cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10933987
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - Irr+RC

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from mice that werethat were irradiated to ablate adult neurogenesis and housed in a regular cage (Irr+RC). 

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

All imaged mice were female. Refer to the original publication for additional information. 
description: ACKNOWLEDGEMENTS

We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.5281/zenodo.10933988
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - Irr+RC

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from mice that werethat were irradiated to ablate adult neurogenesis and housed in a regular cage (Irr+RC). 

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

All imaged mice were female. Refer to the original publication for additional information. 
description: ACKNOWLEDGEMENTS

We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.15468/dl.d7mrgw
title: Occurrence Download

description: A dataset containing 568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Geometry POLYGON((-79.90025 -4.64604,-63.05526 -4.64604,-63.05526 10.48899,-79.90025 10.48899,-79.90025 -4.64604))",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 568 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070577-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.drjcw3
title: Occurrence Download

description: A dataset containing 188 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Labidocera scotti Giesbrecht, 1897"
 ]
}

 The dataset includes 188 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122244-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5uhhj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nasturtium officinale subsp. rotundifolium A.P.Khokhr."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042917-220831081235567/datasets/export for details.
DOI: 10.5281/zenodo.10914284
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - EE dataset

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from mice that were housed in an enriched environment (EE). 

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

All imaged mice were female. Refer to the original publication for additional information. 
description: We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.5281/zenodo.10914285
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - EE dataset

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from mice that were housed in an enriched environment (EE). 

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

All imaged mice were female. Refer to the original publication for additional information. 
description: We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.15468/dl.p42sq5
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Raja cortezensis McEachran & Miyake, 1988"
 ]
}

 The dataset includes 22 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029736-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sakhym
title: Occurrence Download

description: A dataset containing 1623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Colombia",
 "Geometry POLYGON((-79.97182 3.93705,-68.68604 3.93705,-68.68604 11.69543,-79.97182 11.69543,-79.97182 3.93705))",
 "HasGeospatialIssue is false",
 "MediaType is one of (Image, Video)",
 "Month is one of (January, February, March, April, May, December, October, August, July, June, September, November)",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Orchidaceae",
 "Year 2020-2022"
 ]
}

 The dataset includes 1623 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070570-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10913385
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - hM4Di Silencing

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from CNO-induced chemogenetic silencing experiments in hM4Di+ and hM4Di-(control) mice. There is another Zenodo dataset with the remaining hM4Di-(control) mice here. The folder for each mouse includes baseline (pre) and post-CNO (cno) recordings.

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

Refer to the original publication for additional information. The sex of individual mice is as follows:

 




Group
Mouse #
Sex
Group
Mouse #
Sex


hM4Di+
M1
M
hM4Di-
M1
M


 
M2
M
 
M2
M


 
M3
F
 
M3
M


 
M4
F
 
 
 


 
M5
M
 
 
 


 
M6
M
 
 
 


 
M7
M
 
 
 


 
M8
F
 
 
 


 
M9
F
 
 
 
description: ACKNOWLEDGEMENTS

We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.5281/zenodo.10913386
title: Adult neurogenesis improves spatial information encoding in the mouse hippocampus - hM4Di Silencing

description: In vivo two-photon imaging dataset for Frechou et al. "Adult neurogenesis improves spatial information encoding in the mouse hippocampus"

This dataset includes data from CNO-induced chemogenetic silencing experiments in hM4Di+ and hM4Di-(control) mice. There is another Zenodo dataset with the remaining hM4Di-(control) mice here. The folder for each mouse includes baseline (pre) and post-CNO (cno) recordings.

For each recording we included raw imaging data consisting of:



Individual frames (.tif files) from 3 consecutive 3 min Ca2+ imaging movies (which were concatenated for analysis)

Microscope settings metadata (Experiment.xml)

Mouse location data (Episode001.h5 in SyncData folder) containing rotary encoder and RFID data


Some analyzed data is also included:



Suite2p analysis data (Suite2p folder)

fluorescence.npy contains raw fluorescence data (the F output of Suite2p data extraction). Rows are individual cells and columns are frames (i.e. timepoints) acquired at 15.253 Hz.

positions.npy contains the position of the mouse on the treadmill belt indexed from 0 to 100.


