cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5190144
title: Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination

description: Submissions for the Tractostorm 2 Project [1]  from our collaborators (raters) are available for new analysis.
Contains regions of interest (ROIs) as well as resulting bundles. Segmentations were performed with MI-Brain [2] (MI-Brain)


Initial data is the same as in the initial Tractostorm Project [3]
Contains the data as sent to collaborators and the written document containing the dissection protocol in detail.


[1] Rheault, Francois, et al. "Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination." Human Brain Mapping (2022).
[2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." Proceedings of the ISMRM Diffusion study group workshop, Lisbon. 2016.
[3] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." Human brain mapping 41.7 (2020): 1859-1874.


Data Organization:
The 5 HCP subjects were duplicated 4 times each.
193441 -> A111, B218, C317, D418
219231 -> A127, B228, C320, D426
286650 -> A136, B237, C338, D436
486759 -> A149, B246, C344, D443
615441 -> A156, B252, C359, D450

Bundles can be segmented automatically using the scilpy toolbox.
scil_filter_tractogram.py ${INPUT} ${OUTPUT} ${OPTIONS}



	
${INPUT} would be the whole brain tractogram of an HCP subject in data_to_segment.zip
	
${OUTPUT} would be the bundle filename (preferably .trk format)
	
${OPTIONS} would be the sequence of ROIs to apply, one for each bundle.
	

		
CC: '--drawn_roi CENTRAL_CC.nii.gz any include --drawn_roi LOWER_AXIAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude --drawn_roi POST_C_R.nii.gz any exclude --drawn_roi PRE_C_R.nii.gz any exclude'
		
AF_L: '--drawn_roi CENTRAL_CS_L.nii.gz any include --drawn_roi MEDIAL_SAGITTAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any include --drawn_roi PRE_C_L.nii.gz any include --drawn_roi TEMPORAL_ENTRY.nii.gz any include --drawn_roi TEMPORAL_STEM.nii.gz any exclude'
		
PYT_L: '--drawn_roi IC_L.nii.gz any include --drawn_roi MO_L.nii.gz any include --drawn_roi MB_L.nii.gz any include --drawn_roi MO_L_NOT.nii.gz any exclude --drawn_roi MID_SAGITTAL_PLANE.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude'
DOI: 10.5281/zenodo.5190145
title: Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination

description: Initial data is the same as in the initial Tractostorm Project [1]<br> This repository contains the data as sent to collaborators and the writen document containing the dissection protocol in details.<br> Segmentation were performed with MI-Brain [2] (version MI-Brain-2020.04.09_r2e0ff5-linux-x86_64) The submissions from our collaborators (raters) will be added in the next year, following instructions from the publisher or depending on usage in the context of a conference challenge.<br> <br> [1] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." <em>Human brain mapping</em> 41.7 (2020): 1859-1874.<br> [2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." <em>Proceedings of the ISMRM Diffusion study group workshop, Lisbon</em>. 2016.
description: Initial upload, more will follow in 2021-2022
description: {"references": ["Rheault, Francois, et al. \"Tractostorm: The what, why, and how of tractography dissection reproducibility.\" Human brain mapping 41.7 (2020): 1859-1874.", "Rheault, Francois, et al. \"MI-Brain, a software to handle tractograms and perform interactive virtual dissection.\" Proceedings of the ISMRM Diffusion study group workshop, Lisbon. 2016."]}
DOI: 10.5281/zenodo.6473141
title: Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination

description: Submissions for the Tractostorm 2 Project [1]  from our collaborators (raters) are available for new analysis.
Contains regions of interest (ROIs) as well as resulting bundles. Segmentations were performed with MI-Brain [2] (MI-Brain)


Initial data is the same as in the initial Tractostorm Project [3]
Contains the data as sent to collaborators and the written document containing the dissection protocol in detail.


[1] Rheault, Francois, et al. "Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination." Human Brain Mapping (2022).
[2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." Proceedings of the ISMRM Diffusion study group workshop, Lisbon. 2016.
[3] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." Human brain mapping 41.7 (2020): 1859-1874.


