cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xk4muy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hexagrammos pingi Wu & Wang, 1931",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006344-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.24870666.v3
title: Supporting information: Energy dissipation during shear along experimental rough faults

description: Supporting information: Energy dissipation during shear along experimental rough faults
DOI: 10.15468/dl.u7q57z
title: Occurrence Download

description: A dataset containing 1620 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mushrooms Flora of Nepal at National Herbarium and Plant Laboratories (KATH)"
 ]
}

 The dataset includes 1620 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006348-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jg663p
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caretta cepedii Merrem, 1820",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006349-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ynyq9t
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caretta esculenta Merrem, 1820",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006350-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.12604488
title: Hysteresis and Irreversibility of Global Dryness in Response to CO2 Mitigation Efforts
DOI: 10.5281/zenodo.12604489
title: Hysteresis and Irreversibility of Global Dryness in Response to CO2 Mitigation Efforts
DOI: 10.6084/m9.figshare.24257542
title: Supporting information for "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "

description: Supporting information of the manuscript "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "These are the files created for the project titled " Can upwelling regions be potential thermal refugia for marine fishes during climate warming" The "Average_richness" file shows the total pixel richness, which is the sum of the different binary maps developed. The "Average Suitability" folder contains the average value of all species suitability maps. The "Difference_suitability" and "Difference_richness" files show the subtraction results between suitability and richness, respectively, for the present and different RCP scenarios for the periods 2040-2050 and 2090-2100. The "Exploratory_figures" folder displays the maximum, mean, and minimum temperatures at which the species are reported. The Jaccard turnover results are stored in the "Jaccard" folder. The filenames indicate the period (Present, 2040-2050 (2050), and 2090-2100 (2100)), the RCP scenarios (6.0 (6) and 8.5 (8)), and the filtered used (0,50,100 and 500 for 0 km filter, 50 km filter, 100 km filter, and 500 km filter respectevely). The two folders named "Species_figure" and "Species_raster" contain separate results for each species. The "Species_figure" folder displays the results graphically, while the "Species_raster" folder has files in raster format (.tif). Both folders have subfolders indicating which database was used to create the maps, such as 0, 50 and 100 km.The folder named "Calibration_results" contains the results of the model calibration achieved in this study. Within this folder, the subfolder "train" displays the data used for every species in each of the ten runs to create the minimum volume ellipses. The subfolder "raw" displays all the results from every possible combination of models. Lastly, the subfolder "weight" displays the average results of the chosen model. Finally, Pearson correlationship of databases with more than 30 occurrences are shown in the folder “Correlationship”. To replicate our results, please access the "Code_replication" folder, which includes the required scripts and databases. Please, open first the “rProj” file in rstudio and follow the numbered scripts. Note that the unnumbered scripts are functions to run the models.Finally, we stored the occurrences downloaded from the Ocean Biodiversity Information System (OBIS) and Vertnet, along with their references, using the 'robis' and 'vertnet' packages, respectively (“Occurrences” folder). For the data obtained from the Global Biodiversity Information Facility (GBIF), we stored it as data keys and the number of records to create a derived dataset, which can be accessed and cited following the next link: https://doi.org/10.15468/dd.8wacqq.
DOI: 10.6084/m9.figshare.24257542.v2
title: Supporting information for "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "

description: Supporting information of the manuscript "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "These are the files created for the project titled " Can upwelling regions be potential thermal refugia for marine fishes during climate warming" The "Average_richness" file shows the total pixel richness, which is the sum of the different binary maps developed. The "Average Suitability" folder contains the average value of all species suitability maps. The "Difference_suitability" and "Difference_richness" files show the subtraction results between suitability and richness, respectively, for the present and different RCP scenarios for the periods 2040-2050 and 2090-2100. The "Exploratory_figures" folder displays the maximum, mean, and minimum temperatures at which the species are reported. The Jaccard turnover results are stored in the "Jaccard" folder. The filenames indicate the period (Present, 2040-2050 (2050), and 2090-2100 (2100)), the RCP scenarios (6.0 (6) and 8.5 (8)), and the filtered used (0,50,100 and 500 for 0 km filter, 50 km filter, 100 km filter, and 500 km filter respectevely). The two folders named "Species_figure" and "Species_raster" contain separate results for each species. The "Species_figure" folder displays the results graphically, while the "Species_raster" folder has files in raster format (.tif). Both folders have subfolders indicating which database was used to create the maps, such as 0, 50 and 100 km.The folder named "Calibration_results" contains the results of the model calibration achieved in this study. Within this folder, the subfolder "train" displays the data used for every species in each of the ten runs to create the minimum volume ellipses. The subfolder "raw" displays all the results from every possible combination of models. Lastly, the subfolder "weight" displays the average results of the chosen model. Finally, Pearson correlationship of databases with more than 30 occurrences are shown in the folder “Correlationship”. To replicate our results, please access the "Code_replication" folder, which includes the required scripts and databases. Please, open first the “rProj” file in rstudio and follow the numbered scripts. Note that the unnumbered scripts are functions to run the models.Finally, we stored the occurrences downloaded from the Ocean Biodiversity Information System (OBIS) and Vertnet, along with their references, using the 'robis' and 'vertnet' packages, respectively (“Occurrences” folder). For the data obtained from the Global Biodiversity Information Facility (GBIF), we stored it as data keys and the number of records to create a derived dataset, which can be accessed and cited following the next link: https://doi.org/10.15468/dd.8wacqq.
DOI: 10.6084/m9.figshare.24257542.v1
title: Supporting information for "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "

description: Supporting information of the manuscript "Can upwelling regions be potential thermal refugia for marine fishes during climate warming? "These are the files created for the project titled " Can upwelling regions be potential thermal refugia for marine fishes during climate warming" The "Average_richness" file shows the total pixel richness, which is the sum of the different binary maps developed. The "Average Suitability" folder contains the average value of all species suitability maps. The "Difference_suitability" and "Difference_richness" files show the subtraction results between suitability and richness, respectively, for the present and different RCP scenarios for the periods 2040-2050 and 2090-2100. The "Exploratory_figures" folder displays the maximum, mean, and minimum temperatures at which the species are reported. The Jaccard turnover results are stored in the "Jaccard" folder. The filenames indicate the period (Present, 2040-2050 (2050), and 2090-2100 (2100)), the RCP scenarios (6.0 (6) and 8.5 (8)), and the filtered used (0,50,100 and 500 for 0 km filter, 50 km filter, 100 km filter, and 500 km filter respectevely). The two folders named "Species_figure" and "Species_raster" contain separate results for each species. The "Species_figure" folder displays the results graphically, while the "Species_raster" folder has files in raster format (.tif). Both folders have subfolders indicating which database was used to create the maps, such as 0, 50 and 100 km.The folder named "Calibration_results" contains the results of the model calibration achieved in this study. Within this folder, the subfolder "train" displays the data used for every species in each of the ten runs to create the minimum volume ellipses. The subfolder "raw" displays all the results from every possible combination of models. Lastly, the subfolder "weight" displays the average results of the chosen model. Finally, Pearson correlationship of databases with more than 30 occurrences are shown in the folder “Correlationship”. To replicate our results, please access the "Code_replication" folder, which includes the required scripts and databases. Please, open first the “rProj” file in rstudio and follow the numbered scripts. Note that the unnumbered scripts are functions to run the models.Finally, we stored the occurrences downloaded from the Ocean Biodiversity Information System (OBIS) and Vertnet, along with their references, using the 'robis' and 'vertnet' packages, respectively (“Occurrences” folder). For the data obtained from the Global Biodiversity Information Facility (GBIF), we stored it as data keys and the number of records to create a derived dataset, which can be accessed and cited following the next link: https://doi.org/10.15468/dd.8wacqq.
DOI: 10.15468/dl.wnssz2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caretta thunbergi Merrem, 1820",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006351-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26132890
title: <b>DBPFNet</b><b>: A double branch parallel fusion neural network method for land subsidence susceptibility mapping with InSAR observation data</b>

