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A Global Review of Long-range Transported Lead Concentration and Isotopic Ratio Records in Snow and Ice (Supplementary Data)
<p><strong>This is the supplemental material for:</strong></p> <p>Brooks, H.L., Miner, K.R., Kreutz, K.J., Winski, D.A., (in review). A Global Review of Long-range Transported Lead Concentration and Isotopic Ratio Records in Snow and Ice. </p> <p><strong>Purpose:</strong></p> <p>This systematic literature review contextualizes current data availability and examines spatial and temporal gaps in the long-range transported Pb analyses (concentration and isotope ratios) in ice and snow samples. Additionally, we note areas of needed community improvement. It is our hope that researchers will also benefit from a queryable set of references, allowing for quick access to the records appropriate to address multiple research questions. </p> <p><strong>Available Files:</strong></p> <p><em><strong>Table A1:</strong></em> Metadata for Pb records -- Individual sample sites</p> <p><em><strong>Table A2:</strong></em> Metadata for Pb records -- Transect sample sites</p> <p><em><strong>Table A3:</strong></em> Records grouped into 23 regions</p> <p><em><strong>Supplement_fig_25Aug2024: </strong></em>Additional figures supporting main manuscript</p> <p><em><strong>Supplement_method_25Aug2024: </strong></em>Methodology used for the systematic literature review</p> <p><em><strong>Supplement_citations_25Aug2024:</strong></em> Citations for all records included in the systematic literature review</p> <p><em><strong>citations_export.bib:</strong></em> Export of all systematic literature review citation data as bibtex format. Easy import to citation managers (Zotero, Mendley, Endnote, etc)</p> <p><em><strong>indexedReferences.csv:</strong></em> CSV dump of citations_export.bib indexed with citation keys used in TableA.3</p> <p><em><strong>tables.RDS: </strong></em>TableA.1, TableA.2, and indexed References formatted for easy import into R</p> <p><em><strong>tables.sqlite: </strong></em>TableA.1, TableA.2, and indexed References formatted for SQL queries in SQLite</p> <p><em><strong>readme_tables_sqlite.md:</strong></em> Examples of SQLite queries</p> <p> </p> <p><strong>Systematic Literature Review Methodology:</strong></p> <p>To address the current spatial and temporal distribution of long-range transported Pb deposited in the cryosphere (snow-pits and ice cores), we completed a systematic literature review, following the methodology outlined by Booth et al (2016). We completed an “exhaustive coverage [search], citing all relevant literature" (Booth et al., 2016), using the search terms “Lead (Pb) isotopes and concentration in surface snow, snow pits, and ice cores”. We performed an initial comprehensive literature search on these search terms on Web of Science Collection databases in September 2020 and May 2023. Records evaluated for relevance using the title and abstract. Removal of clearly off-topic papers (e.g., the chemistry of penguin feces) gathered in the search due to the dual meaning of “lead” reduced the paper count to 326 titles. The full text of the remaining publications was evaluated with clear explicit criteria for inclusion and exclusion, based on the following criteria.</p> <ol> <li> <ol> <li>Only studies examining long-traveled background atmospheric lead signals were considered. All point source pollution studies examining the localized effects of traffic, road salt, mines, industry, power plants, human activity at base camp stations, etc, were excluded. An exception was made for samples which were taken at sufficient depths in the analyzed record to predate the pollution source or where wind trajectory did not transport pollution to the collection site regardless of close geographic proximity.</li> <li> <p>Only studies of natural, undisturbed snowpacks and ice cores were examined. Studies which sampled snow from urban structures were excluded. Point source studies of emissions detail the localized effects of traffic, road salt, mines, industry, power plants, and human activity at base camp stations. While meaningful for understanding the direct emissions from various sources and developing new technology aimed at reducing source emissions, point source emission studies do not contribute to the understanding of regional and global signals. Additionally, studies examining the volcanic signal in snow following major modern eruptions were excluded, as this was classified as disturbed snow.