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metadata.yaml
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about: []
access:
- schemaKey: AccessRequirements
status: dandi:OpenAccess
acknowledgement: DHK and MN acknowledge support from the United States Army grant
MURI W911NF1910280 and the National Institutes of Health grants U19NS128613 and
R01AT012312.
assetsSummary:
approach:
- name: microscopy approach; cell population imaging
schemaKey: ApproachType
dataStandard:
- identifier: RRID:SCR_015242
name: Neurodata Without Borders (NWB)
schemaKey: StandardsType
measurementTechnique:
- name: two-photon microscopy technique
schemaKey: MeasurementTechniqueType
- name: analytical technique
schemaKey: MeasurementTechniqueType
- name: surgical technique
schemaKey: MeasurementTechniqueType
numberOfBytes: 5324803662
numberOfFiles: 14
numberOfSubjects: 9
schemaKey: AssetsSummary
species:
- identifier: http://purl.obolibrary.org/obo/NCBITaxon_10090
name: Mus musculus - House mouse
schemaKey: SpeciesType
variableMeasured:
- TwoPhotonSeries
- ImagingPlane
- OpticalChannel
- ProcessingModule
- PlaneSegmentation
citation: Zhao, Yue; Boster, Kimberly; Kelley, Douglas; Raicevic, Nikola (2023) BrainFlowZZZ
(Version 0.230602.1307) [Data set]. DANDI archive. https://doi.org/10.48324/dandi.000491/0.230602.1307
contributor:
- affiliation: []
email: yuezhao@rochester.edu
includeInCitation: true
name: Zhao, Yue
roleName:
- dcite:ContactPerson
- dcite:DataManager
- dcite:Maintainer
schemaKey: Person
- affiliation:
- identifier: https://ror.org/022kthw22
name: University of Rochester
schemaKey: Affiliation
identifier: 0000-0001-5178-128X
includeInCitation: true
name: Boster, Kimberly
roleName:
- dcite:Researcher
schemaKey: Person
- affiliation:
- identifier: https://ror.org/022kthw22
name: University of Rochester
schemaKey: Affiliation
email: d.h.kelley@rochester.edu
identifier: 0000-0001-9658-2954
includeInCitation: true
name: Kelley, Douglas
roleName:
- dcite:ContactPerson
- dcite:ProjectLeader
- dcite:ProjectManager
schemaKey: Person
- awardNumber: MURI W911NF1910280
contactPoint: []
identifier: https://ror.org/035w1gb98
includeInCitation: false
name: United States Department of the Army
roleName:
- dcite:Funder
schemaKey: Organization
- awardNumber: U19NS128613 and R01AT012312
contactPoint: []
identifier: https://ror.org/01cwqze88
includeInCitation: false
name: National Institutes of Health
roleName:
- dcite:Funder
schemaKey: Organization
- affiliation:
- identifier: https://ror.org/022kthw22
name: University of Rochester
schemaKey: Affiliation
email: nraicevi@u.rochester.edu
includeInCitation: true
name: Raicevic, Nikola
roleName:
- dcite:Author
schemaKey: Person
dateCreated: '2023-04-26T03:36:47.214653+00:00'
datePublished: '2023-06-02T13:07:32.205531+00:00'
description: "Dataset from the 2023 manuscript titled **_Sizes and Shapes of Perivascular
Spaces Surrounding Murine Pial Arteries_** by Raicevic et al. DOI: 10.21203/rs.3.rs-2587250/v1.