Both NumPy(.npy) files are the output of the Preprocessing.py code, part of the analysis pipeline used for data analysis in the original publication, which can be found at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis

Refer to the original publication for additional information. The sex of individual mice is as follows:

 




Group
Mouse #
Sex
Group
Mouse #
Sex


hM4Di+
M1
M
hM4Di-
M1
M


 
M2
M
 
M2
M


 
M3
F
 
M3
M


 
M4
F
 
 
 


 
M5
M
 
 
 


 
M6
M
 
 
 


 
M7
M
 
 
 


 
M8
F
 
 
 


 
M9
F
 
 
 
description: ACKNOWLEDGEMENTS

We thank Dr. Jake Jordan, Roland Ferger, Elizabeth Wood, Dr. Maria Gulinello, Kevin Fisher, Dr. Mimi Kim and Dr. Sacha Sokoloski for technical advice, assistance and discussions. M.A.F. was supported by a Fulbright Scholarship. M.A.F. and K.D.M. were funded by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. J.T.G. was supported by the Whitehall Foundation (Research Grant 2019-05-71) and the National Institutes of Health (NINDS R01NS125252-01A1). R.C.C. was supported by the National Institutes of Health (NEI R01EY030578, NIDA RF1DA056400). Confocal microscopy experiments were supported by a  shared instrumentation grant (1S10OD025295-01A1). This article is dedicated to the memory of Dr. Paul S. Frenette (1965-2021) who provided invaluable encouragement and support for this project.
DOI: 10.15468/dl.d4n93e
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nasturtium sagittatum R.Br., 1812"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042928-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mr59un
title: Occurrence Download

description: A dataset containing 14180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carex buxbaumii Wahlenb.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14180 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029705-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xstvbg
title: Occurrence Download

description: A dataset containing 7075 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (United States of America, Canada)",
 "MediaType is Image",
 "TaxonKey is Diervilla lonicera Mill."
 ]
}

 The dataset includes 7075 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097934-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.haavrj
title: Occurrence Download

description: A dataset containing 3313 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Labidocera wollastoni (Lubbock, 1857)"
 ]
}

 The dataset includes 3313 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122247-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3susg4
title: Occurrence Download

description: A dataset containing 7052 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carcharhinus tilstoni (Whitley, 1950)"
 ]
}

 The dataset includes 7052 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029706-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esw5tq
title: Occurrence Download

description: A dataset containing 175 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Puma concolor concolor"
 ]
}

 The dataset includes 175 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070600-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bt77w
title: Occurrence Download

description: A dataset containing 12817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Betula pubescens Ehrh."
 ]
}

 The dataset includes 12817 records from 268 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122264-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brbf6a
title: Occurrence Download

description: A dataset containing 706 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leptophis diplotropis (Günther, 1872)"
 ]
}

 The dataset includes 706 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029712-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xe3pbj
title: Occurrence Download

description: A dataset containing 260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Colombia",
 "Geometry POLYGON((-79.97182 3.93705,-68.68604 3.93705,-68.68604 11.69543,-79.97182 11.69543,-79.97182 3.93705))",
 "HasGeospatialIssue is false",
 "MediaType is Image",
 "Month is August",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset includes 260 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070591-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dskpqj
title: Occurrence Download

description: A dataset containing 1522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carex cherokeensis Schwein.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1522 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029724-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rktuax
title: Occurrence Download

description: A dataset containing 875 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Labidocera minuta Giesbrecht, 1889"
 ]
}

 The dataset includes 875 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122235-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqcgx7
title: Occurrence Download

description: A dataset containing 2297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Occurrence evidence)",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Arbutus xalapensis Kunth"
 ]
}

 The dataset includes 2297 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097945-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.