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Figure 2 in Determination of an efficient and reliable method for PCR detection of borrelial DNA from engorged ticks
Figure 2. Results of PCR amplification – A1. Efficient PCR with clear band of 250bp presented as successful amplification, determined by using a positive control; All amplified bands with sizes differing from the positive control were defined as non-specific alleles; Four types of different PCR results: A2. Non-specific alleles; A3. Poor amplification; A4. A combination of poor amplification and non-specific alleles; B. Unsuccessful amplification detected in paired DNA extraction, after using DNA obtained from mouthparts (B1), whereas target region was amplified for the same sample but using DNA obtained from a part of scutum (B2); a 50 bp DNA ladder (BioLabs, New England) (A, B).
Large-scale annotated dataset for cochlear hair cell detection and classification
<p>Our sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5 - 15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following <i>in-vivo</i> and <i>in-vitro</i>ototoxic drug application. The dataset includes over 107,000 hair cells which have been manually identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease. </p><p>Associated code is provided here: https://github.com/indzhykulianlab/hcat-data</p>
VISIONE Feature Repository for VBS: Multi-Modal Features and Detected Objects from VBSLHE Dataset
<p>This repository contains a diverse set of features extracted from the VBSLHE dataset (laparoscopic gynecology) . These features will be utilized in the VISIONE system [Amato et al. 2023, Amato et al. 2022] in the next editions of the Video Browser Showdown (VBS) competition (<a href="https://www.videobrowsershowdown.org/">https://www.videobrowsershowdown.org/</a>). </p> <p>We used a snapshot of the dataset provided by the Medical University of Vienna and Toronto that can be downloaded using the instructions provided at <a href="https://download-dbis.dmi.unibas.ch/mvk/">https://download-dbis.dmi.unibas.ch/mvk/</a>. It comprises 75 video files. We divided each video into video shots with a maximum duration of 5 seconds.</p> <p>This repository is released under a Creative Commons Attribution license. If you use it in any form for your work, please cite the following paper:</p> <blockquote> <p>@inproceedings{amato2023visione, title={VISIONE at Video Browser Showdown 2023}, author={Amato, Giuseppe and Bolettieri, Paolo and Carrara, Fabio and Falchi, Fabrizio and Gennaro, Claudio and Messina, Nicola and Vadicamo, Lucia and Vairo, Claudio}, booktitle={International Conference on Multimedia Modeling}, pages={615--621}, year={2023}, organization={Springer} } </p> </blockquote> <p> </p> <p>This repository (v2) comprises the following files:</p> <ul> <li><em><strong>msb.tar.gz </strong></em> contains tab-separated files (.tsv) for each video. Each tsv file reports, for each video segment, the timestamp and frame number marking the start/end of the video segment, along with the timestamp of the extracted middle frame and the associated identifier ("id_visione").</li> <li><em><strong>extract-keyframes-from-msb.tar.gz</strong></em> contains a Python script designed to extract the middle frame of each video segment from the MSB files. To run the script successfully, please ensure that you have the original VBSLHE videos available.</li> <li><em><strong>features-aladin.tar.gz†</strong></em><strong> </strong>contains <a href="https://github.com/mesnico/ALADIN">ALADIN</a> [Messina N. et al. 2022] features extracted for all the segment's middle frames.</li> <li><em><strong>features-clip-laion.tar.gz†</strong></em> contains <a href="https://huggingface.co/laion/CLIP-ViT-H-14-laion2B-s32B-b79K">CLIP ViT-H/14 - LAION-2B </a>[Schuhmann et al. 2022] features extracted for all the segment's middle frames.</li> <li><em><strong>features-clip-openai.tar.gz† </strong></em>contains <a href="https://huggingface.co/openai/clip-vit-large-patch14">CLIP ViT-L/14</a> [Radford et al. 2021] features extracted for all the segment's middle frames.</li> <li><em><strong>features-clip2video.tar.gz† </strong></em>contains <a href="https://github.com/CryhanFang/CLIP2Video">CLIP2Video</a> [Fang H. et al. 2021] extracted for all the video segments. <strong> </strong></li> <li><em><strong>objects-frcnn-oiv4.tar.gz* </strong></em>contains the objects detected using <a href="http://tfhub.dev/google/faster_rcnn/openimages_v4/inception_resnet_v2/1">Faster R-CNN+Inception ResNet</a> (trained on the Open Images V4 [Kuznetsova et al. 2020]).</li> <li><em><strong>objects-mrcnn-lvis.tar.gz*</strong></em> contains the objects detected using Mask R-CNN [He et al. 2017] (trained on LVIS).</li> <li><em><strong>objects-vfnet64-coco.tar.gz*</strong></em> contains the objects detected using VfNet [Zhang et al. 2021] (trained on COCO dataset).