</p> </li> <li>Studies must specify the sampling localities by providing a minimum of latitude and longitude. Where sampling locations are only referenced by colloquial names, the distance from point source pollution cannot be verified. Therefore, such studies were excluded.</li> <li> <p>Records of <sup>210</sup>Pb in snow and ice were excluded. <sup>210</sup>Pb is useful for establishing chronology in young snow and ice due to its small half life (~ 22.3 years). But it is not useful for consideration of old records and the source constraint of <sup>210</sup>Pb into the atmosphere is poorly constrained over time (Nijampurkar & Clausen, 1990). Therefore, it cannot be considered in conjunction with Pb isotopes and concentrations. Records of <sup>210</sup>Pb in snow and ice were excluded.</p> </li> <li> <p>Pb isotopes and concentrations taken from cryoconites (soil-like composites of dust, industrial soot, and microbial mats of photosynthetic bacteria) were excluded from this literature review. Cryoconites are important to glacial systems as they alter the albedo of the glacier surface, and therefore affect the glacier melt rate (Fountain et al., 2004). However, they must be considered separately from surface snow, snow pits, and ice cores due to the drastic differences in formation and biologic nature.</p> </li> <li> <p>The publication must be available to the author (<em>e.g.,</em> through the University Library, from collaborators)</p> </li> </ol> </li> </ol> <p>To ensure that the literature search conducted on the Web of Science was robust and complete, citations were checked to ensure inclusion in the literature search results and included when missing. Publications were indexed into Table A.1 and Table A.2. Following the completion of publication indexing, Table A.1 and Table A.2 were evaluated against the 23 regions (Table A.3) -- 20 from RGI 7.0 (RGI 7.0 Consortium, 2023) and 3 author defined regions -- to identify areas/papers that may have been missed in the initial search. Areas with few or no results were searched again using Google Scholar and Web of Science.</p> <p>Based on these searches, we sought to understand the current spatial and temporal coverage of these records, shed light on gaps in the previous research and make recommendations on mitigating these gaps going forward. We used tables and graphics, included in the main text and the supplement, to summarize the characteristics of the compiled records. In the main text, we discuss the limitations and gaps within the current long-range transported Pb literature, and recommend paths to mitigate these gaps. Finally, in the main text, we illustrate an example of how researchers can query this record compilation, allowing for quick access to the records appropriate to address their research questions.</p> <p><strong>Methodology Bibliography:</strong></p> <p>Booth, A., Sutton, A., & Papaioannou, D. (2016). Systematic approaches to a successful literature review (Second edition). Sage.</p> <p>Fountain, A. G., Tranter, M., Nylen, T. H., Lewis, K. J., & Mueller, D. R. (2004). Evolution of cryoconite holes and their contribution to meltwater runoff from glaciers in the McMurdo dry valleys, Antarctica. Journal of Glaciology, 50(168), 35–45. https://doi.org/10.3189/172756504781830312</p> <p>Nijampurkar, V. N., & Clausen, H. B. (1990). A century old record of lead-210 fallout on the greenland ice sheet. Tellus Series B Chemical and Physical Meteorology, 42(1), 29–38. https://doi.org/10.1034/j.1600-0889.1990.00005.</p> <p>RGI 7.0 Consortium. (2023). Randolph glacier inventory—A dataset of global glacier outlines, version 7.0. (Version 7.0) [Dataset]. NSIDC: National Snow and Ice Data Center. https://doi.org/doi:10.5067/f6jmovy5navz</p>
FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures
<h2>General</h2> <p>For more details and the most up-to-date information please consult our project page: <a href="https://kainmueller-lab.github.io/fisbe" target="_blank" rel="noopener">https://kainmueller-lab.github.io/fisbe</a>.</p> <h2>Summary</h2> <ul> <li>A new dataset for neuron instance segmentation in 3d multicolor light microscopy data of fruit fly brains <ul> <li>30 completely labeled (segmented) images</li> <li>71 partly labeled images</li> <li>altogether comprising ∼600 expert-labeled neuron instances (labeling a single neuron takes between 30-60 min on average, yet a difficult one can take up to 4 hours)</li> </ul> </li> <li>To the best of our knowledge, the first real-world benchmark dataset for instance segmentation of long thin filamentous objects</li> <li>A set of metrics and a novel ranking score for respective meaningful method benchmarking</li> <li>An evaluation of three baseline methods in terms of the above metrics and score</li> </ul> <h2>Abstract</h2> <p>Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.</p> <h2>Dataset documentation:</h2> <p>We provide a detailed documentation of our dataset, following the <a href="https://arxiv.org/abs/1803.09010" target="_blank" rel="noopener">Datasheet for Datasets</a> questionnaire:</p> <p><em>>> <a href="https://kainmueller-lab.github.io/fisbe/datasheet" target="_blank" rel="noopener">FISBe Datasheet</a></em></p> <p>Our dataset originates from the <a href="https://www.janelia.org/project-team/flylight" target="_blank" rel="noopener">FlyLight project</a>, where the authors released a large image collection of nervous systems of ~74,000 flies, <a href="https://gen1mcfo.janelia.org/cgi-bin/gen1mcfo.cgi" target="_blank" rel="noopener">available for download</a> under CC BY 4.0 license.</p> <h2>Files</h2> <ul> <li>fisbe_v1.0_{completely,partly}.zip <ul> <li>contains the image and ground truth segmentation data; there is one <em>zarr</em> file per sample, see below for more information on how to access <em>zarr</em> files.</li> </ul> </li> <li>fisbe_v1.0_mips.zip <ul> <li>maximum intensity projections of all samples, for convenience.</li> </ul> </li> <li>sample_list_per_split.txt <ul> <li>a simple list of all samples and the subset they are in, for convenience.</li> </ul> </li> <li>view_data.py <ul> <li>a simple python script to visualize samples, see below for more information on how to use it.</li> </ul> </li> <li>dim_neurons_val_and_test_sets.json <ul> <li>a list of instance ids per sample that are considered to be of low intensity/dim; can be used for extended evaluation.</li> </ul> </li> <li>Readme.md <ul> <li>general information</li> </ul> </li> </ul> <h2>How to work with the image files</h2> <p>Each sample consists of a single 3d MCFO image of neurons of the fruit fly.<br>For each image, we provide a pixel-wise instance segmentation for all separable neurons.<br>Each sample is stored as a separate <em>zarr</em> file (<a href="https://zarr.readthedocs.io" target="_blank" rel="noopener">zarr</a> is a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.").<br>The image data ("raw") and the segmentation ("gt_instances") are stored as two arrays within a single zarr file.<br>The segmentation mask for each neuron is stored in a separate channel.<br>The order of dimensions is CZYX.</p> <p>We recommend to work in a virtual environment, e.g., by using conda:</p> <p><code>conda create -y -n flylight-env -c conda-forge python=3.9</code><br><code>conda activate flylight-env</code></p> <h3>How to open <em>zarr</em> files</h3> <ol> <li>Install the python zarr package: <pre><code>pip install zarr</code></pre> </li> <li>Opened a zarr file with:<br> <p><code>import zarr</code><br><code>raw = zarr.open(<path_to_zarr>, mode='r', path="volumes/raw")</code><br><code>seg = zarr.open(<path_to_zarr>, mode='r', path="volumes/gt_instances")</code></p> <p><code># optional:</code><br><code>import numpy as np</code><br><code>raw_np = np.array(raw)</code></p> </li> </ol> <p>Zarr arrays are read lazily on-demand.<br>Many functions that expect numpy arrays also work with zarr arrays.<br>Optionally, the arrays can also explicitly be converted to numpy arrays.</p> <h3>How to view <em>zarr</em> image files</h3> <p>We recommend to use <a href="https://napari.org" target="_blank" rel="noopener">napari</a> to view the image data.