Data Organization:
The 5 HCP subjects were duplicated 4 times each.
193441 -> A111, B218, C317, D418
219231 -> A127, B228, C320, D426
286650 -> A136, B237, C338, D436
486759 -> A149, B246, C344, D443
615441 -> A156, B252, C359, D450

Bundles can be segmented automatically using the scilpy toolbox.
scil_filter_tractogram.py ${INPUT} ${OUTPUT} ${OPTIONS}



	
${INPUT} would be the whole brain tractogram of an HCP subject in data_to_segment.zip
	
${OUTPUT} would be the bundle filename (preferably .trk format)
	
${OPTIONS} would be the sequence of ROIs to apply, one for each bundle.
	

		
CC: '--drawn_roi CENTRAL_CC.nii.gz any include --drawn_roi LOWER_AXIAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude --drawn_roi POST_C_R.nii.gz any exclude --drawn_roi PRE_C_R.nii.gz any exclude'
		
AF_L: '--drawn_roi CENTRAL_CS_L.nii.gz any include --drawn_roi MEDIAL_SAGITTAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any include --drawn_roi PRE_C_L.nii.gz any include --drawn_roi TEMPORAL_ENTRY.nii.gz any include --drawn_roi TEMPORAL_STEM.nii.gz any exclude'
		
PYT_L: '--drawn_roi IC_L.nii.gz any include --drawn_roi MO_L.nii.gz any include --drawn_roi MB_L.nii.gz any include --drawn_roi MO_L_NOT.nii.gz any exclude --drawn_roi MID_SAGITTAL_PLANE.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude'
DOI: 10.15468/dl.6z3hzc
title: Occurrence Download

description: A dataset containing 3487 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.65401 -55.54076,-62.63763 -55.92302,-60.64206 -43.43572,-54.2409 -38.19194,-49.17331 -36.06573,-32.84597 -6.78684,-53.53427 11.31209,-67.32942 13.67663,-79.63655 11.31209,-81.71253 -4.03814,-75.28251 -21.64415,-77.65401 -55.54076))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Anairetes reguloides (Orbigny & Lafresnaye, 1837)"
 ]
}

 The dataset includes 3487 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044721-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ajke73
title: Occurrence Download

description: A dataset containing 43637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus colchicus Linnaeus, 1758",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Machine Observation, Observation, Occurrence evidence)",
 "Year 2008-2024",
 "Country is United States of America",
 "StateProvince is Montana"
 ]
}

 The dataset includes 43637 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044722-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14538407
title: Data for Solvated Initial Conditions Paper

description: Scripts, input files and molecular dynamics trajectories for paper (preprint available at https://doi.org/10.26434/chemrxiv-2024-nfsqp)about ideal ways to compute initial conditions for nonadiabatic dynamics simulations of chromophores in solution.
DOI: 10.5281/zenodo.14538408
title: Data for Solvated Initial Conditions Paper

description: Scripts, input files and molecular dynamics trajectories for paper (preprint available at https://doi.org/10.26434/chemrxiv-2024-nfsqp)about ideal ways to compute initial conditions for nonadiabatic dynamics simulations of chromophores in solution.
DOI: 10.15468/dl.2kg33m
title: Occurrence Download

description: A dataset containing 18040 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bromus japonicus Houtt."
 ]
}

 The dataset includes 18040 records from 498 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044723-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28075223
title: Fonio (Digitaria exilis) Assembly Files

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' LAZY1, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.6084/m9.figshare.28075223.v1
title: Fonio Assembly Files

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' LAZY1, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.6084/m9.figshare.28075223.v2
title: Fonio (Digitaria exilis) Assembly Files

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' LAZY1, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.6084/m9.figshare.28075244
title: Fonio (Digitaria exilis) Time of Day Expression Data

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' <i>LAZY1</i>, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.6084/m9.figshare.28075244.v2
title: Fonio (Digitaria exilis) Time of Day Expression Data

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' <i>LAZY1</i>, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.6084/m9.figshare.28075244.v1
title: Fonio Time of Day Expression Data

description: Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' <i>LAZY1</i>, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.
DOI: 10.15468/dl.nszzut
title: Occurrence Download

description: A dataset containing 192009 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens parviflora DC."
 ]
}

 The dataset includes 192009 records from 797 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044724-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10258727
title: WallStreetBets 2022
DOI: 10.5281/zenodo.14538469
title: Data Files for Climate-based Maize Loss Rate Simulations

description: This archive contains data files from an open source pipeline looking at how crop insurance rates may change in the future within the US Corn Belt using SCYM and CHC-CMIP6. These are available under a Creative Commons license. Unless otherwise specified, these report on SSP245.