</li> </ul> <p>*Please be sure to use the <strong>v2 version </strong>of this repository, since v1 feature files may contain inconsistencies that have now been corrected</p> <p><em><strong>*Note on the object annotations:</strong></em> Within an object archive, there is a jsonl file for each video, where each row contains a record of a video segment (the <em>"_id"</em> corresponds to the <em>"id_visione"</em> used in the msb.tar.gz) . Additionally, there are three arrays representing the objects detected, the corresponding scores, and the bounding boxes. The format of these arrays is as follows:</p> <ul> <li><em>"object_class_names"</em>: vector with the class name of each detected object.</li> <li><em>"object_scores"</em>: scores corresponding to each detected object.</li> <li><em>"object_boxes_yxyx"</em>: bounding boxes of the detected objects in the format <em>(ymin, xmin, ymax, xmax).</em></li> </ul> <p> </p> <p><em><strong>†Note on the cross-modal features: </strong></em>The extracted multi-modal features (ALADIN, CLIPs, CLIP2Video) enable internal searches within the VBSLHE dataset using the query-by-image approach (features can be compared with the dot product). However, to perform searches based on free text, the text needs to be transformed into the joint embedding space according to the specific network being used (see links above). Please be aware that t<strong>he service for transforming text into features is not provided within this repository and should be developed independently using the original feature repositories linked above.</strong></p> <p>We have plans to release the code in the future, allowing the reproduction of the VISIONE system, including the instantiation of all the services to transform text into cross-modal features. However, this work is still in progress, and the code is not currently available.</p> <p> </p> <p><strong>References:</strong></p> <p>[Amato et al. 2023] Amato, G.et al., 2023, January. VISIONE at Video Browser Showdown 2023. In International Conference on Multimedia Modeling (pp. 615-621). Cham: Springer International Publishing.</p> <p>[Amato et al. 2022] Amato, G. et al. (2022). VISIONE at Video Browser Showdown 2022. In: , et al. MultiMedia Modeling. MMM 2022. Lecture Notes in Computer Science, vol 13142. Springer, Cham. </p> <p>[Fang H. et al. 2021] Fang H. et al., 2021. Clip2video: Mastering video-text retrieval via image clip. arXiv preprint arXiv:2106.11097.</p> <p>[He et al. 2017] He, K., Gkioxari, G., Dollár, P. and Girshick, R., 2017. Mask r-cnn. In Proceedings of the IEEE international conference on computer vision (pp. 2961-2969).</p> <p>[Kuznetsova et al. 2020] Kuznetsova, A., Rom, H., Alldrin, N., Uijlings, J., Krasin, I., Pont-Tuset, J., Kamali, S., Popov, S., Malloci, M., Kolesnikov, A. and Duerig, T., 2020. The open images dataset v4. International Journal of Computer Vision, 128(7), pp.1956-1981.</p> <p>[Lin et al. 2014] Lin, T.Y., Maire, M., Belongie, S., Hays, J., Perona, P., Ramanan, D., Dollár, P. and Zitnick, C.L., 2014, September. Microsoft coco: Common objects in context. In European conference on computer vision (pp. 740-755). Springer, Cham.</p> <p>[Messina et al. 2022] Messina N. et al., 2022, September. Aladin: distilling fine-grained alignment scores for efficient image-text matching and retrieval. In Proceedings of the 19th International Conference on Content-based Multimedia Indexing (pp. 64-70).</p> <p>[Radford et al. 2021] Radford A. et al., 2021, July. Learning transferable visual models from natural language supervision. In International conference on machine learning (pp. 8748-8763). PMLR.</p> <p>[Schuhmann et al. 2022] Schuhmann C. et al., 2022. Laion-5b: An open large-scale dataset for training next generation image-text models. Advances in Neural Information Processing Systems, 35, pp.25278-25294.</p> <p>[Zhang et al. 2021] Zhang, H., Wang, Y., Dayoub, F. and Sunderhauf, N., 2021. Varifocalnet: An iou-aware dense object detector. In Proceedings of the IEEE/CV</p>
VISIONE Feature Repository for VBS: Multi-Modal Features and Detected Objects from MVK Dataset
<p>This repository contains a diverse set of features extracted from the marine video (underwater) dataset (MVK) . These features were utilized in the VISIONE system [Amato et al. 2023, Amato et al. 2022] during the latest editions of the Video Browser Showdown (VBS) competition (<a href="https://www.videobrowsershowdown.org/">https://www.videobrowsershowdown.org/</a>). </p> <p>We used a snapshot of the MVK dataset from 2023, that can be downloaded using the instructions provided at <a href="https://download-dbis.dmi.unibas.ch/mvk/">https://download-dbis.dmi.unibas.ch/mvk/</a>. It comprises 1,372 video files. We divided each video into 1 second segments. </p> <p>This repository is released under a Creative Commons Attribution license. If you use it in any form for your work, please cite the following paper:</p> <blockquote> <pre>@inproceedings{amato2023visione, title={VISIONE at Video Browser Showdown 2023}, author={Amato, Giuseppe and Bolettieri, Paolo and Carrara, Fabio and