cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35077/act-top
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 889787076

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 889787076', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', OrganName:'Brain', SampleLocalID:'889787076', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24458', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.5281/zenodo.7860313
title: Soil moisture and climate data from SmartCityTrees sensors in Amersfoort

description: Within the frame of the SCOREwater project, the City of Amersfoort commissioned Hoefakker to install Teneo soil moisture and climate monitor sensors at several locations in the Schothorst neighbourhood and the Central Railway area. These sensors have been branded as "SmartCityTrees" by Hoefakker. The sensors measure soil moisture, temperature and humidity. Schothorst and the Central Railway area differ in groundwater levels. In Schothorst the groundwater levels are higher (average height: 0.7 meter to 1.0 meter below ground level) than in the Central Railway area (average height: lower than 1.6 meter below ground level). The lowest soil moisture sensors are placed on 1.2 meter below ground level. As a result, in the Schothorst area the sensors are located close to or in the groundwater during winter. In the Central Railway area they are located far above the groundwater level. This makes both areas interesting to include. What all soil moisture sensors have in common is that they are all located nearby trees and in public spaces. Locations differ in terms of: being in the sun or in the shade, being in a green setting (unpaved, such as parks) or being in a paved setting, and being near surface water or not. Because of the differences between the locations the sensors have been installed in, data from the sensors can be used to investigate questions such as: What is the influence of the type of surface on soil moisture levels? Does the nearby presence of surface water affect soil moisture? What is the influence of heat on soil moisture? What is the relation between groundwater levels fluctuance and soil moisture? Are adjustments on in public spaces (on street level) helpful to improve the soil situation for a more climate adaptive city? The soil moisture dataset contains soil moisture VWC (volumetric water content, the ratio of water volume to soil volume). This is a percentage represented as a number between 0 and 1. 0.73 for example is 73%. The climate dataset contains temperature in degrees Celsius and the relative humidity. Relative humidity is a percentage represented as a number between 0 and 1 as well. Time period: from 2021-01-01 to 2022-12-31.
DOI: 10.5281/zenodo.7860312
title: Soil moisture and climate data from SmartCityTrees sensors in Amersfoort

description: Within the frame of the SCOREwater project, the City of Amersfoort commissioned Hoefakker to install Teneo soil moisture and climate monitor sensors at several locations in the Schothorst neighbourhood and the Central Railway area. These sensors have been branded as "SmartCityTrees" by Hoefakker. The sensors measure soil moisture, temperature and humidity. Schothorst and the Central Railway area differ in groundwater levels. In Schothorst the groundwater levels are higher (average height: 0.7 meter to 1.0 meter below ground level) than in the Central Railway area (average height: lower than 1.6 meter below ground level). The lowest soil moisture sensors are placed on 1.2 meter below ground level. As a result, in the Schothorst area the sensors are located close to or in the groundwater during winter. In the Central Railway area they are located far above the groundwater level. This makes both areas interesting to include. What all soil moisture sensors have in common is that they are all located nearby trees and in public spaces. Locations differ in terms of: being in the sun or in the shade, being in a green setting (unpaved, such as parks) or being in a paved setting, and being near surface water or not. Because of the differences between the locations the sensors have been installed in, data from the sensors can be used to investigate questions such as: What is the influence of the type of surface on soil moisture levels? Does the nearby presence of surface water affect soil moisture? What is the influence of heat on soil moisture? What is the relation between groundwater levels fluctuance and soil moisture? Are adjustments on in public spaces (on street level) helpful to improve the soil situation for a more climate adaptive city? The soil moisture dataset contains soil moisture VWC (volumetric water content, the ratio of water volume to soil volume). This is a percentage represented as a number between 0 and 1. 0.73 for example is 73%. The climate dataset contains temperature in degrees Celsius and the relative humidity. Relative humidity is a percentage represented as a number between 0 and 1 as well. Time period: from 2021-01-01 to 2022-12-31.
DOI: 10.35077/act-toy
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893412652

