Leaves from genetically unique Juglans regia plants were scanned using X-ray micro-computed tomography (microCT) on the X-ray μCT beamline (8.3.2) at the Advanced Light Source (ALS) in Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA USA). Soil samples were collected in Fall of 2017 from the riparian oak forest located at the Russell Ranch Sustainable Agricultural Institute at the University of California Davis. The soil was sieved through a 2 mm mesh and was air dried before imaging. A single soil aggregate was scanned at 23 keV using the 10x objective lens with a pixel resolution of 650 nanometers on beamline 8.3.2 at the ALS. Additionally, a drought stressed almond flower bud (Prunus dulcis) from a plant housed at the University of California, Davis, was scanned using a 4x lens with a pixel resolution of 1.72 µm on beamline 8.3.2 at the ALS Raw tomographic image data was reconstructed using TomoPy. Reconstructions were converted to 8-bit tif or png format using ImageJ or the PIL package in Python before further processing. Images were annotated using Intel’s Computer Vision Annotation Tool (CVAT) and ImageJ. Both CVAT and ImageJ are free to use and open source. Leaf images were annotated in following Théroux-Rancourt et al. (2020). Specifically, Hand labeling was done directly in ImageJ by drawing around each tissue; with 5 images annotated per leaf. Care was taken to cover a range of anatomical variation to help improve the generalizability of the models to other leaves. All slices were labeled by Dr. Mina Momayyezi and Fiona Duong.To annotate the flower bud and soil aggregate, images were imported into CVAT. The exterior border of the bud (i.e. bud scales) and flower were annotated in CVAT and exported as masks. Similarly, the exterior of the soil aggregate and particulate organic matter identified by eye were annotated in CVAT and exported as masks. To annotate air spaces in both the bud and soil aggregate, images were imported into ImageJ. A gaussian blur was applied to the image to decrease noise and then the air space was segmented using thresholding. After applying the threshold, the selected air space region was converted to a binary image with white representing the air space and black representing everything else. This binary image was overlaid upon the original image and the air space within the flower bud and aggregate was selected using the “free hand” tool. Air space outside of the region of interest for both image sets was eliminated. The quality of the air space annotation was then visually inspected for accuracy against the underlying original image; incomplete annotations were corrected using the brush or pencil tool to paint missing air space white and incorrectly identified air space black. Once the annotation was satisfactorily corrected, the binary image of the air space was saved. Finally, the annotations of the bud and flower or aggregate and organic matter were opened in ImageJ and the associated air space mask was overlaid on top of them forming a three-layer mask suitable for training the fully convolutional network. All labeling of the soil aggregate and soil aggregate images was done by Dr. Devin Rippner. These images and annotations are for training deep learning models to identify different constituents in leaves, almond buds, and soil aggregates Limitations: For the walnut leaves, some tissues (stomata, etc.) are not labeled and only represent a small portion of a full leaf. Similarly, both the almond bud and the aggregate represent just one single sample of each. The bud tissues are only divided up into buds scales, flower, and air space. Many other tissues remain unlabeled. For the soil aggregate annotated labels are done by eye with no actual chemical information. Therefore particulate organic matter identification may be incorrect. Resources in this dataset:Resource Title: Annotated X-ray CT images and masks of a Forest Soil Aggregate. File Name: forest_soil_images_masks_for_testing_training.zipResource Description: This aggregate was collected from the riparian oak forest at the Russell Ranch Sustainable Agricultural Facility. The aggreagate was scanned using X-ray micro-computed tomography (microCT) on the X-ray μCT beamline (8.3.2) at the Advanced Light Source (ALS) in Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA USA) using the 10x objective lens with a pixel resolution of 650 nanometers. For masks, the background has a value of 0,0,0; pores spaces have a value of 250,250, 250; mineral solids have a value= 128,0,0; and particulate organic matter has a value of = 000,128,000. These files were used for training a model to segment the forest soil aggregate and for testing the accuracy, precision, recall, and f1 score of the model.Resource Title: Annotated X-ray CT images and masks of an Almond bud (P. Dulcis). File Name: Almond_bud_tube_D_P6_training_testing_images_and_masks.zipResource Description: Drought stressed almond flower bud (Prunis dulcis) from a plant housed at the University of California, Davis, was scanned by X-ray micro-computed tomography (microCT) on the X-ray μCT beamline (8.3.2) at the Advanced Light Source (ALS) in Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA USA) using the 4x lens with a pixel resolution of 1.72 µm using. For masks, the background has a value of 0,0,0; air spaces have a value of 255,255, 255; bud scales have a value= 128,0,0; and flower tissues have a value of = 000,128,000. These files were used for training a model to segment the almond bud and for testing the accuracy, precision, recall, and f1 score of the model.Resource Software Recommended: Fiji (ImageJ),url: https://imagej.net/software/fiji/downloads Resource Title: Annotated X-ray CT images and masks of Walnut leaves (J. Regia) . File Name: 6_leaf_training_testing_images_and_masks_for_paper.zipResource Description: Stems were collected from genetically unique J. regia accessions at the 117 USDA-ARS-NCGR in Wolfskill Experimental Orchard, Winters, California USA to use as scion, and were grafted by Sierra Gold Nursery onto a commonly used commercial rootstock, RX1 (J. microcarpa × J. regia). We used a common rootstock to eliminate any own-root effects and to simulate conditions for a commercial walnut orchard setting, where rootstocks are commonly used. The grafted saplings were repotted and transferred to the Armstrong lathe house facility at the University of California, Davis in June 2019, and kept under natural light and temperature. Leaves from each accession and treatment were scanned using X-ray micro-computed tomography (microCT) on the X-ray μCT beamline (8.3.2) at the Advanced Light Source (ALS) in Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA USA) using the 10x objective lens with a pixel resolution of 650 nanometers. For masks, the background has a value of 170,170,170; Epidermis value= 85,85,85; Mesophyll value= 0,0,0; Bundle Sheath Extension value= 152,152,152; Vein value= 220,220,220; Air value = 255,255,255.Resource Software Recommended: Fiji (ImageJ),url: https://imagej.net/software/fiji/downloads

