dandiarchive-dataset/s3://dandiarchive/dandisets/000491/0.230602.1307/dandiset.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://dandiarchive.org/dandiset/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  3×1 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```"
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: []