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893412652', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'893412652', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24377', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.5517/ccdc.csd.cc2803p3
title: CCDC 2085484: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803q4
title: CCDC 2085485: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803r5
title: CCDC 2085486: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803s6
title: CCDC 2085487: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803t7
title: CCDC 2085488: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803v8
title: CCDC 2085489: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2803w9
title: CCDC 2085490: Experimental Crystal Structure Determination

description: Related Article: Thomas G. F. Marsh, Alessia Santambrogio, Ben J. Murray, Lee T. Boulton, Juan A. Aguilar, Dmitry S. Yufit, Graham Sandford, William D. G. Brittain|2023|Eur.J.Org.Chem.|26|e202300058|doi:10.1002/ejoc.202300058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28q37c
title: CCDC 2106612: Experimental Crystal Structure Determination

description: Related Article: Hiroto Fujisaki, Tomoya Ishizuka, Hiroaki Kotani, Yoshihito Shiota, Kazunari Yoshizawa, Takahiko Kojima|2023|Nature (London)|616|476|doi:10.1038/s41586-023-05821-2
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cjr8y
title: CCDC 2190840: Experimental Crystal Structure Determination

description: Related Article: Xiao-Fei Liu, Ke Zhang, Lin-Lin Wang, He Wang, Jian Huang, Xun-Ting Zhang, Xiao-Bing Lu, Wen-Zhen Zhang|2022|J.Org.Chem.|88|5212|doi:10.1021/acs.joc.2c01816
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.35077/act-try
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893503755

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893503755', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'893503755', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24378', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.6084/m9.figshare.22687714
title: S25_BMDM_WT_16_hours_LPS_rep1.bam

description: sample1
DOI: 10.6084/m9.figshare.22687714.v1
title: S25_BMDM_WT_16_hours_LPS_rep1.bam

description: sample1
DOI: 10.5281/zenodo.7860326
title: Apparent temperature data

description: This dataset includes apparent temperature data from thermal walks organized by the City of Amersfoort (COA) to be able to evaluate how people perceive temperature at certain locations. The subjective opinions of the participants of the thermal walk are complemented by measurements from a sensor measuring air temperature, wind speed and humidity.
DOI: 10.5281/zenodo.7860325
title: Apparent temperature data

description: This dataset includes apparent temperature data from thermal walks organized by the City of Amersfoort (COA) to be able to evaluate how people perceive temperature at certain locations. The subjective opinions of the participants of the thermal walk are complemented by measurements from a sensor measuring air temperature, wind speed and humidity.
DOI: 10.35077/act-tub
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893647190

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893647190', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'893647190', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24475', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.35077/act-tug
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893714311

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 893714311', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'893714311', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24376', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'
DOI: 10.5281/zenodo.7860332
title: Cell cycle heterogeneity in pancreatic ductal adenocarcinoma

description: Multiplexed, single-cell imaging data for PDAC cell lines.
DOI: 10.5281/zenodo.7860331
title: Cell cycle heterogeneity in pancreatic ductal adenocarcinoma

description: Multiplexed, single-cell imaging data for PDAC cell lines.
DOI: 10.35077/act-use
title: Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 894360289

description: Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
description: https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
description: DATASET METADATA: title:'Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 894360289', GeneralModality:'cell morphology', Technique:'Patch-seq' SPECIMEN METADATA: LocalID:'H19.03.314', Species:'Human', NCBITaxonomy:'NCBI:txid9606', Age:'33', Ageunit:'years', Sex:'Male', Genotype:'culture, enhancer AAV', OrganName:'Brain', SampleLocalID:'894360289', Atlas:'Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24469', Locations:'MTG' INSTRUMENT METADATA: MicroscopeType:'Brightfield', MicroscopeManufacturerAndModel:'Zeiss AxioImager Z2 microscope', ObjectiveImmersion:'Oil' IMAGE METADATA: xAxis:'NA', yAxis:'NA', zAxis:'NA', Number:'NA', displayColor:'NA', stepSizeX:'0.114', stepSizeY:'0.114', stepSizeZ:'0.44'