43 research outputs found
W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping
In fluorescence microscopy live-cell imaging, there is a critical trade-off
between the signal-to-noise ratio and spatial resolution on one side, and the
integrity of the biological sample on the other side. To obtain clean
high-resolution (HR) images, one can either use microscopy techniques, such as
structured-illumination microscopy (SIM), or apply denoising and
super-resolution (SR) algorithms. However, the former option requires multiple
shots that can damage the samples, and although efficient deep learning based
algorithms exist for the latter option, no benchmark exists to evaluate these
algorithms on the joint denoising and SR (JDSR) tasks. To study JDSR on
microscopy data, we propose such a novel JDSR dataset, Widefield2SIM (W2S),
acquired using a conventional fluorescence widefield and SIM imaging. W2S
includes 144,000 real fluorescence microscopy images, resulting in a total of
360 sets of images. A set is comprised of noisy low-resolution (LR) widefield
images with different noise levels, a noise-free LR image, and a corresponding
high-quality HR SIM image. W2S allows us to benchmark the combinations of 6
denoising methods and 6 SR methods. We show that state-of-the-art SR networks
perform very poorly on noisy inputs. Our evaluation also reveals that applying
the best denoiser in terms of reconstruction error followed by the best SR
method does not necessarily yield the best final result. Both quantitative and
qualitative results show that SR networks are sensitive to noise and the
sequential application of denoising and SR algorithms is sub-optimal. Lastly,
we demonstrate that SR networks retrained end-to-end for JDSR outperform any
combination of state-of-the-art deep denoising and SR networksComment: ECCVW 2020. Project page: \<https://github.com/ivrl/w2s
Automatic Hotspots Detection for Intracellular Calcium Analysis in Fluorescence Microscopic Videos
In recent years, life-cell imaging techniques and their software applications have become powerful tools to investigate complex biological mechanisms such as calcium signalling. In this paper, we propose an automated framework to detect areas inside cells that show changes in their calcium concentration i.e. the regions of interests or hotspots, based on videos taken after loading living mouse cardiomyocytes with fluorescent calcium reporter dyes. The proposed system allows an objective and efficient analysis through the following four key stages: (1) Pre-processing to enhance video quality, (2) First level segmentation to detect candidate hotspots based on adaptive thresholding on the frame level, (3) Second-level segmentation to fuse and identify the best hotspots from the entire video by proposing the concept of calcium fluorescence hit-ratio, and (4) Extraction of the changes of calcium fluorescence over time per hotspot. From the extracted signals, different measurements are calculated such as maximum peak amplitude, area under the curve, peak frequency, and inter-spike interval of calcium changes. The system was tested using calcium imaging data collected from Heart muscle cells. The paper argues that the automated proposal offers biologists a tool to speed up the processing time and mitigate the consequences of inter-intra observer variability
A functional variant in the Stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork
There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.This research was supported by grants from the Spanish Ministry of Science and Innovation (AGL2009-09779 and AGL2012-33529). RRF is recipient of a PhD scholarship from the Spanish Ministry of Science and Innovation (BES-2010-034607). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of manuscript
Deciphering chemical order/disorder and material properties at the single-atom level
Correlating 3D arrangements of atoms and defects with material properties and
functionality forms the core of several scientific disciplines. Here, we
determined the 3D coordinates of 6,569 iron and 16,627 platinum atoms in a
model iron-platinum nanoparticle system to correlate 3D atomic arrangements and
chemical order/disorder with material properties at the single-atom level. We
identified rich structural variety and chemical order/disorder including 3D
atomic composition, grain boundaries, anti-phase boundaries, anti-site point
defects and swap defects. We show for the first time that experimentally
measured 3D atomic coordinates and chemical species with 22 pm precision can be
used as direct input for first-principles calculations of material properties
such as atomic magnetic moments and local magnetocrystalline anisotropy. This
work not only opens the door to determining 3D atomic arrangements and chemical
order/disorder of a wide range of nanostructured materials with high precision,
but also will transform our understanding of structure-property relationships
at the most fundamental level.Comment: 21 pages, 4 figure
Three-dimensional winged nanocone optical antennas
We introduce 3D optical antennas based on winged nanocones. The antennas support particle plasmon oscillations with current distributions that facilitate transformation of transverse far-field radiation to strong longitudinal local fields near the cone apices. We characterize the optical responses of the antennas by their extinction spectra and by second-harmonic generation microscopy with cylindrical vector beams. The results demonstrate a new 3D polarization- controllable optical antenna for applications in apertureless near-field microscopy, spectroscopy, and plasmonic sensing. (C) 2014 Optical Society of Americ
Artefacts mediating practices across time and space: sociocultural studies of material conditions for learning and remembering
The theme of this symposium is to explore the material conditions of learning and remembering from a sociocultural perspective. We do this in four different empirical contexts. Learning and remembering are understood as meaning-making processes that are dependent on and co-constituted by mediating tools that enable practices to extend across time and space. Our interests are precisely in what ways the “tools” people employ in these studies mediate activities of learning and remembering, and how they contribute to the organization of collective forms of knowing. We also address how we analyze the specific material features of tools that co-determine the unfolding of the activities