Falchi, Fabrizio and Gennaro, Claudio and Messina, Nicola and Vadicamo, Lucia and Vairo, Claudio}, booktitle={International Conference on Multimedia Modeling}, pages={615--621}, year={2023}, organization={Springer} }</pre> </blockquote> <p> </p> <p>This repository comprises the following files:</p> <ul> <li><strong><em>msb.tar.gz </em></strong> contains tab-separated files (.tsv) for each video. Each tsv file reports, for each video segment, the timestamp and frame number marking the start/end of the video segment, along with the timestamp of the extracted middle frame and the associated identifier ("id_visione"). </li> <li><em><strong>extract-keyframes-from-msb.tar.gz</strong></em> contains a Python script designed to extract the middle frame of each video segment from the MSB files. To run the script successfully, please ensure that you have the original MVK videos available.</li> <li><strong><em>features-aladin.tar.gz<sup>†</sup></em> </strong>contains <a href="https://github.com/mesnico/ALADIN">ALADIN</a> [Messina N. et al. 2022] features extracted for all the segment's middle frames. </li> <li><em><strong>features-clip-laion.tar.gz<sup>†</sup></strong></em> contains <a href="https://huggingface.co/laion/CLIP-ViT-H-14-laion2B-s32B-b79K">CLIP ViT-H/14 - LAION-2B </a>[Schuhmann et al. 2022] features extracted for all the segment's middle frames.</li> <li><em><strong>features-clip-openai.tar.gz<sup>†</sup> </strong></em>contains <a href="https://huggingface.co/openai/clip-vit-large-patch14">CLIP ViT-L/14</a> [Radford et al. 2021] features extracted for all the segment's middle frames. </li> <li><em><strong>features-clip2video.tar.gz<sup>†</sup> </strong></em>contains <a href="https://github.com/CryhanFang/CLIP2Video">CLIP2Video</a> [Fang H. et al. 2021] extracted for all the 1s video segments. <strong> </strong></li> <li><em><strong>objects-frcnn-oiv4.tar.gz<sup>*</sup> </strong></em>contains the objects detected using <a href="http://tfhub.dev/google/faster_rcnn/openimages_v4/inception_resnet_v2/1">Faster R-CNN+Inception ResNet</a> (trained on the Open Images V4 [Kuznetsova et al. 2020]). </li> <li><em><strong>objects-mrcnn-lvis.tar.gz<sup>*</sup></strong></em> contains the objects detected using Mask R-CNN [He et al. 2017] (trained on LVIS).</li> <li><em><strong>objects-vfnet64-coco.tar.gz<sup>*</sup></strong></em> contains the objects detected using VfNet [Zhang et al. 2021] (trained on COCO dataset).</li> </ul> <p>*Please be sure to use the <strong>v2 version </strong>of this repository, since v1 feature files may contain inconsistencies that have now been corrected</p> <p><em><strong>*Note on the object annotations:</strong></em> Within an object archive, there is a jsonl file for each video, where each row contains a record of a video segment (the <em>"_id"</em> corresponds to the <em>"id_visione"</em> used in the msb.tar.gz) . Additionally, there are three arrays representing the objects detected, the corresponding scores, and the bounding boxes. The format of these arrays is as follows:</p> <ul> <li><em>"object_class_names"</em>: vector with the class name of each detected object.</li> <li><em>"object_scores"</em>: scores corresponding to each detected object.</li> <li><em>"object_boxes_yxyx"</em>: bounding boxes of the detected objects in the format <em>(ymin, xmin, ymax, xmax).</em></li> </ul> <p> </p> <p><em><strong><sup>†</sup>Note on the cross-modal features: </strong></em>The extracted multi-modal features (ALADIN, CLIPs, CLIP2Video) enable internal searches within the MVK dataset using the query-by-image approach (features can be compared with the dot product). However, to perform searches based on free text, the text needs to be transformed into the joint embedding space according to the specific network being used (see links above). Please be aware that t<strong>he service for transforming text into features is not provided within this repository and should be developed independently using the original feature repositories linked above.</strong></p> <p>We have plans to release the code in the future, allowing the reproduction of the VISIONE system, including the instantiation of all the services to transform text into cross-modal features. However, this work is still in progress, and the code is not currently available.</p> <p> </p> <p><strong>References:</strong></p> <p>[Amato et al. 2023] Amato, G.et al., 2023, January. VISIONE at Video Browser Showdown 2023. In International Conference on Multimedia Modeling (pp. 615-621). Cham: Springer International Publishing.</p> <p>[Amato et al. 2022] Amato, G. et al. (2022). VISIONE at Video Browser Showdown 2022. In: , et al. MultiMedia Modeling. MMM 2022. Lecture Notes in Computer Science, vol 13142. Springer, Cham. </p> <p>[Fang H. et al. 2021] Fang H. et al., 2021. Clip2video: Mastering video-text retrieval via image clip. arXiv preprint arXiv:2106.11097.</p> <p>[He et al. 2017] He, K., Gkioxari, G., Dollár, P. and Girshick, R., 2017. Mask r-cnn. In Proceedings of the IEEE international conference on computer vision (pp. 2961-2969).