMC-1.

Approximate Full Adders for Energy Efficient Image Processing Applications

2021 ◽  
pp. 2150235
Author(s):  
M. C. Parameshwara
Keyword(s):  
Energy Efficient ◽  
State Of The Art ◽  
Signal To Noise Ratio ◽  
Full Adder ◽  
Signal To Noise ◽  
Design Metrics ◽  
Standard Cell Library ◽  
Cell Library ◽  
Fair Comparison ◽  
Power Delay Product

This paper proposes six novel approximate 1-bit full adders (AFAs) for inexact computing. The six novel AFAs namely AFA1, AFA2, AFA3, AFA4, AFA5, and AFA6 are derived from state-of-the-art exact 1-bit full adder (EFA) architectures. The performance of these AFAs is compared with reported AFAs (RAAs) in terms of design metrics (DMs) and peak-signal-to-noise-ratio (PSNR). The DMs under consideration are power, delay, power-delay-product (PDP), energy-delay-product (EDP), and area. For a fair comparison, the EFAs and proposed AFAs along with RAAs are described in Verilog, simulated, and synthesized using Cadences’ RC tool, using generic 180 nm standard cell library. The unconstrained synthesis results show that: among all the proposed AFAs, the AFA1 and AFA2 are found to be energy-efficient adders with high PSNR. The AFA1 has a total [Formula: see text][Formula: see text][Formula: see text]W, [Formula: see text][Formula: see text]ps, [Formula: see text][Formula: see text]fJ, [Formula: see text][Formula: see text]Js, [Formula: see text][Formula: see text][Formula: see text]m2, and [Formula: see text][Formula: see text]dB. And the AFA2 has the total [Formula: see text][Formula: see text][Formula: see text]W, [Formula: see text][Formula: see text]ps, [Formula: see text][Formula: see text]fJ, [Formula: see text][Formula: see text]Js, [Formula: see text][Formula: see text][Formula: see text]m2, and [Formula: see text][Formula: see text]dB.

scholarly journals An Adaptive Image Inpainting Method Based on Continued Fractions Interpolation

2018 ◽  
Vol 2018 ◽  
pp. 1-16 ◽  
Author(s):  
Lei He ◽  
Yan Xing ◽  
Kangxiong Xia ◽  
Jieqing Tan
Keyword(s):  
Continued Fractions ◽  
State Of The Art ◽  
Signal To Noise Ratio ◽  
Subjective Evaluation ◽  
Image Inpainting ◽  
Rational Interpolation ◽  
Objective Evaluation ◽  
Experimental Results ◽  
Signal To Noise

In view of the drawback of most image inpainting algorithms by which texture was not prominent, an adaptive inpainting algorithm based on continued fractions was proposed in this paper. In order to restore every damaged point, the information of known pixel points around the damaged point was used to interpolate the intensity of the damaged point. The proposed method included two steps; firstly, Thiele’s rational interpolation combined with the mask image was used to interpolate adaptively the intensities of damaged points to get an initial repaired image, and then Newton-Thiele’s rational interpolation was used to refine the initial repaired image to get a final result. In order to show the superiority of the proposed algorithm, plenty of experiments were tested on damaged images. Subjective evaluation and objective evaluation were used to evaluate the quality of repaired images, and the objective evaluation was comparison of Peak Signal to Noise Ratios (PSNRs). The experimental results showed that the proposed algorithm had better visual effect and higher Peak Signal to Noise Ratio compared with the state-of-the-art methods.

