scholarly journals Griottes: a generalist tool for network generation from segmented tissue images

2022 ◽  
Author(s):  
Gustave Ronteix ◽  
Valentin Bonnet ◽  
Sebastien Sart ◽  
Jeremie Sobel ◽  
Elric Esposito ◽  
...  

Microscopy techniques and image segmentation algorithms have improved dramatically this decade, leading to an ever increasing amount of biological images and a greater reliance on imaging to investigate biological questions. This has created a need for methods to extract the relevant information on the behaviors of cells and their interactions, while reducing the amount of computing power required to organize this information. This task can be performed by using a network representation in which the cells and their properties are encoded in the nodes, while the neighborhood interactions are encoded by the links. Here we introduce Griottes, an open-source tool to build the "network twin" of 2D and 3D tissues from segmented microscopy images. We show how the library can provide a wide range of biologically relevant metrics on individual cells and their neighborhoods, with the objective of providing multi-scale biological insights. The library's capacities are demonstrated on different image and data types. This library is provided as an open-source tool that can be integrated into common image analysis workflows to increase their capacities.

2021 ◽  
Author(s):  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Martin Högbom ◽  
Hugo Lebrette

Microcrystal electron diffraction (MicroED) has the potential to considerably impact the field of structural biology. Indeed, the method can solve atomic structures of a wide range of molecules, beyond the reach of single particle cryo-electron microscopy, exploiting crystals too small for X-ray diffraction (XRD) even using X-ray free-electron lasers. However, until the first unknown protein structure – a R2-like ligand binding oxidase from Sulfolobus acidocaldarius (SaR2lox) – was recently solved at 3.0 Å resolution, MicroED had only been used to study known protein structures previously obtained by XRD. Here, after adapting sample preparation protocols, the structure of the SaR2lox protein originally solved by MicroED was redetermined by XRD at 2.1 Å resolution. In light of the higher resolution XRD data and taking into account experimental differences of the methods, the quality of the MicroED structure is examined. The analysis demonstrates that MicroED provided an overall accurate model, revealing biologically relevant information specific to SaR2lox, such as the absence of an ether cross-link, but did not allow to detect the presence of a ligand visible by XRD in the protein binding pocket. Furthermore, strengths and weaknesses of MicroED compared to XRD are discussed in the perspective of this real-life protein example. The study provides fundaments to help MicroED become a method of choice for solving novel protein structures.


2021 ◽  
Author(s):  
Sehi L'Yi ◽  
Qianwen Wang ◽  
Fritz Lekschas ◽  
Nils Gehlenborg

The combination of diverse data types and analysis tasks in genomics has resulted in the development of a wide range of visualization techniques and tools. However, most existing tools are tailored to a specific problem or data type and offer limited customization, making it challenging to optimize visualizations for new analysis tasks or datasets. To address this challenge, we designed Gosling—a grammar for interactive and scalable genomics data visualization. Gosling balances expressiveness for comprehensive multi-scale genomics data visualizations with accessibility for domain scientists. Our accompanying JavaScript toolkit called Gosling.js provides scalable and interactive rendering. Gosling.js is built on top of an existing platform for web-based genomics data visualization to further simplify the visualization of common genomics data formats. We demonstrate the expressiveness of the grammar through a variety of real-world examples. Furthermore, we show how Gosling supports the design of novel genomics visualizations. An online editor and examples of Gosling.js and its source code are available at https://gosling.js.org.


2020 ◽  
Vol 25 ◽  
pp. 41-54
Author(s):  
Tuyen Le ◽  
H. David Jeong ◽  
Stephen B. Gilbert ◽  
Evgeny Chukharev-Hudilainen