</p> <p>[Kuznetsova et al. 2020] Kuznetsova, A., Rom, H., Alldrin, N., Uijlings, J., Krasin, I., Pont-Tuset, J., Kamali, S., Popov, S., Malloci, M., Kolesnikov, A. and Duerig, T., 2020. The open images dataset v4. International Journal of Computer Vision, 128(7), pp.1956-1981.</p> <p>[Lin et al. 2014] Lin, T.Y., Maire, M., Belongie, S., Hays, J., Perona, P., Ramanan, D., Dollár, P. and Zitnick, C.L., 2014, September. Microsoft coco: Common objects in context. In European conference on computer vision (pp. 740-755). Springer, Cham.</p> <p>[Messina et al. 2022] Messina N. et al., 2022, September. Aladin: distilling fine-grained alignment scores for efficient image-text matching and retrieval. In Proceedings of the 19th International Conference on Content-based Multimedia Indexing (pp. 64-70).</p> <p>[Radford et al. 2021] Radford A. et al., 2021, July. Learning transferable visual models from natural language supervision. In International conference on machine learning (pp. 8748-8763). PMLR.</p> <p>[Schuhmann et al. 2022] Schuhmann C. et al., 2022. Laion-5b: An open large-scale dataset for training next generation image-text models. Advances in Neural Information Processing Systems, 35, pp.25278-25294.</p> <p>[Zhang et al. 2021] Zhang, H., Wang, Y., Dayoub, F. and Sunderhauf, N., 2021. Varifocalnet: An iou-aware dense object detector. In Proceedings of the IEEE/CV</p>
RafanoSet: Dataset of raw, manual and automatically annotated Raphanus Raphanistrum weed images for object detection and segmentation in Heterogenous Agriculture Environment
<p>This dataset is a collection of raw and annotated Multispectral (MS) images acquired in a heterogenous agricultural environment with MicaSense RedEdge-M camera. The spectra particularly Green, Blue, Red, Red Edge and Near Infrared (NIR) were acquired at sub-metre level.. <br><br>The MS images were labelled manually using VIA and automatically using Grounding DINO in combination with Segment Anything Model. The segmentation masks obtained using these two annotation techniqes over as well as the source code to perform necessary image processing operations are provided in the repository. The images are focussed over Horseradish (Raphanus Raphanistrum) infestations in Triticum Aestivum (wheat) crops.</p> <p>The nomenclature of sequecncing and naming images and annotations has been in this format: IMG_<scene number>_<spectral channel number><br><strong>_1</strong>: Blue<br><strong>_2</strong>: Green<br><strong>_3</strong>: Red<br><strong>_4</strong>: Near Infrared<br><strong>_5</strong>: RedEdge<br><br>Example: An image name <strong>IMG_0200_3 </strong>represents the scene number<strong> 200</strong> in <strong>Red channel</strong></p> <p>This dataset 'RafanoSet'is categorized in 6 directories namely 'Raw Images', 'Manual Annotations', 'Automated Annotations', 'Binary Masks - Manual', 'Binary Masks - Automated' and 'Codes'. The sub-directory 'Raw Images' consists of manually acquired 85 images in .PNG format. over 17 different scenes. The sub-directory 'Manual Annotations' consists of annotation file 'region_data' in COCO segmentation format. The sub-directory 'Automated Annotations' consists of 80 automatically annotated images in .JPG format and 80 .XML files in Pascal VOC annotation format.</p> <p>The scientific framework of image acquisition and annotations are explained in the Data in Brief paper which is the course of peer review. This is just a prerequisite to the data article. <br><br>Field experimentation roles:</p> <p>The image acquisition was performed by Mariano Crimaldi, a researcher, on behalf of Department of Agriculture and the hosting institution University of Naples Federico II, Italy.</p> <p>Shubham Rana has been the curator and analyst for the data under the supervision of his PhD supervisor Prof. Salvatore Gerbino. They are affiliated with Department of Engineering, University of Campania 'Luigi Vanvitelli'. </p> <p>Domenico Barretta, Department of Engineering has been associated in consulting and brainstorming role particularly with data validation, annotation management and litmus testing of the datasets.</p>
Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection
<p>Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on phylogenetic inference and introgression detection.</p>
Fig. 5 in Detection and characterization of diverse coccidian protozoa shed by California sea lions
Fig. 5. Indirect fluorescence antibody test of California sea lion sporulated oocyst cultures. Zoites derived from cultivated oocysts from animal CSL10089 (A), CSL10092 (B), and CSL10100 (C) were tested using serum from a Sarcocystis neurona-infected horse. Image D shows reactivity of serum from the S. neurona-infected horse to S. neurona culture isolate snUCD-1. Image E shows a lack of seroreactivity of negative control serum from a S. neurona-negative horse to zoite culture from CSL10089. Scale bars are 15 Mm.