</p> <ol> <li>Install napari: <pre><code>pip install "napari[all]"</code></pre> </li> <li>Save the following Python script: <br> <p><code>import zarr, sys, napari</code></p> <p><code>raw = zarr.load(sys.argv[1], mode='r', path="volumes/raw")</code><br><code>gts = zarr.load(sys.argv[1], mode='r', path="volumes/gt_instances")</code></p> <p><code>viewer = napari.Viewer(ndisplay=3)</code><br><code>for idx, gt in enumerate(gts):</code><br><code> viewer.add_labels(</code><br><code> gt, rendering='translucent', blending='additive', name=f'gt_{idx}')</code><br><code>viewer.add_image(raw[0], colormap="red", name='raw_r', blending='additive')</code><br><code>viewer.add_image(raw[1], colormap="green", name='raw_g', blending='additive')</code><br><code>viewer.add_image(raw[2], colormap="blue", name='raw_b', blending='additive')</code><br><code>napari.run()</code></p> </li> <li>Execute: <pre><code>python view_data.py <path-to-file>/R9F03-20181030_62_B5.zarr</code></pre> </li> </ol> <h2>Metrics</h2> <ul> <li>S: Average of avF1 and C</li> <li>avF1: Average F1 Score</li> <li>C: Average ground truth coverage</li> <li>clDice_TP: Average true positives clDice</li> <li>FS: Number of false splits</li> <li>FM: Number of false merges</li> <li>tp: Relative number of true positives</li> </ul> <p>For more information on our selected metrics and formal definitions please see <a href="https://arxiv.org/abs/2404.00130" target="_blank" rel="noopener">our paper</a>.</p> <h2>Baseline</h2> <p>To showcase the FISBe dataset together with our selection of metrics, we provide evaluation results for three baseline methods, namely <a href="https://github.com/Kainmueller-Lab/PatchPerPix" target="_blank" rel="noopener">PatchPerPix (ppp)</a>, <a href="https://github.com/google/ffn" target="_blank" rel="noopener">Flood Filling Networks (FFN)</a> and a non-learnt application-specific <a href="https://www.biorxiv.org/content/10.1101/2020.06.07.138941v1" target="_blank" rel="noopener">color clustering from Duan et al.</a>.<br>For detailed information on the methods and the quantitative results please see <a href="https://arxiv.org/abs/2404.00130" target="_blank" rel="noopener">our paper</a>.</p> <h2>License</h2> <p>The FlyLight Instance Segmentation Benchmark (FISBe) dataset is licensed under the <a href="https://creativecommons.org/licenses/by/4.0" target="_blank" rel="noopener">Creative Commons Attribution 4.0 International (CC BY 4.0) license</a>.</p> <h2>Citation</h2> <p>If you use <em>FISBe</em> in your research, please use the following BibTeX entry: </p> <pre><code>@misc{mais2024fisbe, title = {FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures}, author = {Lisa Mais and Peter Hirsch and Claire Managan and Ramya Kandarpa and Josef Lorenz Rumberger and Annika Reinke and Lena Maier-Hein and Gudrun Ihrke and Dagmar Kainmueller}, year = 2024, eprint = {2404.00130}, archivePrefix ={arXiv}, primaryClass = {cs.CV} }</code></pre> <h2>Acknowledgments</h2> <p>We thank Aljoscha Nern for providing unpublished MCFO images as well as Geoffrey W. Meissner and the entire FlyLight Project Team for valuable<br>discussions.<br>P.H., L.M. and D.K. were supported by the HHMI Janelia Visiting Scientist Program.<br>This work was co-funded by Helmholtz Imaging.</p> <h2>Changelog</h2> <p>There have been no changes to the dataset so far.<br>All future change will be listed <a href="https://kainmueller-lab.github.io/fisbe/changelog" target="_blank" rel="noopener">on the changelog page</a>.</p> <h2>Contributing</h2> <p>If you would like to contribute, have encountered any issues or have any suggestions, please <a href="https://github.com/Kainmueller-Lab/fisbe/issues" target="_blank" rel="noopener">open an issue</a> for the FISBe dataset in the accompanying github repository.</p> <p>All contributions are welcome!</p>
Supplemental Figures for "On the comparative utility of entropic learning versus deep learning for long-range ENSO prediction"
<p>Supplemental figures for the paper "On the comparative utility of entropic learning versus deep learning for long-range ENSO prediction".</p>
HALOC Dataset | WiFi CSI-based Long-Range Person Localization Using Directional Antennas
<p><strong>WiFi CSI-based Long-Range Person Localization Using Directional Antennas</strong></p> <p>This repository contains the HAllway LOCalization (HALOC) dataset and WiFi system CAD files as proposed in <a href="https://openreview.net/forum?id=AOJFcEh5Eb" target="_blank" rel="noopener">[1]</a>.</p> <p><strong>PyTroch Dataloader</strong></p> <p>A minimal PyTorch dataloader for the HALOC dataset is provided at: <a href="https://github.com/StrohmayerJ/HALOC" target="_blank" rel="noopener">https://github.com/StrohmayerJ/HALOC</a></p> <p><strong>Dataset Description</strong></p> <p>The HALOC dataset comprises six sequences (in .csv format) of synchronized WiFi Channel State Information (CSI) and 3D position labels. Each row in a given .csv file represents a single WiFi packet captured via ESP-IDF, with CSI and 3D coordinates stored in the "data" and ("x", "y", "z") fields, respectively.