Open data standards (e.g. LandXML, TransXML, CityGML) are a key to addressing the interoperability issue in exchanging civil information modeling (CIM) data throughout the project life-cycle. Since these schemas include rich sets of data types covering a wide range of assets and disciplines, model view definitions (MVDs) which define subsets of a schema are required to specify what types of data to be shared in accordance with a specific exchange scenario. The traditional procedure for generating and implementing MVDs is time-consuming and laborious as entities and attributes relevant to a particular data exchange context are manually identified by domain experts. This paper presents a method that can locate relevant information from a source XML data schema for a specific domain based on the user's keyword. The study employs a semantic resource of civil engineering terms to understand the semantics of a keyword-based query. The study also introduces a novel context-based search technique for retrieving related entities and their referenced objects. The developed method was tested on a gold standard of several LandXML subschemas. The experiment results show that the semantic MVD retrieval algorithm achieves a mean average precision of nearly 90%. The research is original, being a novel method for extracting partial civil information models given a keyword from the end user. The method is expected to become a fundamental tool assisting professionals in extracting data from complex digital datasets.


2021 ◽  
Author(s):  
Rebekah Rodriguez ◽  
Martin Boerwinkle ◽  
Paul Silvia

To expand the tools available to arts researchers in psychology, we present the Open Gallery for Arts Research (OGAR), a free, open-source tool for studying visitor behavior within an online gallery environment. OGAR is highly extensible, allowing researchers to modify the environment to test different hypotheses, and it affords assessing a wide range of outcome variables. After describing the tool and its development, we present a proof-of-concept study that evaluates OGAR’s usability and performance and illustrates some ways that it can be used to study the psychology of virtual visits. With a sample of 44 adults from an online participant panel who freely explored OGAR, we observed that OGAR had good usability based on high scores on the System Usability Scale and rare instances of self-reported nausea, among other usability markers. Furthermore, using position and viewing data provided by OGAR, we found that participants navigated the gallery and interacted with the artwork in predictable and coherent ways that resembled visitor behavior in real-world art museums. OGAR appears to be a useful tool for researchers and art professionals interested in how people navigate and experience virtual and real art spaces.


2021 ◽  
Author(s):  
Giacomo Nodjoumi ◽  
Luca Guallini ◽  
Roberto Orosei ◽  
Luca Penasa ◽  
Angelo Pio Rossi

<p>The objective of this work is to present a new Free and Open-Source Software (FOSS) to read and convert to multiple data formats data acquired by the Mars Advanced Radar for Subsurface and Ionosphere Sounding (MARSIS) instrument on board Mars Express (MEX) orbiting Mars since 2005.</p><p>MARSIS is an orbital synthetic aperture radar sounder that operates with dual-frequency between 1.3 and 5.5 MHz and wavelengths between 230 and 55 m for subsurface sounding. The Experiment Data Record (EDR) and Reduced Data Record (RDR) datasets are available for download on public access platforms such as the Planetary Science Archive fo ESA and the PDS-NASA Orbital Data Explorer (ODE).</p><p>These datasets have been widely used for different research, focused to study the subsurface of the red planet up to a depth of a few kilometres, and especially for studying ice caps and looking for subsurface ice and water deposits, producing relevant results. (Lauro et al., 2020; Orosei et al., 2020)</p><p>The Python tool presented here is capable of reading common data types used to distribute MARSIS dataset and then converting into multiple data formats. Users can interactively configure data source, destination, pre-processing and type of outputs among:</p><ul><li>Geopackages: for GIS software, is a single self-contained file containing a layer in which are stored all parameters for each file processed.</li> <li>Numpy array dump: for fast reading and analysis of original data for both frequencies.</li> <li>PNG images: for fast inspections, created for each frequency, and saved. Image pre-processing filters, such as image-denoising, standardization and normalization, can be selected by user.</li> <li>SEG-Y: for analysing data with seismic interpretation and processing software, see e.g. OpendTect, consist of a SEG-Y file for each frequency.</li> </ul><p>SEG-Y capability is the most relevant feature, since is not present in any of other FOSS tool and give to researchers the possibility to visualize radargrams in advanced software, specific for seismic interpretation and analysis, making it possible to interpret the data in a fully three-dimensional environment.</p><p>This tool, available on zenodo (Nodjoumi, 2021), has been developed completely in Python 3, relying only on open-source libraries, compatible with principal operating systems and with parallel processing capabilities, granting easy scalability and usability across a wide range of computing machines. It is also highly customizable since it can be expanded adding processing steps before export or new types of output. An additional module to ingest data directly into PostgreSQL/PostGIS and a module to interact directly with ACT-REACT interface of data platforms are under development.</p><p>Acknowledgments:</p><p>This study is within the Europlanet 2024 RI, and it has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 871149. </p><p>References:</p><p>Lauro, S. E. et al. (2020) ‘Multiple subglacial water bodies below the south pole of Mars unveiled by new MARSIS data’, doi: 10.1038/s41550-020-1200-6.</p><p>Nodjoumi, G. (2021) 'MARSIS-xDR-READER', doi: 10.5281/zenodo.4436199</p><p>Orosei, R. et al. (2020) ‘The global search for liquid water on mars from orbit: Current and future perspectives’, doi: 10.3390/life10080120.</p>


