cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13790068
title: Long-range axonal projections analyses of the mouse brain

description: Accompanying data and analyses of the article "Generating brain-wide connectome using synthetic axonal morphologies". The code to reproduce the figures is available at this repository.

Main contents:



SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, Peng et al. 2021, Winnubst et al. 2019) after morphology-workflows Repair post-processing steps.

atlas: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)

out_a_p: output of the axon projection anaylsis and clustering on the 3601 morphologies of the dataset.



axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.

clustering_output.csv: output of the GMM clustering.

config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.



circuit: contains files describing the circuit synthesized with Blue Brain's circuit-build*.



bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).

sonata: files that contain nodes and edges of the circuit.

auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with Voxcell.

conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with ConnectomeUtilities.Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.



local_axons: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.

synthesized_MOp5_LRAs: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. 

out_a_p_synth_MOp5: axonal projection analysis of the synthesized MOp5 axons.

synthesized_isocortex_cells: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with MorphIO.

synthesized_isocortex_LRAs: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. 


Additional files:



flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.

config_a_s.cfg: configuration file used to synthesize the long-range axons with the axon-synthesis code.

target_pts: tufts common ancestors for the synthesized MOp5 axons.

brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.


*These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.
DOI: 10.5281/zenodo.13790069
title: Long-range axonal projections analyses of the mouse brain

description: Accompanying data and analyses of the article "Generating brain-wide connectome using synthetic axonal morphologies". The code to reproduce the figures is available at this repository.

Main contents:



SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, Peng et al. 2021, Winnubst et al. 2019) after morphology-workflows Repair post-processing steps.

atlas : atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)

out_a_p : output of the axonal projection* anaylsis and clustering on the 3601 morphologies of the dataset.



axon_lengths_12.csv, axon_terminals_12.csv : the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.

clustering_output.csv : output of the GMM clustering.

config_a_p.cfg : configuration file used to produce this analysis, with running the axonal projection code.



circuit : contains files describing the circuit synthesized with Blue Brain's circuit-build*.



bioname : parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).

sonata : files that contain nodes and edges of the circuit.

auxiliary : various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with Voxcell.

conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with ConnectomeUtilities.Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.



local_axons : biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.

synthesized_MOp5_LRAs : 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. 

out_a_p_synth_MOp5 : axonal projection analysis of the synthesized MOp5 axons.

synthesized_isocortex_cells : all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with MorphIO.

synthesized_isocortex_LRAs : 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. 


Additional files:



flatmap_both.nrrd : file used to generate a flat map visualization of the mouse isocortex, shown in the article.

config_a_s.cfg : configuration file used to synthesize the long-range axons with the axon-synthesis* code.

target_pts : tufts common ancestors for the synthesized MOp5 axons.


*These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.
DOI: 10.5281/zenodo.13950932
title: Long-range axonal projections analyses of the mouse brain

description: Accompanying data and analyses of the article "Generating brain-wide connectome using synthetic axonal morphologies". The code to reproduce the figures is available at this repository.

Main contents:



SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, Peng et al. 2021, Winnubst et al. 2019) after morphology-workflows Repair post-processing steps.

atlas: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)

out_a_p: output of the axonal projection* anaylsis and clustering on the 3601 morphologies of the dataset.



axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.

clustering_output.csv: output of the GMM clustering.

config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.



circuit: contains files describing the circuit synthesized with Blue Brain's circuit-build*.



bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).

sonata: files that contain nodes and edges of the circuit.

auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with Voxcell.

conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with ConnectomeUtilities.Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.



local_axons: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.

synthesized_MOp5_LRAs: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. 

out_a_p_synth_MOp5: axonal projection analysis of the synthesized MOp5 axons.

synthesized_isocortex_cells: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with MorphIO.

synthesized_isocortex_LRAs: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. 


Additional files:



flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.

config_a_s.cfg: configuration file used to synthesize the long-range axons with the axon-synthesis* code.

target_pts: tufts common ancestors for the synthesized MOp5 axons.

brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.


*These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.
DOI: 10.5281/zenodo.13950969
title: Long-range axonal projections analyses of the mouse brain

description: Accompanying data and analyses of the article "Generating brain-wide connectome using synthetic axonal morphologies". The code to reproduce the figures is available at this repository.