\ \n\n## Overview\nThe **14 datasets** from **9 subjects** include the original
3D two photon microscopy data from three channels which show tracer in the vessel,
PVSs, and microspheres. Additionally, each dataset also includes the final binary
segmentation of the PVS and vessel used to generate the model and statistics in
the manuscript. Additional details regarding the subjects, tracer injection, image
acquisition, and segmentation can be found in the manuscript at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9949243/.\n\n##
Content\nFor easier navigation, below is a mapping between the NWB file names and
the datasets referenced in the manuscript.\n1. sub-21-07-19-b-act (Mouse 6, dataset
K)\n2. sub-21-09-01-b-act (Mouse 8, dataset M)\n3. sub-21-09-20-b-act (Mouse 9,
dataset N)\n4. sub-21-10-08-b-act (Mouse 7, dataset L)\n5. sub-BPN-M4 (Mouse 3,
dataset E and F)\n6. sub-BPN-M6 (Mouse 4, dataset G and H)\n7. sub-BPN-M7 (Mouse
5, dataset I and J)\n8. sub-BPN-OLD-M2 (Mouse 1, dataset A and B)\n9. sub-BPN-OLD-M3
(Mouse 2, dataset C and D)\n\n## Data Reading Instructions\nThe .nwb files can be
viewed using PyNWB or MatNWB. To install and set up, please visit <https://www.nwb.org/how-to-use/>.
Below, we show how to open and view an .nwb file using MatNWB. \n### Loading the
image data\n```matlab\nnwb = nwbRead(PATH_TO_NWB_FILE);\n\n% first check what color
channels are present\n>> nwb.acquisition\nans = \n 3\xD71 Set array with properties:\n
\ TwoPhotonSeriesChanA: [types.core.TwoPhotonSeries]\n TwoPhotonSeriesChanB:
[types.core.TwoPhotonSeries]\n TwoPhotonSeriesChanC: [types.core.TwoPhotonSeries]\n```\nThe
above code load the .nwb file and the output tells us that there are three channels
present in the nwb file, which are ChanA, ChanB, and ChanC. Then, to load the actual
data from a channel,\n```matlab\n% load the image data from ChanA\n>> chanAdata
= nwb.acquisition.get('TwoPhotonSeriesChanA').data.load();\n\n% check its shape\n>>
size(chanAdata)\nans =\n 1 512 512 181\n```\n### Loading the segmentation
masks\nFor an overview of the mask for ChanA, for example,\n```matlab\n>> nwb.processing.get('ophys').nwbdatainterface.get('ImageSegmentation').planesegmentation.get('PlaneSegmentationChanA').image_mask.data\nans
= \n DataStub with properties:\n filename: '.\\sub-BPN-M4_ses-20210524-m1_obj-1c8nyxo_ophys.nwb'\n
\ path: '/processing/ophys/ImageSegmentation/PlaneSegmentationChanA/image_mask'\n
\ dims: [512 512 181]\n ndims: 3\n dataType: 'logical'\n```\nTo load
the actual mask data into array (may take several seconds to load),\n```matlab\n%
load mask from ChanA\n>> mask = nwb.processing.get('ophys').nwbdatainterface.get('ImageSegmentation').planesegmentation.get('PlaneSegmentationChanA').image_mask.data.load();\n\n%
check its shape\n>> size(mask)\nans =\n 512 512 181\n```"
doi: 10.48324/dandi.000491/0.230602.1307
ethicsApproval: []
id: DANDI:000491/0.230602.1307
identifier: DANDI:000491
keywords: []
license:
- spdx:CC-BY-4.0
manifestLocation:
- https://dandiarchive.s3.amazonaws.com/dandisets/000491/0.230602.1307/assets.yaml
name: BrainFlowZZZ
protocol: []
publishedBy:
endDate: '2023-06-02T13:07:32.205531+00:00'
id: urn:uuid:2165d23e-389e-4efd-8ccf-c841c4648cd4
name: DANDI publish
schemaKey: PublishActivity
startDate: '2023-06-02T13:07:32.205531+00:00'
wasAssociatedWith:
- id: urn:uuid:ed323eeb-c2bd-4cb1-8c6e-cbccda4c4e30
identifier: RRID:SCR_017571
name: DANDI API
schemaKey: Software
version: 0.1.0
relatedResource: []
repository: https://dandiarchive.org
schemaKey: Dandiset
schemaVersion: 0.6.4
studyTarget: []
url: https://dandiarchive.org/dandiset/000491/0.230602.1307
version: 0.230602.1307
wasGeneratedBy: []