We present Meta4P (MetaProteins-Peptides-PSMs Parser), an easy-to-use bioinformatic application designed to integrate label-free quantitative metaproteomic data with taxonomic and functional annotations. Meta4P can retrieve, filter, and process identification and quantification data from three levels of inputs (proteins, peptides, PSMs) in different file formats. Abundance data can be combined with taxonomic and functional information and aggregated at different and customizable levels, including taxon-specific functions and pathways. Meta4P output tables, available in various formats, are ready to be used as inputs for downstream statistical analyses. This user-friendly tool is expected to provide a useful contribution to the field of metaproteomic data analysis, helping make it more manageable and straightforward.

Manually disambiguated ground-truth for the Gnome GTK project supporting the replication of the results presented in the article "gambit – An Open Source Name Disambiguation Tool for Version Control Systems".

Please request access via zenodo.

This repository contains the data and results from the paper "Code Smells Detection via Code Review: An Empirical Study" submitted to ESEM 2020. 1. data folder The data folder contains the retrieved 269 reviews that discuss code smells. Each review includes four parts: Code Change URL, Code Smell Term, Code Smell Discussion, and Source Code URL. 2. scripts floder The scripts folder contains the Python script that was used to search for code smell terms and the list of code smell terms. smell-term/general_smell_terms.txt contains general code smell terms, such as "code smell". smell-term/specific_smell_terms.txt contains specific code smell terms, such as "dead code". smell-term/misspelling_terms_of_smell.txt contains the misspelling terms of 'smell', such as "ssell". get_changes.py is used for getting code changes from OpenStack. get_comments.py is used for getting review comments for each code change. smell_search.py is used for searching review comments that contain code smell terms. 3. project folder The project folder contains the MAXQDA project files. The files can be opened by MAXQDA 12 or higher versions, which are available at https://www.maxqda.com/ for download. You may also use the free 14-day trial version of MAXQDA 2018, which is available at https://www.maxqda.com/trial for download. Data Labeling & Encoding for RQ2.mx12 is the results of data labeling and encoding for RQ2, which were analyzed by the MAXQDA tool. Data Labeling & Encoding for RQ3.mx12 is the results of data labeling and encoding for RQ3, which were analyzed by the MAXQDA tool.

Label-free quantification based on data-independent acquisition (DIA) workflows is increasingly popular. Several software tools have been recently published or are commercially available. The present study focuses on the critical evaluation of three different software packages (Progenesis, synapter and ISOQuant) supporting ion-mobility enhanced DIA data. In order to benchmark the label-free quantification performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, E.coli). This model data set simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and down-regulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on the variation of reported protein quantities between technical replicates.

Labeled high-resolution orthoimagery time-series of an alluvial river corridor; Elwha River, Washington, USA.

Daniel Buscombe, Marda Science LLC

There are two datasets in this data release:

1. Model training dataset. A manually (or semi-manually) labeled image dataset that was used to train and evaluate a machine (deep) learning model designed to identify subaerial accumulations of large wood, alluvial sediment, water, and vegetation in orthoimagery of alluvial river corridors in forested catchments.