</p> <p>The sequences are divided into training, validation, and test subsets as follows:</p> <table> <tbody> <tr> <td><strong>Subset</strong></td> <td><strong>Sequences</strong></td> </tr> <tr> <td>Training</td> <td>0.csv, 1.csv, 2.csv and 3.csv</td> </tr> <tr> <td>Validation</td> <td>4.csv</td> </tr> <tr> <td>Test</td> <td>5.csv</td> </tr> </tbody> </table> <p> </p> <p><strong>WiFi System CAD files</strong></p> <p>We provide CAD files for the 3D printable parts of the proposed WiFi system consisting of the main housing (housing.stl), the lid (lid.stl), and the carrier board (carrier.stl) featuring mounting points for the Nvidia Jetson Orin Nano and the ESP32-S3-DevKitC-1 module. </p> <p><strong>Download and Use</strong><br>This data may be used for non-commercial research purposes only. If you publish material based on this data, we request that you include a reference to our paper [1].</p> <p>[1] Strohmayer, J., and Kampel, M. (2024). “WiFi CSI-based Long-Range Person Localization Using Directional Antennas”, <em>The Second Tiny Papers Track at ICLR 2024</em>, May 2024, Vienna, Austria. <a href="https://openreview.net/forum?id=AOJFcEh5Eb" target="_blank" rel="noopener">https://openreview.net/forum?id=AOJFcEh5Eb</a></p> <p>BibTeX citation:</p> <pre>@inproceedings{<br>strohmayer2024wifi,<br>title={WiFi {CSI}-based Long-Range Person Localization Using Directional Antennas},<br>author={Julian Strohmayer and Martin Kampel},<br>booktitle={The Second Tiny Papers Track at ICLR 2024},<br>year={2024},<br>url={https://openreview.net/forum?id=AOJFcEh5Eb}<br>}</pre>
Nanoparticle clustering in supraparticles to control magnetic long-range interactions
<p>This data publication is based on the metadata and datasets underlying the manuscript: Nanoparticle clustering in supraparticles to control magnetic long-range interactions</p> <p>To tailor superparamagnetic iron oxide nanoparticles (SPIONs) to the specific needs of diverse application fields, it is essential to understand not only their intrinsic properties but also their interactions with each other. Theoretical models predicting/explaining the magnetization behavior of macroscopic samples containing millions of SPIONs are intricate due to the complexity of the underlying relaxation mechanisms in alternating fields. This study introduces supraparticles (SPs) as model architectures to empirically investigate magnetic interactions within and between large SPION clusters (> 100 nanoparticles). For this purpose, nanoparticle dispersions containing SPIONs and silica nanoparticles (SiO<sub>2</sub> NPs) as non‐magnetic building blocks are spray‐dried to form binary SPs. Selective salt‐induced agglomeration of the two building block types before spray‐drying is utilized to tailor SP architectures, including control over SPION cluster size, shape, and proximity. Magnetic particle spectroscopy (MPS), operating under ambient conditions, reveals altered magnetization behavior for different cluster structures. Not only the nearest SPION neighbors, but the whole cluster structure up to several micrometers is decisive for the magnetization behavior. This highlights the importance of long‐range magnetic interactions. This work presents a versatile approach for designing model architectures to advance empirical interaction studies between SPIONs in macroscopic samples.</p>
Data and Code for the paper 'Indication of long-range correlations governing city size'
<div> <h1>Summary</h1> <p>This repository contains the preprocessed data necessary for constructing the city network as described in the related paper, as well as the code to do the Shortest-path Fluctuation Analysis (SFA) on those networks.</p> <div> <h2>Under the <code>data</code> folder</h2> <ul> <li> <p>In the <code>Node_list</code> folder, each <em><code>CSV</code></em> file has the name convention like <code>AL_1000_node_list.csv</code>, for example, this means the table contains the list of <strong>nodes</strong> that make up the network for <strong>Austria</strong> (as country code, <code>AL</code>) at the spatial clustering distance threshold of <strong>1000</strong>m. The table has 3 columns with column names, and without row names.