description: The compressed package (Beijing_plains.rar) contains the code files implemented by an under review paper ("DBPFNet: A double branch parallel fusion neural network method for land subsidence susceptibility mapping with InSAR observation data").The Beijing_plains.rar contains four files, the code, the Image, the Label, and the Result.
DOI: 10.15468/dl.zuxf9c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelone mydas Boulenger, 1889",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006352-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.12604354
title: Advances in volumetric super-resolution microscopy and single-particle tracking (associated codes and datasets)

description: Overview

This Zenodo repository contains datasets and code relating to the thesis entitled "Advances in volumetric super-resolution microscopy and single-particle tracking" by Sam G. Daly (Yusuf Hamied Department of Chemistry, University of Cambridge).

Managed/updated versions my be avalible at https://github.com/TheLeeLab.

The Excel Workbook 'MicrolensRelayCalculator' is designed to help in the design of MLAs for SMLFM.

Available Datasets

Chapter 4



Simulated localisation data for various PSFs: standard, astigmatism, double helix, SMLFM, and tetrapod; 4000 detected photons, 20 emitters per frame, 200 frames.

Microtubule imaging in a fixed HeLa cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames.


Chapter 5



B cell receptor imaging on a fixed B cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

SPT of the B cell receptor on a live B cell (PALM); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed Jurkat T cell embedded in agarose (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

PD-1 imaging on a fixed T cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed T cell (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.


Chapter 6



SPT of ACBD3 in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.

SPT of TMD mutant (length: 27) in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.


Available Code



Autofocus (BeanShell): Counteracts axial drift in SMLFM experiments.

Calibration (BeanShell): Controls the piezo scanner for axial calibrations in 3D-SMLM.

3D Reconstruction (Matlab): Reconstructs 2D-localised SMLFM data in 3D. Maintained version available on GitHub.

Fiducial correction (Matlab): Removes focal drift artifacts from 3D localisation data.

Temporal grouping (Python): Removes multiple single-molecule blinking events.

3D tracking (Matlab): Converts 3D localisations into tracks and calculates diffusion quantities.

Matching (Matlab): Determines PPV, sensitivity, and Jaccard index from localisation data.

Membrane curvature (Python): Determines the frequency of 3D localisations at a given membrane curvature.


Supported by The Royal Society (RGF\EA\181021)
DOI: 10.5281/zenodo.12528021
title: Advances in volumetric super-resolution microscopy and single-particle tracking (associated codes and datasets)

description: Overview

This Zenodo repository contains datasets and code relating to the thesis entitled "Advances in volumetric super-resolution microscopy and single-particle tracking" by Sam G. Daly (Yusuf Hamied Department of Chemistry, University of Cambridge).

Managed/updated versions my be avalible at https://github.com/TheLeeLab.

The Excel Workbook 'MicrolensRelayCalculator' is designed to help in the design of MLAs for SMLFM.

Available Datasets

Chapter 4



Simulated localisation data for various PSFs: standard, astigmatism, double helix, SMLFM, and tetrapod; 4000 detected photons, 20 emitters per frame, 200 frames.

Microtubule imaging in a fixed HeLa cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames.


Chapter 5



B cell receptor imaging on a fixed B cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

SPT of the B cell receptor on a live B cell (PALM); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed Jurkat T cell embedded in agarose (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

PD-1 imaging on a fixed T cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed T cell (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.


Chapter 6



SPT of ACBD3 in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.

SPT of TMD mutant (length: 27) in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.


Available Code



Autofocus (BeanShell): Counteracts axial drift in SMLFM experiments.

Calibration (BeanShell): Controls the piezo scanner for axial calibrations in 3D-SMLM.