2. Model output dataset. A labeled image dataset that uses the aforementioned model to estimate subaerial accumulations of large wood, alluvial sediment, water, and vegetation in a larger orthoimagery dataset of alluvial river corridors in forested catchments.

All of these label data are derived from raw gridded data that originate from the U.S. Geological Survey (Ritchie et al., 2018). That dataset consists of 14 orthoimages of the Middle Reach (MR, in between the former Aldwell and Mills reservoirs) and 14 corresponding Lower Reach (LR, downstream of the former Mills reservoir) of the Elwha River, Washington, collected between the period 2012-04-07 and 2017-09-22. That orthoimagery was generated using SfM photogrammetry (following Over et al., 2021) using a photographic camera mounted to an aircraft wing. The imagery capture channel change as it evolved under a ~20 Mt sediment pulse initiated by the removal of the two dams. The two reaches are the ~8 km long Middle Reach (MR) and the lower-gradient ~7 km long Lower Reach (LR).

The orthoimagery have been labeled (pixelwise, either manually or by an automated process) according to the following classes (inter class in the label data in parentheses):

1. vegetation / other (0)

2. water (1)

3. sediment (2)

4. large wood (3)

1. Model training dataset.

Imagery was labeled using a combination of the open-source software Doodler (Buscombe et al., 2021; https://github.com/Doodleverse/dash_doodler) and hand-digitization using QGIS at 1:300 scale, rasterizeing the polygons, and gridded and clipped in the same way as all other gridded data. Doodler facilitates relatively labor-free dense multiclass labeling of natural imagery, enabling relatively rapid training dataset creation. The final training dataset consists of 4382 images and corresponding labels, each 1024 x 1024 pixels and representing just over 5% of the total data set. The training data are sampled approximately equally in time and in space among both reaches. All training and validation samples purposefully included all four label classes, to avoid model training and evaluation problems associated with class imbalance (Buscombe and Goldstein, 2022).

Data are provided in geoTIFF format. The imagery and label grids (imagery) are reprojected to be co-located in the NAD83(2011) / UTM zone 10N projection, and to consist of 0.125 x 0.125m pixels.

Pixel-wise labels measurements such as these facilitate development and evaluation of image segmentation, image classification, object-based image-analysis (OBIA), and object-in-image detection models, and numerous potential other machine learning models for the general purposes of river corridor classification, description, enumeration, inventory, and process or state quantification. For example this dataset may serve in transfer learning contexts for application in different river or coastal environments or for different tasks or class ontologies.

Files:

1. Labels_used_for_model_training_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 63 MB, label tiffs

2. Model_training_ images1of4.zip, 1.5 GB, imagery tiffs

3. Model_training_ images2of4.zip, 1.5 GB, imagery tiffs

4. Model_training_ images3of4.zip, 1.7 GB, imagery tiffs

5. Model_training_ images4of4.zip, 1.6 GB, imagery tiffs

2. Model output dataset.

Imagery was labeled using a deep-learning based semantic segmentation model (Buscombe, 2023) trained specifically for the task using the Segmentation Gym (Buscombe and Goldstein, 2022) modeling suite. We use the software package Segmentation Gym (Buscombe and Goldstein, 2022) to fine-tune a Segformer (Xie et al., 2021) deep learning model for semantic image segmentation. We take the instance (i.e. model architecture and trained weights) of the model of Xie et al. (2021), itself fine-tuned on ADE20k dataset (Zhou et al., 2019) at resolution 512x512 pixels, and fine-tune it on our 1024x1024 pixel training data consisting of 4-class label images.

The spatial extent of the imagery in the MR is 455157.2494695878122002,5316532.9804129302501678 : 457076.1244695878122002,5323771.7304129302501678. Imagery width is 15351 pixels and imagery height is 57910 pixels. The spatial extent of the imagery in the LR is 457704.9227139975992031,5326631.3750646486878395 : 459241.6727139975992031,5333311.0000646486878395. Imagery width is 12294 pixels and imagery height is 53437 pixels. Data are provided in Cloud-Optimzed geoTIFF (COG) format. The imagery and label grids (imagery) are reprojected to be co-located in the NAD83(2011) / UTM zone 10N projection, and to consist of 0.125 x 0.125m pixels. All grids have been clipped to the union of extents of active channel margins during the period of interest.