</p> <ul> <li> <p>Each row in the table is a record of one node, the <strong><em>node ID</em></strong> is the <code>row_id</code> of the record in the table, the first record has a row_id of <strong>0</strong>.</p> </li> <li> <p>The <strong>first</strong> column in the table is the <em><code>X</code></em> coordinate of the mass center of the node.</p> </li> <li> <p>The <strong>second</strong> column in the table is the <em><code>Y</code></em> coordinate of the mass center of the node.</p> </li> <li> <p>The <strong>third</strong> column in the table is the <strong>Size</strong> of the node, i.e., the number of pixels of this city.</p> </li> </ul> </li> <li> <p>In the <code>Edge_list</code> folder, each <em><code>TXT</code></em> file has the name convention like <code>AL_1000_edges.txt</code>, for example, this means the table contains the list of <strong>edges</strong> that make up the network for <strong>Austria</strong> (as country code, <code>AL</code>) at the spatial clustering distance threshold of <strong>1000</strong>m. The table has 2 columns without column name, without row name.</p> <ul> <li> <p>Each row in the table is a record of one edge that is composed of a pair of nodes, the <strong><em>node ID</em></strong> is the <code>row_id</code> of that node in the <strong>node_list</strong> table.</p> </li> <li> <p>The <strong>first</strong> column in the table is the <strong><em>ID</em></strong> of the node on one side of an edge.</p> </li> <li> <p>The <strong>second</strong> column in the table is the <strong><em>ID</em></strong> of the node on the other side of an edge.</p> </li> </ul> </li> </ul> </div> <div> <h2>Under the <code>code</code> folder</h2> <ul> <li> <p>The <code>SFA_args_LSPT_out.cpp</code> file contains the <strong>C++</strong> code to do the SFA calculation, detailed information can be found in the documentation of the code file.</p> </li> <li> <p>The <code>SFA_config.ini</code> file contains some configuration parameters for running the compiled program, details can also be found in the file. This file has to be put in the same folder as the compiled executable file.</p> </li> </ul> </div> </div>
Data set for "Diverse long-range axonal projections of excitatory layer 2/3 neurons in mouse barrel cortex"
<p>Data set for: Yamashita T, Vavladeli A, Pala A, Galan K, Crochet S, Petersen SSA, Petersen CCH (2018) Diverse long-range axonal projections of excitatory layer 2/3 neurons in mouse barrel cortex. Front Neuroanat 12: 33. https://doi.org/10.3389/fnana.2018.00033</p> <p>There are 25 files in this data upload:</p> <p>1. '2018_Yamashita_FrontNeuroanat.pdf' - this a pdf version of the online publication.</p> <p>2. 'Yamashita_Figure2_Quantification.xlsx' - this is a Microsoft Excel file giving the locations of high density axonal projections from layer 2/3 pyramidal neurons in the mouse C2 barrel column in the coordinate frame of Paxinos & Franklin (2001) The mouse brain in stereotaxic coordinates. Academic Press. The data are plotted in Figure 2 of Yamashita et al., 2018.</p> <p>3. 'Yamashita_Figure7_Quantification.xlsx' - this is a Microsoft Excel file giving the dendritic length, number of dendrites, number of dendritic nodes and total axonal length, as well as the axonal length in the different projection zones for each reconstructed neuron. The data are plotted in Figure 7 of Yamashita et al., 2018.</p> <p>4. 'Yamashita_SupMov1_S2P_AP049.mov' - this is a QuickTime video file, showing the 3D structure of neuron AP049 featured in Figure 3 of Yamashita et al., 2018.</p> <p>5. 'Yamashita_SupMov2_M1P_TY308.mov' - this is a QuickTime video file, showing the 3D structure of neuron TY308 featured in Figure 5 of Yamashita et al., 2018.</p> <p>6. 'AV198.zip' - this zipped folder contains data relating to mouse AV198: a) 'AV198_stack.tif' the z-stack of whole-brain fluorescence images from expression of tdTomato in layer 2/3 neurons of the C2 barrel column of mouse AV198. b) 'AV198_ROI_Box.zip' can be loaded into FIJI (https://fiji.sc) and indicates projection regions by a box. c) 'AV198_ROI_Point.zip' can be loaded into FIJI (https://fiji.sc) and indicates projection regions by a point. d) 'AV198_Paxinos' is a folder showing the coronal fluorescent brain sections in pdf format overlaid on the equivalent drawing from Paxinos & Franklin (2001) The mouse brain in stereotaxic coordinates. Academic Press.</p> <p>7. 