Fig. 3 in Detection and characterization of diverse coccidian protozoa shed by California sea lions
Fig. 3. Three California sea lion haul-out sites (red circles) on the central California coast where fecal samples were collected from free-ranging animals. Field sample identifiers for test-positive samples are given (Ãno-, PL- and WR-) at each location. Coccidian parasite genotypes and species amplified in sample DNA are indicated in parentheses: A, Coccidia A; B, Coccidia B; Sn, Sarcocystis neurona-like; unchar, uncharacterized species. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.).
Dataset for training Dev-ResNet for detection of developmental events in Lymnaea stagnalis
<p>Dataset for training <a href="https://github.com/EmbryoPhenomics/dev-resnet">Dev-ResNet</a> for detection of developmental events in<em> Lymnaea stagnalis. </em></p> <p> </p> <p>The following naming scheme is used for the individual GIF files:</p> <p>Example: "./video/20C_A_B1_315hr.gif"</p> <ul> <li><strong>"./video/"</strong> --> Source folder.</li> <li><strong>"20C" </strong> --> Treatment, here incubation temperature.</li> <li><strong>"A"</strong> --> Egg mass label.</li> <li><strong>"B1" </strong> --> Individual embryo label.</li> <li><strong>"315hr" </strong>--> Hours since first cell division.</li> </ul> <p> </p>
RASP: A new method for single puncta detection in complex cellular backgrounds
<p>Super-resolution and single-molecule microscopy are increasingly applied to complex biological systems. A major challenge of this approach is that fluorescent puncta must be detected in the low signal, high noise, heterogeneous background environments of cells and tissue. We present RASP, Radiality Analysis of Single Puncta, a bioimaging-segmentation method that solves this problem. RASP removes false positive puncta that other analysis methods detect, and detects features over a broad range of spatial scales: from single proteins to complex cell phenotypes. RASP outperforms the state-of-the-art in precision and speed, using image gradients to separate Gaussian-shaped objects from background. We demonstrate RASP's power by showing it can extract spatial correlations between microglia, neurons, and alpha-synuclein oligomers in the human brain. This sensitive, computationally efficient approach enables fluorescent puncta and cellular features to be distinguished in cellular and tissue environments with a sensitivity down to the level of the single protein. </p>
Benchmark for energy efficient obstacle detection on head mounted wearable for the vision impaired
<p>Here we present a novel benchmark dataset with the associated challenge, that is to detect obstacles based on head-mounted sensors and lightweight wearable devices to assist Blind and Visually Impaired individuals (BVIs) navigate in indoor environments. The challenge encompasses three objectives: (1) as accurately as possible to detect the obstacles on the pathway that likely lead to a collision; (2) as durably as possible on a given amount of battery power for the detection algorithm or model to run; (3) as reliably as possible to compensate natural head turns so nearby objects would not trigger false alarms. The data provided in the benchmark are collected from the following head mounted sensors: (i) nine low-cost ultrasonic sensors; (ii) one high-end ultrasonic sensor with a larger detection range but higher power consumption; (iii) a 9-Degrees of Freedom (DOF) Inertial Measurement Unit (IMU). The resulting dataset consists of more than 188,000 unique sequences obtained from multiple subjects walking in three different indoor scenarios. This benchmark is to facilitate and encourage accurate yet fast obstacle detection solutions that can really benefit BVIs. </p>
Geodetic anomaly detection and analysis in the Campi Flegrei caldera (Italy) deformation pattern of the 2021-2023 escalating unrest phase
<p>Data used within the manuscript: "<strong><span>First evidence of a geodetic anomaly in the Campi Flegrei caldera (Italy) ground deformation pattern revealed by DInSAR and GNSS measurements during the 2021-2023 escalating unrest phase</span>"</strong></p> <p> </p> <p>Archive content:</p> <ul> <li><code>DTSLOS_CNRIREA_20150325_20231021_FB9K</code>: Line of Sight displacement time series retrieved by applying the P-SBAS algorithm to Sentinel-1 data set acquired from ascending orbits (Track 44) over Campi Flegrei caldera in the 20150325 - 20231021 interval. Data format is according to the <a href="https://gitlab.com/epos-tcs-satdata/doc/-/blob/main/TCS_SATD_Product_Description.md#los-displacement-time-series-dtslos" target="_blank" rel="noopener noreferrer">EPOS specification</a>.