Reach-wide pixel-wise measurements such as these facilitate comparison of wood and sediment storage at any scale or location. These data may be useful for studying the morphodynamics of wood-sediment interactions in other geomorphically complex channels, wood storage in channels, the role of wood in ecosystems and conservation or restoration efforts.

Files:

1. Elwha_MR_labels_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 9.67 MB, label COGs from Elwha River Middle Reach (MR)

2. ElwhaMR_ imagery_ part1_ of 2.zip, 566 MB, imagery COGs from Elwha River Middle Reach (MR)

3. ElwhaMR imagery_ part2_ of_ 2.zip, 618 MB, imagery COGs from Elwha River Middle Reach (MR)

3. Elwha_LR_labels_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 10.96 MB, label COGs from Elwha River Lower Reach (LR)

4. ElwhaLR_ imagery_ part1_ of 2.zip, 622 MB, imagery COGs from Elwha River Middle Reach (MR)

5. ElwhaLR imagery_ part2_ of_ 2.zip, 617 MB, imagery COGs from Elwha River Middle Reach (MR)

This dataset was created using open-source tools of the Doodleverse, a software ecosystem for geoscientific image segmentation, by Daniel Buscombe (https://github.com/dbuscombe-usgs) and Evan Goldstein (https://github.com/ebgoldstein). Thanks to the contributors of the Doodleverse!. Thanks especially Sharon Fitzpatrick (https://github.com/2320sharon) and Jaycee Favela for contributing labels.

References

• Buscombe, D. (2023). Doodleverse/Segmentation Gym SegFormer models for 4-class (other, water, sediment, wood) segmentation of RGB aerial orthomosaic imagery (v1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8172858

• Buscombe, D., Goldstein, E. B., Sherwood, C. R., Bodine, C., Brown, J. A., Favela, J., et al. (2021). Human-in-the-loop segmentation of Earth surface imagery. Earth and Space Science, 9, e2021EA002085. https://doi.org/10.1029/2021EA002085

• Buscombe, D., & Goldstein, E. B. (2022). A reproducible and reusable pipeline for segmentation of geoscientific imagery. Earth and Space Science, 9, e2022EA002332. https://doi.org/10.1029/2022EA002332 See: https://github.com/Doodleverse/segmentation_gym

• Over, J.R., Ritchie, A.C., Kranenburg, C.J., Brown, J.A., Buscombe, D., Noble, T., Sherwood, C.R., Warrick, J.A., and Wernette, P.A., 2021, Processing coastal imagery with Agisoft Metashape Professional Edition, version 1.6—Structure from motion workflow documentation: U.S. Geological Survey Open-File Report 2021–1039, 46 p., https://doi.org/10.3133/ofr20211039.

• Ritchie, A.C., Curran, C.A., Magirl, C.S., Bountry, J.A., Hilldale, R.C., Randle, T.J., and Duda, J.J., 2018, Data in support of 5-year sediment budget and morphodynamic analysis of Elwha River following dam removals: U.S. Geological Survey data release, https://doi.org/10.5066/F7PG1QWC.

• Xie, E., Wang, W., Yu, Z., Anandkumar, A., Alvarez, J.M. and Luo, P., 2021. SegFormer: Simple and efficient design for semantic segmentation with transformers. Advances in Neural Information Processing Systems, 34, pp.12077-12090.

• Zhou, B., Zhao, H., Puig, X., Xiao, T., Fidler, S., Barriuso, A. and Torralba, A., 2019. Semantic understanding of scenes through the ade20k dataset. International Journal of Computer Vision, 127, pp.302-321.

Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183) metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤0.19) when quantifying the two internal standards and had higher abundance correlation (≥0.92) when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html.

This repository holds the necessary data and code as well as a descriptive Readme file that was used for our publication "A formative usability study of workflow management systems in label-free digital pathology" by Markus Jelonek et al. (2022), submitted to F1000Research. Abstract: We present a formative usability study that investigates the usability of different workflow management systems in the field of biomedical data analysis. Specifically, we study a task in the field of so-called label-free digital pathology and investigate one graphical user interface based workflow and one script-based workflow to solve the task. Our main intention is to gain first insights into the systematic study of usability in the context of biomedical image analysis, and formulate experiences and guidelines for future usability studies dealing with workflow management systems. Embedded in a specific setup dealing with label-free digital pathology, the core question behind our contribution is how usability studies for scientific workflow management can be conducted, and how they can be used systematically to improve such tools. Further, we address specific questions about the resource utilisation and management of usability studies, including the recruitment of participants as well as the design of specific workflows to be investigated. This research was funded by the German Research Foundation (DFG), grant number MO 2804/1-1, assigned to Axel Mosig.