Main contents:



SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, Peng et al. 2021, Winnubst et al. 2019) after morphology-workflows Repair post-processing steps.

atlas: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)

out_a_p: output of the axon projection anaylsis and clustering on the 3601 morphologies of the dataset.



axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.

clustering_output.csv: output of the GMM clustering.

config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.



circuit: contains files describing the circuit synthesized with Blue Brain's circuit-build*.



bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).

sonata: files that contain nodes and edges of the circuit.

auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with Voxcell.

conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with ConnectomeUtilities.Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.



local_axons: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.

synthesized_MOp5_LRAs: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. 

out_a_p_synth_MOp5: axonal projection analysis of the synthesized MOp5 axons.

synthesized_isocortex_cells: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with MorphIO.

synthesized_isocortex_LRAs: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. 


Additional files:



flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.

config_a_s.cfg: configuration file used to synthesize the long-range axons with the axon-synthesis code.

target_pts: tufts common ancestors for the synthesized MOp5 axons.

brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.


*These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.
DOI: 10.7910/dvn/hhsjy8/2xd6q5
title: img_636_1898220.jpg

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DOI: 10.7910/dvn/hhsjy8/6mjbvl
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DOI: 10.7910/dvn/hhsjy8/oaxedh
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DOI: 10.7910/dvn/hhsjy8/rdtygs
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DOI: 10.7910/dvn/sfzzah/hmqjom
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-smoked tilapia.tab

description: Value Chain Processors data Version 6 - Smoked Tilapia
DOI: 10.7910/dvn/sfzzah/ixks0k
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-farmed fish.tab

description: Value Chain Processors data Version 6 - Farmed Fish
DOI: 10.7910/dvn/sfzzah/nmiasy
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-frozen tilapia.tab

description: Value Chain Processors data Version 6 - Frozen Tilapia
DOI: 10.7910/dvn/sfzzah/ujmvbb
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-smoked catfish.tab

description: Value Chain Processors data Version 6 - Smoked Catfish
DOI: 10.7910/dvn/sfzzah/wsxl4p
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-parts fish.tab

description: Value Chain Processors data Version 6 - parts fish
DOI: 10.7910/dvn/zcvyag/sfpmiy
title: Contributions_Envi_Exp_bycandidate.tab

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DOI: 10.7910/dvn/zcvyag/shjuyo
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DOI: 10.7910/dvn/hhsjy8/7rlxwz
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DOI: 10.7910/dvn/sfzzah/3zhii4
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-Farmed fish.tab

description: Value chain Retailers Data - version 5- Farmed fish
DOI: 10.7910/dvn/sfzzah/4hnrru
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-frozen tilapia.tab

description: Value chain Retailers Data - version 5-frozen tilapia.
DOI: 10.7910/dvn/sfzzah/au5h0b
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-fresh catfish.tab

description: Value chain Retailers Data - version 5-fresh catfish
DOI: 10.7910/dvn/sfzzah/fiz9p5
title: VC_Processors_Data_Cleaning_Errors_Removed_v6-Value chain actors survey.tab

description: Value Chain Processors data Version 6 - Value Chain Actors Survey
DOI: 10.7910/dvn/sfzzah/kkqqwy
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-fresh tilapia.tab

description: Value chain Retailers Data - version 5-fresh tilapia
DOI: 10.7910/dvn/sfzzah/of2gfk
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-dry catfish.tab

description: Value chain Retailers Data - version 5 - dry catfish
DOI: 10.7910/dvn/zcvyag/8vvf9h
title: Db_Contrib_Pollut_Ind_byparty.tab

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DOI: 10.7910/dvn/zcvyag/bvhapb
title: Db_Contrib_Aggr_bysector.tab

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DOI: 10.7910/dvn/zcvyag/c8aljw
title: DB final estimation.tab

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DOI: 10.7910/dvn/zcvyag/jbu3tb
title: DB governor estimations.tab

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DOI: 10.7910/dvn/zcvyag/upqxv5
title: Db_Contrib_Environ_Org_byparty.tab

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DOI: 10.7910/dvn/zcvyag/utfjh4
title: Final regressions - Tables.do