</li> <li><code>DTSLOS_CNRIREA_20150324_20231020_UJBI</code>: Line of Sight displacement time series retrieved by applying the P-SBAS algorithm to Sentinel-1 data set acquired from descending orbits (Track 22) over Campi Flegrei caldera in the 20150324 - 20231020 interval. Data format is according to the <a href="https://gitlab.com/epos-tcs-satdata/doc/-/blob/main/TCS_SATD_Product_Description.md#los-displacement-time-series-dtslos" target="_blank" rel="noopener noreferrer">EPOS specification</a>.</li> <li><code>Campi_Flegrei_GNSS_Weekly_Timeseries</code>: Weekly displacement time series of Campi Flegrei caldera GNSS network from 2016 to 2023.</li> </ul>
Dragon_Pi: IoT Side-Channel Power Data Intrusion Detection Dataset and Unsupervised Convolutional Autoencoder for Intrusion Detection
<h2><strong>Dragon_Pi</strong></h2> <div> <div>For a more in depth description of the Dragon_Pi dataset, please consult the journal article of the same name:</div> <div>Lightbody <em>et al.</em>, Future Internet, 2024, <a href="https://doi.org/10.3390/fi16030088">https://doi.org/10.3390/fi16030088</a> - specifically Section 3.2: Dataset Overview.</div> <div> </div> </div> <p>Dragon_Pi is an intrusion detection dataset for IoT devices. In the field of IoT security there are few datasets, and those which do exist tend to focus solely on network traffic. The Dragon_Pi dataset seeks to provide not only more data for the field of IoT security, but also, data of a somewhat under-published type: linear time series power consumption data.</p> <p>Dragon_Pi is a fully labelled Intrusion Detection dataset for IoT devices. It is composed of both normal and under-attack power consumption data obtained from two separate testbeds - one using a DragonBoard 410c and the other a Raspberry Pi Model 3 - Hence the moniker <em>Dragon_Pi</em>. </p> <p>These testbeds were set up with predefined normal behavour as described in the attached publications. The normal linear time series power consumption was sampled from the testbed under these normal conditions. Both testbeds were then attacked using some common attacks on IoT - the linear time series power consumption captured under these condtions as well. </p> <p>Specifically, the testbeds were subjected to the Port Scan (using Nmap), SSH Brute Force (using Hydra) and SYNFlood Denial of Service (using Hping3) attacks. These attacks were repeated to gain insight to what their signatures looked like and also how varying the tool settings effected the resultant signature. A fourth type of scenario was also conducted on the testbeds - the "Capture the Flag" scenarios. In these files multiple attack types were used with a more specific target - to exfiltrate a hidden file from the testbeds.</p> <p>Each file has three hierarchical levels of annotation for <strong>each sample</strong> within:</p> <ol> <li>A simple "Normal or Anomaly" label for the specific sample</li> <li>A specifc attack type label e.g. "SSH Bruteforce", for the specific sample</li> <li>A specific tool setting for that attack e.g. "Hydra_T16", for the specific sample</li> </ol> <p>Users can decide for themselves what level of annotation they require for their specific task. </p> <p>Each file in the Dragon_Pi dataset is accompanied by its own legend file. This file explains the contents of the specific .csv file and the specific indexes of the events within.</p> <p>The Dragon_Pi dataset consists of approximately 67 files, as shown in Table 1. Compressed, the datset totals approximately 13GB. Completely decompressed the dataset is approximately 80GB ( 30GB Pi data, 50 GB Dragon data). </p> <div> </div> <div> <table> <tbody> <tr> <td>Label Type</td> <td>Specific Label </td> <td>Number of Files DragonBoard 410c</td> <td>Number of Files Raspberry Pi</td> </tr> <tr> <td>Normal </td> <td>Normal </td> <td>3 </td> <td>2</td> </tr> <tr> <td>Port Scan Attack </td> <td>Nmap_T5</td> <td>2</td> <td>1</td> </tr> <tr> <td> </td> <td>Nmap_T4</td> <td>1</td> <td>1</td> </tr> <tr> <td> </td> <td>Nmap_T3</td> <td>1</td> <td>1</td> </tr> <tr> <td> </td> <td>Nmap_T2</td> <td>1</td> <td>1</td> </tr> <tr> <td>SSH Brute Force</td> <td>Hydra_T32</td> <td>4</td> <td>2</td> </tr> <tr> <td> </td> <td>Hydra_T16</td> <td>16</td> <td>2</td> </tr> <tr> <td> </td> <td>Hydra_T3</td> <td>8</td> <td>2</td> </tr> <tr> <td> </td> <td>Hydra_T1</td> <td>5</td> <td>2</td> </tr> <tr> <td>SYNFlood DOS</td> <td>SYNFlood DOS</td> <td>1</td> <td>1</td> </tr> <tr> <td>Capture the Flag</td> <td>Misc Attacks</td> <td>3</td> <td>5</td> </tr> </tbody> </table> </div> <div>Table 1. Enumeration of the in the Dragon_Pi dataset.