In spite of its central role in biology and disease, protein turnover is a largely understudied aspect of most proteomic studies due to the complexity of computational workflows that analyze in vivo turnover rates. To address this need, we developed a new computational tool, TurnoveR, to accurately calculate protein turnover rates from mass spectrometric analysis of metabolic labeling experiments in Skyline, a free and open-source proteomics software platform. TurnoveR is a straightforward graphical interface that enables seamless integration of protein turnover analysis into a traditional proteomics workflow in Skyline, allowing users to take advantage of the advanced and flexible data visualization and curation features built into the software. The computational pipeline of TurnoveR performs critical steps to determine protein turnover rates, including isotopologue demultiplexing, precursor-pool correction, statistical analysis, and generation of data reports and visualizations. This workflow is compatible with many mass spectrometric platforms and recapitulates turnover rates and differential changes in turnover rates between treatment groups calculated in previous studies. We expect that the addition of TurnoveR to the widely used Skyline proteomics software will facilitate wider utilization of protein turnover analysis in highly relevant biological models, including aging, neurodegeneration, and skeletal muscle atrophy.

The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.

The OSDG Community Dataset (OSDG-CD) is a public dataset of thousands of text excerpts, which were validated by over 1,400 OSDG Community Platform (OSDG-CP) citizen scientists from over 140 countries, with respect to the Sustainable Development Goals (SDGs). Dataset Information In support of the global effort to achieve the Sustainable Development Goals (SDGs), OSDG is realising a series of SDG-labelled text datasets. The OSDG Community Dataset (OSDG-CD) is the direct result of the work of more than 1,400 volunteers from over 130 countries who have contributed to our understanding of SDGs via the OSDG Community Platform (OSDG-CP). The dataset contains tens of thousands of text excerpts (henceforth: texts) which were validated by the Community volunteers with respect to SDGs. The data can be used to derive insights into the nature of SDGs using either ontology-based or machine learning approaches. 📘 The file contains 43,0210 (+390) text excerpts and a total of 310,328 (+3,733) assigned labels. To learn more about the project, please visit the OSDG website and the official GitHub page. Explore a detailed overview of the OSDG methodology in our recent paper "OSDG 2.0: a multilingual tool for classifying text data by UN Sustainable Development Goals (SDGs)". Source Data The dataset consists of paragraph-length text excerpts derived from publicly available documents, including reports, policy documents and publication abstracts. A significant number of documents (more than 3,000) originate from UN-related sources such as SDG-Pathfinder and SDG Library. These sources often contain documents that already have SDG labels associated with them. Each text is comprised of 3 to 6 sentences and is about 90 words on average. Methodology All the texts are evaluated by volunteers on the OSDG-CP. The platform is an ambitious attempt to bring together researchers, subject-matter experts and SDG advocates from all around the world to create a large and accurate source of textual information on the SDGs. The Community volunteers use the platform to participate in labelling exercises where they validate each text's relevance to SDGs based on their background knowledge. In each exercise, the volunteer is shown a text together with an SDG label associated with it – this usually comes from the source – and asked to either accept or reject the suggested label. There are 3 types of exercises: All volunteers start with the mandatory introductory exercise that consists of 10 pre-selected texts. Each volunteer must complete this exercise before they can access 2 other exercise types. Upon completion, the volunteer reviews the exercise by comparing their answers with the answers of the rest of the Community using aggregated statistics we provide, i.e., the share of those who accepted and rejected the suggested SDG label for each of the 10 texts. This helps the volunteer to get a feel for the platform. SDG-specific exercises where the volunteer validates texts with respect to a single SDG, e.g., SDG 1 No Poverty. All SDGs exercise where the volunteer validates a random sequence of texts where each text can have any SDG as its associated label. After finishing the introductory exercise, the volunteer is free to select either SDG-specific or All SDGs exercises. Each exercise, regardless of its type, consists of 100 texts. Once the exercise is finished, the volunteer can either label more texts or exit the platform. Of course, the volunteer can finish the exercise early. All progress is saved and recorded still. To ensure quality, each text is validated by up to 9 different volunteers and all texts included in the public release of the data have been validated by at least 3 different volunteers. It is worth keeping in mind that all exercises present the volunteers with a binary decision problem, i.e., either accept or reject a suggested label. The volunteers are never asked to select one or more SDGs that a certain text might relate to. The rationale behind this set-up is that asking a volunteer to select from 17 SDGs is extremely inefficient. Currently, all texts are validated against only one associated SDG label. Column Description doi - Digital Object Identifier of the original document text_id - unique text identifier text - text excerpt from the document sdg - the SDG the text is validated against labels_negative - the number of volunteers who rejected the suggested SDG label labels_positive - the number of volunteers who accepted the suggested SDG label agreement - agreement score based on the formula (agreement = \frac{|labels_{positive} - labels_{negative}|}{labels_{positive} + labels_{negative}}) Further Information Do not hesitate to share with us your outputs, be it a research paper, a machine learning model, a blog post, or just an interesting observation. All queries can be directed to community@osdg.ai. This CSV file uses UTF-8 character encoding. For easy access on MS Excel, open the file using Data ...