'AV199.zip' - same as 'AV198.zip' but for mouse AV199.</p> <p>8. 'AV201.zip' - same as 'AV198.zip' but for mouse AV201.</p> <p>9. 'AV202.zip' - same as 'AV198.zip' but for mouse AV202.</p> <p>10. 'AV203.zip' - same as 'AV198.zip' but for mouse AV203.</p> <p>11. 'AP042.ASC' - Neurolucida (http://www.mbfbioscience.com/neurolucida) data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse AP042. Brain contours are also traced.</p> <p>12. 'AP044.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse AP044. Brain contours are also traced.</p> <p>13. 'AP046.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse AP046. Brain contours are also traced.</p> <p>14. 'AP047.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse AP047. Brain contours are also traced.</p> <p>15. 'AP049.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse AP049. Brain contours are also traced.</p> <p>16. 'TY220.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY220. Brain contours are also traced.</p> <p>17. 'TY288.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY288. Brain contours are also traced.</p> <p>18. 'TY300.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY300. Brain contours are also traced.</p> <p>19. 'TY302.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY302. Brain contours are also traced.</p> <p>20. 'TY308.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY308. Brain contours are also traced.</p> <p>21. 'TY310.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY310. Brain contours are also traced.</p> <p>22. 'TY337.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY337. Brain contours are also traced.</p> <p>23. 'TY345.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY345. Brain contours are also traced.</p> <p>24. 'TY367.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY367. Brain contours are also traced.</p> <p>25. 'TY369.ASC' - Neurolucida data file of the 3D reconstruction of axon and dendrite from the single neuron labelled in mouse TY369. Brain contours are also traced.</p>
Data set for "Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices"
<p>Data set for: Liu Y, Bech P, Tamura K, Délez LT, Crochet S, Petersen CCH (2024) Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices. eLife 13: RP97602. https://doi.org/10.7554/eLife.97602</p> <p>There are 3 files in this upload:</p> <p>1. The file named "2024_Liu_eLife.pdf" is the Open Access pdf of the online publication in eLife.</p> <p>2. The file named "Liu_anatomy_data_code.zip" (~35 GB) is a zipped version of a folder "Liu_anatomy_data_code" (~111 GB), which contains the anatomical data analysed in the study along with the Python codes used to generate the published figures 1-7 and their associated figure supplements. </p> <p>3. The file named "Liu_function_data_code.zip" (~10 GB) is a zipped version of a folder "Liu_function_data_code" (~35 GB), which contains the functional data analysed in the study along with the Python codes used to generate the published figure 8 and its associated figure supplement. </p> <p>After unzipping, the Python codes should run as a Jupyter notebook (anatomy .ipynb code) or Python code (function .py code) in Anaconda.</p>
Raw MS data for "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor"
<p>These are the raw HDX/MS data for our paper: "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor."</p>
Data of the publication "Transport and entanglement growth in long-range random Clifford circuits"
<p>Conservation laws can constrain entanglement dynamics in isolated quantum systems, manifest in a slowdown of higher Rényi entropies. Here, we explore this phenomenon in a class of long-range random Clifford circuits with U(1) symmetry where transport can be tuned from diffusive to superdiffusive. We unveil that the different<br> hydrodynamic regimes reflect themselves in the asymptotic entanglement growth according to <span class="math-tex">\(S(t) \propto t^{1/z}\)</span> where<br> the dynamical transport exponent z depends on the probability <span class="math-tex">\(\propto r^{-\alpha}\)</span> of gates spanning a distance r. For<br> sufficiently small <span class="math-tex">\(\alpha\)</span>, we show that the presence of hydrodynamic modes becomes irrelevant such that S(t) behaves<br> similarly in circuits with and without conservation law. We explain our findings in terms of the inhibited operator<br> spreading in U(1)-symmetric Clifford circuits where the emerging light cones can be understood in the context<br> of classical Lévy flights. Our Letter sheds light on the connections between Clifford circuits and more generic<br> many-body quantum dynamics.</p>