</div> <div> </div> <div> </div> <div>For a more in depth description of the Dragon_Pi dataset, please consult the journal article of the same name:</div> <div>Lightbody <em>et al.</em>, Future Internet, 2024, <a href="https://doi.org/10.3390/fi16030088">https://doi.org/10.3390/fi16030088</a> - specifically Section 3.2: Dataset Overview.</div> <div> </div> <div> </div> <div><strong>Publication of this dataset:</strong></div> <div> </div> <div>This dataset was published in Lightbody <em>et al.</em>, Future Internet, 2024, <a href="https://doi.org/10.3390/fi16030088">https://doi.org/10.3390/fi16030088</a>. Consult and cite this article for a more in depth dataset description, as well as an in depth review of first AI Intrusion Detection model trained on this dataset. </div> <div> </div> <div>See article Lightbody <em>et al.</em>, Future Internet, 2023, <a href="https://doi.org/10.3390/fi15050187">https://doi.org/10.3390/fi15050187</a> for a detailed investigation on the attack signatures discovered while creating this dataset. This work was an inital investigation of the dataset and can serve as a part 1 to the Dragon_Pi paper.</div> <div> </div> <div> </div> <div><strong>How to cite this dataset in your work: </strong></div> <div> </div> <div>Please cite these two DOIs when publishing using this dataset:</div> <div> <ol> <li>Dragon_Pi release publication: <a href="https://doi.org/10.3390/fi16030088">https://doi.org/10.3390/fi16030088</a> (most important)</li> <li>Zenodo Dataset DOI: https://doi.org/10.5281/zenodo.10784947</li> </ol> </div> <div> <div> </div> </div> <p> </p>
Testing strengths, limitations and biases of current Pulsar Timing Arrays detection analyses on realistic data
<p>In this project, we carried out an extensive investigation of the performance of current Pulsar Timing Arrays (PTA) analyses on simulated PTA datasets where we modeled the gravitational waves (GW) signal as the incoherent superposition of sinusoidal signals from a cosmic population of super-massive black hole binaries (SMBHBs). Here we publish the dataset referred to in the paper as the <em><strong>SMBHB_set</strong></em>: 100 realisations of PTA datasets with 25 pulsars and a GWB signal of nominal amplitude 2.4e-15. For each realisation, listed from 1001 to 1100, this repository contains the pulsars .par and .tim files, the mcmc chain (sampling over 66 parameters: 60 for pulsars intrinsic noise parameters and log amplitude and slope of a common red noise process), and the SMBHB details for that specific realisation of the GWB. The columns of the <em>MBHB_list.dat</em> files contain (from left to right): log10 MBH chirp mass (in solar masses in the source frame), mass ratio, source redshift, log10 of GW fundamental mode (n=2) in the observer frame, phi and theta angles in the sky, source inclination angle, source polarisation angle, source initial orbital phase, source initial direction of periastron and source initial eccentricity.</p> <p>If you make use of any of this data, please cite:<br><br></p> <div>@article{ refId0,</div> <div> author = {{Valtolina, Serena} and {Shaifullah, Golam} and {Samajdar, Anuradha} and {Sesana, Alberto}},</div> <div> title = {Testing strengths, limitations, and biases of current pulsar timing arrays’ detection analyses on realistic data},</div> <div> DOI= "10.1051/0004-6361/202348084",</div> <div> url= "https://doi.org/10.1051/0004-6361/202348084",</div> <div> journal = {A&A},</div> <div> year = 2024,</div> <div> volume = 683,</div> <div> pages = "A201",</div> <div>}</div>
Automatic detection of clefts and corridors within the sandstone plateau - Szczeliniec Wielki & Szczeliniec Mały mesas, Poland
<p>This dataset presents the method of automatic clefts and corridors detection within areas of highly dissected relief. This methodical approach was developed for a geomorphological study on Szczeliniec Wielki and Szczeliniec Mały sandstone mesas (Stołowe Mts., SW Poland) (Migoń et al. 2023)</p> <p>Contents:</p> <ol> <li>CleftHunter_manual_v1_0.pdf - short method description</li> <li>kernel_examples.zip - set of exemplary kernel files </li> <li>Szczeliniec_Wielki_clefts_threshold_depth_2m.zip - raster dataset of automatically detected clefts within the plateau of Szczeliniec Wielki (.tif)</li> <li>Szczeliniec_Maly_clefts_threshold_depth_2m.zip - raster dataset of automatically detected clefts within the plateau of Szczeliniec Mały (.tif)</li> <li>Szczeliniec_Wielki_mesa_caprock_base.zip - Szczeliniec Wielki caprock zone (.shp, polygon)</li> <li>Szczeliniec_Maly_mesa_caprock_base.zip - Szczeliniec Mały caprock zone (.shp, polygon)</li> <li>Szczeliniec_Wielki_mesa_caprock_hillshade.zip - shaded relief of the Szczeliniec Wielki plateau (.tif)</li> <li>Szczeliniec_Maly_mesa_caprock_hillshade.zip - shaded relief of the Szczeliniec Mały plateau (.tif)</li> </ol> <p>Preferred citation:</p> <p>Migoń P., Duszyński F., Jancewicz K., Kotowska M., Porębna W. (2023), Surface-subsurface connectivity in the morphological evolution of sandstone-capped tabular hills – how much analogy to karst?. Geomorphology vol. 440, Id 108884, 1–22<br>DOI: 10.1016/j.geomorph.2023.108884</p> <p> </p> <p>This research was funded by National Science Centre, Poland, research project no. 2020/39/D/ST10/00861.</p>
Figure 1 in Detection of Male Mediterranean Fruit Flies (Diptera: Tephritidae): Performance of Trimedlure Relative to Capilure and Enriched Ginger Root Oil
Figure 1. Capture of C. capitata males in TML- versus CPL-baited Jackson traps for 3 replicates in an Oahu coffee field. Abscissa represents period of lure ageing, where 0 weeks represents fresh lures. Bar heights indicate mean of 20 traps per lure type; error bars represent + 1 SE. Symbols above bars show results of the Tukey HSD test comparing the 2 lures for each ageing category, where an asterisk indicates P <0.001 and ns indicates no significant difference.
BotHawk: GitHub Bot Account Detection Dataset
<p>The <strong>"BotHawk: GitHub Bot Account Detection Dataset"</strong> is a specialized resource developed for the research and development community focused on identifying and understanding bot accounts within the GitHub ecosystem. This comprehensive dataset offers an in-depth look into the behaviors, contributions, and patterns of bot accounts, distinguishing them from human user activities on GitHub.</p> <p>Designed to enhance the accuracy and efficiency of bot detection algorithms, the BotHawk Dataset encompasses a variety of features, including commit history, issue participation, pull request activities, and other interaction metrics specific to GitHub. It provides an invaluable foundation for developing machine learning models capable of distinguishing between bot-generated and human-generated activities, contributing to more secure and trustworthy interactions within the GitHub platform.</p> <p>This dataset not only serves as a tool for academic research in cybersecurity, machine learning, and software engineering but also offers practical applications for developers and platform administrators seeking to improve the health of their projects by filtering out bot-based noise and manipulation. The BotHawk dataset is instrumental in advancing our comprehension of bot dynamics within the GitHub ecosystem, supporting the broader objective of fostering a secure, transparent, and collaborative open-source community.</p>
Fig. 1 in Evidence for intercontinental parasite exchange through molecular detection and characterization of haematozoa in northern pintails (Anas acuta) sampled throughout the North Pacific Basin
Fig. 1. Approximate locations in North America and East Asia at which northern pintail tissue samples were collected during 2011–2012 to test for haemosporidian infection. Regions (i.e. Alaska, California, and Japan) and sub-regions (Koyukuk-Nowitna NWR, Yukon-Kuskokwim Delta NWR, Izembek NWR, Sacramento Valley, San Joaquin Valley) for sampling locations are indicated (NWR = National Wildlife Refuge). The number of tissue samples per location is indicated in parentheses. Sample tissue was whole blood unless indicated by an asterisk (signifying wing muscle tissue).
HGT breakpoints and events detected by LocalHGT in 2098 real data
<p> </p> <table> <tbody> <tr> <td>filter_hgt_results.zip</td> <td>the HGT breakpoints of all samples, in this folder, each CSV file represents a sample. </td> </tr> <tr> <td>identified_event.csv</td> <td>the HGT events of all samples, the results of all samples are in this file.</td> </tr> <tr> <td>TableS1</td> <td>phenotypes of all samples</td> </tr> <tr> <td>use.zip</td> <td>Microbial abundances of all samples, in this folder, all samples from the same cohort are in a single file.</td> </tr> </tbody> </table> <p> </p>
Auxiliary data release for "Fast marginalization algorithm for optimizing gravitational wave detection, parameter estimation and sky localization"
<p>This release contains parameter estimation runs on synthetic injections, described in https://arxiv.org/abs/2404.02435 .</p> <p>Important note: The posterior samples provided are weighted, the weights are stored in a column named 'weights' . </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.