Modern mass spectrometry setups used in today’s proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNPxl for UV-induced peptide–RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark (Ramus, C.; J. Proteomics 2016, 132, 51–62). The second workflow, RNPxl, represents the first software solution to date for identification of peptide–RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

What’s Included

Introducing the Japanese Newspaper, Books, and Magazine Image Dataset - a diverse and comprehensive collection of images meticulously curated to propel the advancement of text recognition and optical character recognition (OCR) models designed specifically for the Japanese language.

Containing a total of 5000 images, this Japanese OCR dataset offers an equal distribution across newspapers, books, and magazines. Within, you'll find a diverse collection of content, including articles, advertisements, cover pages, headlines, call outs, and author sections from a variety of newspapers, books, and magazines. Images in this dataset showcases distinct fonts, writing formats, colors, designs, and layouts.

To ensure the diversity of the dataset and to build robust text recognition model we allow limited (less than five) unique images from a single resource. Stringent measures have been taken to exclude any personal identifiable information (PII), and in each image a minimum of 80% space is contain visible Japanese text.

Images have been captured under varying lighting conditions – both day and night – along with different capture angles and backgrounds, further enhancing dataset diversity. The collection features images in portrait and landscape modes.

All these images were captured by native Japanese people to ensure the text quality, avoid toxic content and PII text. We used latest iOS and android mobile devices above 5MP camera to click all these images to maintain the image quality. In this training dataset images are available in both JPEG and HEIC formats.

Along with the image data you will also receive detailed structured metadata in CSV format. For each image it includes metadata like device information, source type like newspaper, magazine or book image, and image type like portrait or landscape etc. Each image is properly renamed corresponding to the metadata.

The metadata serves as a valuable tool for understanding and characterizing the data, facilitating informed decision-making in the development of Japanese text recognition models.

We're committed to expanding this dataset by continuously adding more images with the assistance of our native Japanese crowd community.

If you require a custom dataset tailored to your guidelines or specific device distribution, feel free to contact us. We're equipped to curate specialized data to meet your unique needs.

Furthermore, we can annotate or label the images with bounding box or transcribe the text in the image to align with your specific requirements using our crowd community.

This Image dataset, created by FutureBeeAI, is now available for commercial use.

Leverage the power of this image dataset to elevate the training and performance of text recognition, text detection, and optical character recognition models within the realm of the Japanese language. Your journey to enhanced language understanding and processing starts here.

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Synthetic Data Generation Market Size 2024-2028

The synthetic data generation market size is forecast to increase by USD 2.88 billion at a CAGR of 60.02% between 2023 and 2028.

The global synthetic data generation market is expanding steadily, driven by the growing need for privacy-compliant data solutions and advancements in AI technology. Key factors include the increasing demand for data to train machine learning models, particularly in industries like healthcare services and finance where privacy regulations are strict and the use of predictive analytics is critical, and the use of generative AI and machine learning algorithms, which create high-quality synthetic datasets that mimic real-world data without compromising security.
This report provides a detailed analysis of the global synthetic data generation market, covering market size, growth forecasts, and key segments such as agent-based modeling and data synthesis. It offers practical insights for business strategy, technology adoption, and compliance planning. A significant trend highlighted is the rise of synthetic data in AI training, enabling faster and more ethical development of models. One major challenge addressed is the difficulty in ensuring data quality, as poorly generated synthetic data can lead to inaccurate outcomes.
For businesses aiming to stay competitive in a data-driven global landscape, this report delivers essential data and strategies to leverage synthetic data trends and address quality challenges, ensuring they remain leaders in innovation while meeting regulatory demands

What will be the Size of the Market During the Forecast Period?

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Synthetic data generation offers a more time-efficient solution compared to traditional methods of data collection and labeling, making it an attractive option for businesses looking to accelerate their AI and machine learning projects. The market represents a promising opportunity for organizations seeking to overcome the challenges of data scarcity and privacy concerns while maintaining data diversity and improving the efficiency of their artificial intelligence and machine learning initiatives. By leveraging this technology, technology decision-makers can drive innovation and gain a competitive edge in their respective industries.