See README for more details including column-level description of each resource. Funded by the Eric and Wendy Schmidt Center for Data Science and Environment at the University of California, Berkeley.
DOI: 10.15468/dl.a7wdtu
title: Occurrence Download

description: A dataset containing 3244 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus tenuis (Duméril & Bibron, 1837)"
 ]
}

 The dataset includes 3244 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044725-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14538487
title: HD2NetData
DOI: 10.5281/zenodo.14538488
title: HD2NetData
DOI: 10.57841/casdc.0004264
title: 水稻新品种“科天优4312”审定证书及相关材料
DOI: 10.15468/dl.qvnakd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudalsophis biserialis biserialis"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044726-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c8t3sz
title: Occurrence Download

description: A dataset containing 43187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is CardObs : Observations naturalistes issues de l'outil CardObs-Données naturalistes de Pascal Dupont",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 43187 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044727-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13356981
title: Data Files for Climate-based Maize Loss Rate Simulations

description: ⚠️ WARNING: These files are outdated. Please see https://zenodo.org/records/14538469. ⚠️

 

This archive contains data files from an open source pipeline looking at how crop insurance rates may change in the future within the US Corn Belt using SCYM and CHC-CMIP6. These are available under a Creative Commons license. Unless otherwise specified, these report on SSP245.

See README for more details including column-level description of each resource.
DOI: 10.5281/zenodo.13356980
title: Data Files for Climate-based Maize Loss Rate Simulations

description: This archive contains data files from an open source pipeline looking at how crop insurance rates may change in the future within the US Corn Belt using SCYM and CHC-CMIP6. These are available under a Creative Commons license. Unless otherwise specified, these report on SSP245.

See README for more details including column-level description of each resource. Funded by the Eric and Wendy Schmidt Center for Data Science and Environment at the University of California, Berkeley.
DOI: 10.5281/zenodo.14533227
title: Data Files for Climate-based Maize Loss Rate Simulations

description: ⚠️ WARNING: These files are outdated. Please see https://zenodo.org/records/14538469. ⚠️

 

This archive contains data files from an open source pipeline looking at how crop insurance rates may change in the future within the US Corn Belt using SCYM and CHC-CMIP6. These are available under a Creative Commons license. Unless otherwise specified, these report on SSP245.

See README for more details including column-level description of each resource. Funded by the Eric and Wendy Schmidt Center for Data Science and Environment at the University of California, Berkeley.
DOI: 10.5281/zenodo.14537666
title: Gold standard for tractograms and meshes io testing

description: Gold standard for tractograms (trk, tck, trx, dpy, vtk, fib) and meshes (gii, pial, vtk, ply, stl, obj) IO testing for the StatefulTractogram (SFT) and StatefulSurface (SFS) in Dipy.
DOI: 10.5281/zenodo.14538513
title: Gold standard for tractograms and meshes io testing

description: Gold standard for tractograms (trk, tck, trx, dpy, vtk, fib) and meshes (gii, pial, vtk, ply, stl, obj) IO testing for the StatefulTractogram (SFT) and StatefulSurface (SFS) in Dipy.
DOI: 10.5281/zenodo.2651349
title: Gold standard for tractogram io testing

description: Gold standard for tractogram io testing (in dipy)
DOI: 10.5281/zenodo.6576865
title: Gold standard for tractogram io testing

description: Gold standard for tractogram io testing (in dipy)
DOI: 10.5281/zenodo.7767654
title: Gold standard for tractogram io testing

description: Gold standard for tractogram io testing (in dipy)
DOI: 10.5281/zenodo.2651348
title: Gold standard for tractograms and meshes io testing

description: Gold standard for tractograms (trk, tck, trx, dpy, vtk, fib) and meshes (gii, pial, vtk, ply, stl, obj) IO testing for the StatefulTractogram (SFT) and StatefulSurface (SFS) in Dipy.
DOI: 10.5281/zenodo.14279528
title: Gravity and Magnetic Field Reconstruction Using Diffusion Model

description: This is the code and data for Gravity and Magnetic Field Reconstruction Using Diffusion Model
DOI: 10.5281/zenodo.14279529
title: Gravity and Magnetic Field Reconstruction Using Diffusion Model

description: This is the code and data for Gravity and Magnetic Field Reconstruction Using Diffusion Model