3D Reconstruction (Matlab): Reconstructs 2D-localised SMLFM data in 3D. Maintained version available on GitHub.

Fiducial correction (Matlab): Removes focal drift artifacts from 3D localisation data.

Temporal grouping (Python): Removes multiple single-molecule blinking events.

3D tracking (Matlab): Converts 3D localisations into tracks and calculates diffusion quantities.

Matching (Matlab): Determines PPV, sensitivity, and Jaccard index from localisation data.

Membrane curvature (Python): Determines the frequency of 3D localisations at a given membrane curvature.


Supported by The Royal Society (RGF\EA\181021)
DOI: 10.5281/zenodo.12528022
title: Advances in volumetric super-resolution microscopy and single-particle tracking (associated codes and datasets)

description: Overview

This Zenodo repository contains datasets and code relating to the thesis entitled "Advances in volumetric super-resolution microscopy and single-particle tracking" by Sam G. Daly (Yusuf Hamied Department of Chemistry, University of Cambridge).

Managed/updated versions my be avalible at https://github.com/TheLeeLab.

Available Datasets

Chapter 4



Simulated localisation data for various PSFs: standard, astigmatism, double helix, SMLFM, and tetrapod; 4000 detected photons, 20 emitters per frame, 200 frames.

Microtubule imaging in a fixed HeLa cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames.


Chapter 5



B cell receptor imaging on a fixed B cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

SPT of the B cell receptor on a live B cell (PALM); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed Jurkat T cell embedded in agarose (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

PD-1 imaging on a fixed T cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.

Membrane imaging on a fixed T cell (resPAINT); 20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.


Chapter 6



SPT of ACBD3 in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.

SPT of TMD mutant (length: 27) in a live HeLa cell (PALM); 20 ms exposure, 640 and 405 nm excitation, 200 frames.


Available Code



Autofocus (BeanShell): Counteracts axial drift in SMLFM experiments.

Calibration (BeanShell): Controls the piezo scanner for axial calibrations in 3D-SMLM.

3D Reconstruction (Matlab): Reconstructs 2D-localised SMLFM data in 3D. Maintained version available on GitHub.

Fiducial correction (Matlab): Removes focal drift artifacts from 3D localisation data.

Temporal grouping (Python): Removes multiple single-molecule blinking events.

3D tracking (Matlab): Converts 3D localisations into tracks and calculates diffusion quantities.

Matching (Matlab): Determines PPV, sensitivity, and Jaccard index from localisation data.

Membrane curvature (Python): Determines the frequency of 3D localisations at a given membrane curvature.


Supported by The Royal Society (RGF\EA\181021)
DOI: 10.15468/dl.qn28db
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelonia agassizii Bocourt, 1868",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006353-240626123714530/datasets/export for details.
DOI: 10.15468/dl.a7tcej
title: Occurrence Download

description: A dataset containing 3535 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Launaea fragilis (Asso) Pau"
 ]
}

 The dataset includes 3535 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006356-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xze7ju
title: Occurrence Download

description: A dataset containing 1235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Botaurus stellaris (Linnaeus, 1758)",
 "Year 2020-2024"
 ]
}

 The dataset includes 1235 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006355-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8b9h94
title: Occurrence Download

description: A dataset containing 7540 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spodoptera litura (Fabricius, 1775)"
 ]
}

 The dataset includes 7540 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006354-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rz4849
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelonia agassizzii Lehr, 2002",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006357-240626123714530/datasets/export for details.
DOI: 10.15468/dl.mcgd5m
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelonia albiventer Nardo, 1864",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006358-240626123714530/datasets/export for details.
DOI: 10.15468/dl.s77kax
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelonia bicarinata Lesson, 1834",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006359-240626123714530/datasets/export for details.
DOI: 10.15468/dl.95udxv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chelonia castanea Eschscholtz, 1829",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006360-240626123714530/datasets/export for details.