In situ studies of metal–semiconductor interactions with synchrotron radiation

1998 ◽  
Vol 5 (3) ◽  
pp. 1050-1051
Author(s):  
D. E. Sayers ◽  
P. T. Goeller ◽  
B. I. Boyanov ◽  
R. J. Nemanich
Keyword(s):  
Synchrotron Radiation ◽  
Silicon Germanium ◽  
Signal To Noise Ratio ◽  
Thick Films ◽  
Strained Silicon ◽  
Reaction Products ◽  
Signal To Noise ◽  
In Situ Studies ◽  
And Performance

The capabilities and performance of a UHV system for in situ studies of metal–semiconductor interactions are described. The UHV system consists of interconnected deposition and analysis chambers, each of which is capable of maintaining a base pressure of approximately 1 × 10−10 torr. The deposited materials and their reaction products can be studied in situ with RHEED, XAFS, AES, XPS, UPS and ARUPS. Results from a study of the reaction of 0.7- and 1.7-monolayer-thick films of cobalt with strained silicon–germanium alloys are presented. The signal-to-noise ratio obtained in these experiments indicates that the apparatus is capable of supporting in situ EXAFS studies of ∼0.1-monolayer-thick films.

scholarly journals Automated Multimodal image fusion for brain tumor detection

2021 ◽  
Vol 3 (1) ◽  
pp. 68-82
Author(s):  
Harpreet Kaur ◽  
◽  
Deepika Koundal ◽  
Virendar Kadyan ◽  
Navneet Kaur ◽  
...  
Keyword(s):  
Image Fusion ◽  
State Of The Art ◽  
Signal To Noise Ratio ◽  
Visual Image ◽  
Fusion Rule ◽  
Resonance Imaging ◽  
Signal To Noise ◽  
Multiple Images ◽  
Fused Image ◽  
Magnetic Resonance Imaging Mri

In medical domain, various multimodalities such as Computer tomography (CT) and Magnetic resonance imaging (MRI) are integrated into a resultant fused image. Image fusion (IF) is a method by which vital information can be preserved by extracting all important information from the multiple images into the resultant fused image. The analytical and visual image quality can be enhanced by the integration of different images. In this paper, a new algorithm has been proposed on the basis of guided filter with new fusion rule for the fusion of different imaging modalities such as MRI and Fluorodeoxyglucose images of brain for the detection of tumor. The performance of the proposed method has been evaluated and compared with state-of-the-art image fusion techniques using various qualitative as well as quantitative evaluation metrics. From the results, it has been observed that more information has achieved on edges and content visibility is also high as compared to the other techniques which makes it more suitable for real applications. The experimental results are evaluated on the basis of with-reference and without-references metric such as standard deviation, entropy, peak signal to noise ratio, mutual information etc.

scholarly journals Overlap graph-based generation of haplotigs for diploids and polyploids

2018 ◽  
Author(s):  
Jasmijn A. Baaijens ◽  
Alexander Schönhuth
Keyword(s):  
Recent Work ◽  
Genome Assembly ◽  
De Novo ◽  
Iterative Scheme ◽  
State Of The Art ◽  
Simulated Data ◽  
Specific Sequence ◽  
New Approach ◽  
Link Type ◽  
Polyploid Genome

AbstractHaplotype aware genome assembly plays an important role in genetics, medicine, and various other disciplines, yet generation of haplotype-resolved de novo assemblies remains a major challenge. Beyond distinguishing between errors and true sequential variants, one needs to assign the true variants to the different genome copies. Recent work has pointed out that the enormous quantities of traditional NGS read data have been greatly underexploited in terms of haplotig computation so far, which reflects that methodology for reference independent haplotig computation has not yet reached maturity. We present POLYTE (POLYploid genome fitTEr) as a new approach to de novo generation of haplotigs for diploid and polyploid genomes. Our method follows an iterative scheme where in each iteration reads or contigs are joined, based on their interplay in terms of an underlying haplotype-aware overlap graph. Along the iterations, contigs grow while preserving their haplotype identity. Benchmarking experiments on both real and simulated data demonstrate that POLYTE establishes new standards in terms of error-free reconstruction of haplotype-specific sequence. As a consequence, POLYTE outperforms state-of-the-art approaches in various relevant aspects, where advantages become particularly distinct in polyploid settings. POLYTE is freely available as part of the HaploConduct package at https://github.com/HaploConduct/HaploConduct, implemented in Python and C++.

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