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DOI: 10.7910/dvn/hhsjy8/6u7qfe
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DOI: 10.7910/dvn/hhsjy8/caekfg
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DOI: 10.7910/dvn/hhsjy8/pvjg5y
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DOI: 10.7910/dvn/sfzzah/dp6rek
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-smoked tilapia.tab

description: Value chain Retailers Data - version 5-smoked tilapia
DOI: 10.7910/dvn/sfzzah/hfszkt
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-smoked catfish.tab

description: Value chain Retailers Data - version 5-smoked catfish
DOI: 10.7910/dvn/sfzzah/jrghrh
title: VC_wholesalers_cleaning_errors_removed_v4 - Farmed_fish.tab

description: Value chain wholesalers v4 - Farmed Fish
DOI: 10.7910/dvn/sfzzah/kekfui
title: VC_wholesalers_cleaning_errors_removed_v4 - Dried Catfish.tab

description: Value chain wholesalers v4 - Dried Catfish
DOI: 10.7910/dvn/sfzzah/nzppek
title: VC_wholesalers_cleaning_errors_removed_v4 - FreshCatfish.tab

description: Value chain wholesalers v4 - Fresh Catfish
DOI: 10.7910/dvn/sfzzah/ycrsye
title: VC_Retailers_Data_Cleaning_Errors_Removed_v5-Value chain actors survey.tab

description: Value chain Retailers Data - version 5 -Value chain actors survey
DOI: 10.7910/dvn/zcvyag/14oqtr
title: Replication file - Figures.do

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DOI: 10.7910/dvn/zcvyag/g9dgyh
title: Readme.docx

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DOI: 10.7910/dvn/hhsjy8/frvb6m
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DOI: 10.7910/dvn/sfzzah/7n0ntq
title: whl_survey-var-names.tab

description: Variable names
DOI: 10.7910/dvn/sfzzah/pxhp2t
title: VC_wholesalers_cleaning_errors_removed_v4 - Frozen tilapia.tab

description: Value chain wholesalers v4 - Frozen Tilapia
DOI: 10.7910/dvn/sfzzah/rhepkw
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DOI: 10.7910/dvn/sfzzah/ty9qhz
title: VC_wholesalers_cleaning_errors_removed_v4 - Value chain actors survey.tab

description: Value chain wholesalers v4 - Value chain actors survey
DOI: 10.7910/dvn/sfzzah/w478rm
title: VC_wholesalers_cleaning_errors_removed_v4 - Smoked Catfish.tab

description: Value chain wholesalers v4 - Smoked Catfish
DOI: 10.7910/dvn/sfzzah/yr5qis
title: VC_wholesalers_cleaning_errors_removed_v4 - Smoked Tilapia.tab

description: Value chain wholesalers v4 - Smoked Tilapia
DOI: 10.7910/dvn/hhsjy8/8npnwr
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DOI: 10.7910/dvn/hhsjy8/lb8fjr
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DOI: 10.7910/dvn/bb0qqk/aqfge0
title: A library of 22 compounds of plant origin known to have antiviral activity was obtained from the PubChem database.tab

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DOI: 10.7910/dvn/hhsjy8/5bhd0o
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DOI: 10.7910/dvn/hhsjy8/4qdsl9
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DOI: 10.7910/dvn/hhsjy8/qjuzzz
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DOI: 10.7910/dvn/n0e55y
title: Replication Data for: "The Lobbying Disclosure Act at 25: Challenges and Opportunities for Analysis"

description: Replication files of longitudinal counts to produce figures in article.
DOI: 10.7910/dvn/n0e55y/exp4i4
title: lda25_replication_data.tab

description: :unav
DOI: 10.7910/dvn/n0e55y/x1ugee
title: lda25_replication_figures_dofile.do

description: Stata code to produce plots in article
DOI: 10.7910/dvn/hhsjy8/8jmgmd
title: img_651_1672055.jpg

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DOI: 10.7910/dvn/hhsjy8/igbmsy
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DOI: 10.7910/dvn/hhsjy8/jqbvkc
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DOI: 10.15468/dl.dkmdmy
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula chungensis Balf.fil. & Kingdon-Ward"
 ]
}

 The dataset includes 150 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094850-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wtskkr
title: Occurrence Download

description: A dataset containing 103307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chorthippus vagans (Eversmann, 1848), Conocephalus fuscus (Fabricius, 1793), Gomphocerippus rufus (Linnaeus, 1758))",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 103307 records from 499 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0167694-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.