Market Segmentation

The market research report provides comprehensive data (region-wise segment analysis), with forecasts and estimates in 'USD billion' for the period 2024-2028, as well as historical data from 2018-2022 for the following segments.

End-user

  Healthcare and life sciences
  Retail and e-commerce
  Transportation and logistics
  IT and telecommunication
  BFSI and others


Type

  Agent-based modelling
  Direct modelling


Data

  Tabular Data
  Text Data
  Image & Video Data
  Others


Offering Band

  Fully Synthetic Data
  Partially Synthetic Data
  Hybrid Synthetic Data


Application

  Data Protection
  Data Sharing
  Predictive Analytics
  Natural Language Processing
  Computer Vision Algorithms
  Others


Geography

  North America

    US
    Canada
    Mexico


  Europe

    Germany
    UK
    France
    Italy


  APAC

    China
    Japan
    India


  Middle East and Africa



  South America

By End-user Insights

The healthcare and life sciences segment is estimated to witness significant growth during the forecast period. In the thriving healthcare and life sciences sector, synthetic data generation is gaining significant traction as a cost-effective and time-efficient alternative to utilizing real-world data. This market segment's rapid expansion is driven by the increasing demand for data-driven insights and the importance of safeguarding sensitive information. One noteworthy application of synthetic data generation is in the realm of computer vision, specifically with geospatial imagery and medical imaging.

For instance, in healthcare, synthetic data can be generated to replicate medical imaging, such as MRI scans and X-rays, for research and machine learning model development without compromising patient privacy. Similarly, in the field of physical security, synthetic data can be employed to enhance autonomous vehicle simulation, ensuring optimal performance and safety without the need for real-world data. By generating artificial datasets, organizations can diversify their data sources and improve the overall quality and accuracy of their machine learning models.

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The healthcare and life sciences segment was valued at USD 12.60 million in 2018 and showed a gradual increase during the forecast period.

Regional Insights

North America is estimated to contribute 36% to the growth of the global market during the forecast period. Technavio's analysts have elaborately explained the regional trends and drivers that shape the m

This is the complementary material for the paper: "An Industrial Survey on the Relationships between Software Architecture and Source Code", which is currently under review. We provide a brief description of the files.

1. Valid Responses of the Questionnaire.xlsx comprises the 87 valid survey responses that were collected by sending the questionnaire to 1000 participants.

2. Interview Transcript includes eight files (Interview Transcript_IP1.docx - Interview Transcript_IP8.docx) of the interview transcripts from eight practitioners.

3. Data Labeling & Encoding.mx18 is the results of data labeling and encoding that were analyzed by the MAXQDA tool. We extracted the answers of open questions from the questionnaire and interview instrument, labeled them with the number of respondents and interviewees (e.g., Respondent1, Respondent2, Interview Transcript_IP1), and encoded the extracted data using Grounded Theory. The file can be opened by MAXQDA 18 or higher versions, which are available at https://www.maxqda.com/ for download. You may also use the free 14-day trial version of MAXQDA 2018, which is available at https://www.maxqda.com/trial for download.

What’s Included

Introducing the English Product Image Dataset - a diverse and comprehensive collection of images meticulously curated to propel the advancement of text recognition and optical character recognition (OCR) models designed specifically for the English language.

Containing a total of 2000 images, this English OCR dataset offers diverse distribution across different types of front images of Products. In this dataset, you'll find a variety of text that includes product names, taglines, logos, company names, addresses, product content, etc. Images in this dataset showcase distinct fonts, writing formats, colors, designs, and layouts.

To ensure the diversity of the dataset and to build a robust text recognition model we allow limited (less than five) unique images from a single resource. Stringent measures have been taken to exclude any personally identifiable information (PII) and to ensure that in each image a minimum of 80% of space contains visible English text.

Images have been captured under varying lighting conditions – both day and night – along with different capture angles and backgrounds, to build a balanced OCR dataset. The collection features images in portrait and landscape modes.

All these images were captured by native English people to ensure the text quality, avoid toxic content and PII text. We used the latest iOS and Android mobile devices above 5MP cameras to click all these images to maintain the image quality. In this training dataset images are available in both JPEG and HEIC formats.

Along with the image data, you will also receive detailed structured metadata in CSV format. For each image, it includes metadata like image orientation, county, language, and device information. Each image is properly renamed corresponding to the metadata.

The metadata serves as a valuable tool for understanding and characterizing the data, facilitating informed decision-making in the development of English text recognition models.