2020 ◽  
pp. 100001
Author(s):  
Wilko Heitkoetter ◽  
Bruno U. Schyska ◽  
Danielle Schmidt ◽  
Wided Medjroubi ◽  
Thomas Vogt ◽  
...  

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.


Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4288
Author(s):  
Fernanda Malhão ◽  
Ana Catarina Macedo ◽  
Carla Costa ◽  
Eduardo Rocha ◽  
Alice Abreu Ramos

Fucoxanthin (Fx) is a carotenoid derived from marine organisms that exhibits anticancer activities. However, its role as a potential drug adjuvant in breast cancer (BC) treatment is still poorly explored. Firstly, this study investigated the cytotoxic effects of Fx alone and combined with doxorubicin (Dox) and cisplatin (Cis) on a panel of 2D-cultured BC cell lines (MCF7, SKBR3 and MDA-MB-231) and one non-tumoral cell line (MCF12A). Fucoxanthin induced cytotoxicity against all the cell lines and potentiated Dox cytotoxic effects towards the SKBR3 and MDA-MB-231 cells. The combination triggering the highest cytotoxicity (Fx 10 µM + Dox 1 µM in MDA-MB-231) additionally showed significant induction of cell death and genotoxic effects, relative to control. In sequence, the same combination was tested on 3D cultures using a multi-endpoint approach involving bioactivity assays and microscopy techniques. Similar to 2D cultures, the combination of Fx and Dox showed higher cytotoxic effects on 3D cultures compared to the isolated compounds. Furthermore, this combination increased the number of apoptotic cells, decreased cell proliferation, and caused structural and ultrastructural damages on the 3D models. Overall, our findings suggest Fx has potential to become an adjuvant for Dox chemotherapy regimens in BC treatment.


Minerals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 347
Author(s):  
Carsten Laukamp ◽  
Andrew Rodger ◽  
Monica LeGras ◽  
Heta Lampinen ◽  
Ian C. Lau ◽  
...  

Reflectance spectroscopy allows cost-effective and rapid mineral characterisation, addressing mineral exploration and mining challenges. Shortwave (SWIR), mid (MIR) and thermal (TIR) infrared reflectance spectra are collected in a wide range of environments and scales, with instrumentation ranging from spaceborne, airborne, field and drill core sensors to IR microscopy. However, interpretation of reflectance spectra is, due to the abundance of potential vibrational modes in mineral assemblages, non-trivial and requires a thorough understanding of the potential factors contributing to the reflectance spectra. In order to close the gap between understanding mineral-diagnostic absorption features and efficient interpretation of reflectance spectra, an up-to-date overview of major vibrational modes of rock-forming minerals in the SWIR, MIR and TIR is provided. A series of scripts are proposed that allow the extraction of the relative intensity or wavelength position of single absorption and other mineral-diagnostic features. Binary discrimination diagrams can assist in rapidly evaluating mineral assemblages, and relative abundance and chemical composition of key vector minerals, in hydrothermal ore deposits. The aim of this contribution is to make geologically relevant information more easily extractable from reflectance spectra, enabling the mineral resources and geoscience communities to realise the full potential of hyperspectral sensing technologies.


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