Data of the publication "Hydrodynamics in long-range interacting systems with center-of-mass conservation"
<p>In systems with a conserved density, the additional conservation of the center of mass (dipole moment) has been shown to slow down the associated hydrodynamics. At the same time, long-range interactions generally lead to faster transport and information propagation. Here, we explore the competition of these two effects and develop a hydrodynamic theory for long-range center-of-mass-conserving systems. We demonstrate that these systems can exhibit a rich dynamical phase diagram containing subdiffusive, diffusive, and superdiffusive behaviors, with continuously varying dynamical exponents. We corroborate our theory by studying quantum lattice models whose emergent hydrodynamics exhibit these phenomena.</p>
Raw data to "Quantum-critical and dynamical properties of the XXZ bilayer with long-range interactions"
<div> <p>This directory contains the data used to generate the numerical results in the work "Quantum-critical and dynamical properties of the XXZ bilayer with long-range interactions [1]".</p> <p>To get an overview of the organization of the directory and a description of the data we recommend the README.md file.</p> <p>[1]: P. Adelhardt, A. Duft and K. P. Schmidt, Quantum-critical and dynamical properties of the XXZ bilayer with long-range interactions, <a href="https://arxiv.org/abs/2408.13145">arXiv:2408.13145</a></p> <p> </p> </div>
Computational generation of long-range axonal morphologies
<p>This repository contains both the data and scripts to reproduce all figures of the related article.</p> <p>Usually, one should download all the files in a directory and read the README.md file.</p>
Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
<p>MD simulations used in the studies of the publication "<strong>Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations</strong>"</p>
Observing emergent hydrodynamics in a long-range quantum magnet
<p>Here lies the experimental data and the analysis codes for the manuscript titled "Observing emergent hydrodynamics in a long-range quantum magnet" to be published in Science.</p>
FIGURE 4 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 4. Site-specific data for lamina length and lamina width plotted for each taxon. 4A: Lamina length for Platanus neptuni. 4B: Lamina width for P. neptuni. 4C: Lamina length for Eotrigonobalanus furcinervis. 4D: Lamina width for E. furcinervis. 4E: Lamina length for Daphnogene cinnamomifolia. 4F: Lamina width for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.
FIGURE 1 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 1. Map showing the locations of the considered sites, which are numbered according to Table 1.
FIGURE 3 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 3. Site-specific data for lamina area and lamina perimeter plotted for each taxon. 3A: Lamina area for Platanus neptuni. 3B: Lamina perimeter for P. neptuni. 3C: Lamina area for Eotrigonobalanus furcinervis. 3D: Lamina perimeter for E. furcinervis. 3E: Lamina area for Daphnogene cinnamomifolia. 3F: Lamina perimeter for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.
FIGURE 6 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 6. Site-specific data for lamina centroid and leaf length-to-width ratio (LWR) plotted for each taxon. 6A: Lamina centroid for Platanus neptuni. 6B: LWR for P. neptuni. 6C: Lamina centroid for Eotrigonobalanus furcinervis. 6D: LWR for E. furcinervis. 6E: Lamina centroid for Daphnogene cinnamomifolia. 6F: LWR for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.
FIGURE 2 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?
FIGURE 2. Plasticity index (PI) of various leaf traits, for the considered sites and taxa. 2A: PI for lamina area. 2B: PI for lamina length. 2C: PI for lamina perimeter. 2D: PI for lamina width. 2E: PI for lamina circularity. 2F: PI for lamina centroid. Squares: Platanus neptuni. Circles: Daphnogene cinnamomifolia. Triangles: Eotrigonobalanus furcinervis. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.
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.