We're committed to expanding this dataset by continuously adding more images with the assistance of our native English crowd community.

If you require a custom product image OCR dataset tailored to your guidelines or specific device distribution, feel free to contact us. We're equipped to curate specialized data to meet your unique needs.

Furthermore, we can annotate or label the images with bounding box or transcribe the text in the image to align with your specific project requirements using our crowd community.

This Image dataset, created by FutureBeeAI, is now available for commercial use.

Leverage the power of this product image OCR dataset to elevate the training and performance of text recognition, text detection, and optical character recognition models within the realm of the English language. Your journey to enhanced language understanding and processing starts here.

Bitext - Retail Banking Tagged Training Dataset for LLM-based Virtual Assistants

  Overview

This hybrid synthetic dataset is designed to be used to fine-tune Large Language Models such as GPT, Mistral and OpenELM, and has been generated using our NLP/NLG technology and our automated Data Labeling (DAL) tools. The goal is to demonstrate how Verticalization/Domain Adaptation for the [Retail Banking] sector can be easily achieved using our two-step approach to LLM… See the full description on the dataset page: https://huggingface.co/datasets/bitext/Bitext-retail-banking-llm-chatbot-training-dataset.

Bio-orthogonal chemistry has gained widespread use in the study of many biological systems of interest, including protein prenylation. Prenylation is a post-translational modification in which a 15 or 20 carbon isoprenoid chain is transferred onto a cysteine near the C-terminus of a target protein. The three enzymes, protein farnesyltransferase (FTase), geranylgeranyl transferase I (GGTase I), and geranylgeranyl transferase II (GGTase II), that catalyze this process have been shown to exhibit some variability in substrate selection. This trait has been utilized in the past to transfer an array of farnesyl diphosphate analogues with a range of functionality, like an alkyne- containing analogue for copper-catalyzed bioconjugation reactions for example. Reported here is the synthesis of an analogue of the isoprenoid substrate embedded with norbornene functionality (C10NorOPP) for the study of prenylation and development of multifaceted protein-polymer-label conjugates. This analogue undergoes the inverse electron demand Diels Alder reaction with a tetrazine containing tags, allowing for copper-free labeling of proteins in the prenylome. This probe was synthesized in 7 steps with an overall yield of 7%. The use of C10NorOPP for the study of prenylation was explored in metabolic labeling of prenylated proteins in HeLa, COS-7, and astrocyte cells. Furthermore, in HeLa cells, these modified prenylated proteins were identified and quantified using LFQ proteomics, finding 24 enriched prenylated proteins. Additionally, here we utilize the unique chemistry of C10NorOPP in the construction of a multi- protein-polymer conjugate for the targeted labeling of cancer cells. This combines the specificity of the norbornene-tetrazine conjugation with traditional azide-alkyne cycloaddition for the construction of a polymer linked fluorescent trimer increasing cell binding.

Large-scale proteome analysis requires rapid and high-throughput analytical methods. We recently reported a new paradigm in proteome analysis where direct infusion and ion mobility are used instead of liquid chromatography (LC) to achieve rapid and high-throughput proteome analysis. Here, we introduce an improved direct infusion shotgun proteome analysis protocol including label-free quantification (DISPA-LFQ) using CsoDIAq software. With CsoDIAq analysis of DISPA data, we can now identify up to ∼2000 proteins from the HeLa and 293T proteomes, and with DISPA-LFQ, we can quantify ∼1000 proteins from no more than 1 μg of sample within minutes. The identified proteins are involved in numerous valuable pathways including central carbon metabolism, nucleic acid replication and transport, protein synthesis, and endocytosis. Together with a high-throughput sample preparation method in a 96-well plate, we further demonstrate the utility of this technology for performing high-throughput drug analysis in human 293T cells. The total time for data collection from a whole 96-well plate is approximately 8 h. We conclude that the DISPA-LFQ strategy presents a valuable tool for fast identification and quantification of proteins in complex mixtures, which will power a high-throughput proteomic era of drug screening, biomarker discovery, and clinical analysis.

Open Images is a dataset of ~9M images that have been annotated with image-level labels and object bounding boxes.

The training set of V4 contains 14.6M bounding boxes for 600 object classes on 1.74M images, making it the largest existing dataset with object location annotations. The boxes have been largely manually drawn by professional annotators to ensure accuracy and consistency. The images are very diverse and often contain complex scenes with several objects (8.4 per image on average). Moreover, the dataset is annotated with image-level labels spanning thousands of classes.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('open_images_v4', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

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