dandiset.yaml

# DO NOT EDIT THIS FILE LOCALLY. ALL LOCAL UPDATES WILL BE LOST.
# It can be edited online at https://dandiarchive.org/dandiset/000026
# and obtained from the dandiarchive.
'@context': https://raw.githubusercontent.com/dandi/schema/master/releases/0.6.0/context.json
about:
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citation: Mazzamuto, Giacomo; Costantini, Irene; Danila Di Meo; Castelli, Filippo
  Maria; Pesce, Luca; Scardigli, Marina; Pavone, Francesco Saverio; Roffilli, Matteo;
  Silvestri, Ludovico; Brady, Niamh; Ramazzotti, Josephine; Hof, Patrick R.; Boas,
  David A.; Fischl, Bruce; Morgan, Leah; Yang, Jiarui; Chang, Shuaibin; Laffey, Jessie;
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  Balbastre, Yael; Vera, Matthew; Cordero, Devani; Nestor, Kimberly; Ammon, William;
  Nolan, Jackson; Mora, Jocelyn; Pallares, Erendira Garcia; Augustinack, Jean; Diamond,
  Bram; Fogarty, Morgan; Boyd, Emma; Varghese, Merina; Dalca, Adrian V.; Edlow, Brian;
  Frosche, Matthew; Wicinski, Bridget; Chen, I-Chun Anderson; Gavryusev, Vladislav
  (2024) Human brain cell census for BA 44/45 (Version draft) [Data set]. DANDI archive.
  https://dandiarchive.org/dandiset/000026/draft
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dateCreated: '2020-06-24T18:34:50.022000+00:00'
description: Magnetic resonance imaging (MRI) is used to establish a macroscopic reference
  coordinate system of laminar and cytoarchitectural boundaries. Cell counting is
  obtained with both traditional immunohistochemistry, to provide a stereological
  gold standard, and with a custom-made inverted confocal light-sheet fluorescence
  microscope (LSM) for 3D imaging at cellular resolution. Finally, polarization-sensitive
  optical coherence tomography (PSOCT) enables registration of the distorted histological
  cell typing obtained with LSM to the MRI-based atlas coordinate system.
ethicsApproval: []
id: DANDI:000026/draft
identifier: DANDI:000026
keywords:
- multi-modal imaging
- MRI
- OCT
- SPIM
- human cortex
- Broca's area
- Motor cortex
- Stereology
license:
- spdx:CC-BY-4.0
manifestLocation:
- https://api.dandiarchive.org/api/dandisets/000026/versions/draft/assets/
name: Human brain cell census for BA 44/45
protocol:
- https://www.protocols.io/view/high-resolution-ex-vivo-structural-mri-imaging-amp-byt7pwrn
- https://www.protocols.io/view/serial-sectioning-optical-histology-cell-census-ne-bu7mnzk6
- https://www.biorxiv.org/content/10.1101/2021.07.18.452829v1
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  url: https://www.biorxiv.org/content/10.1101/2020.07.28.225011v1
- identifier: Paper
  name: Dual-beam confocal light-sheet microscopy via flexible acousto-optic deflector
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  repository: J. of Biomedical Optics
  schemaKey: Resource
  url: https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-24/issue-10/106504/Dual-beam-confocal-light-sheet-microscopy-via-flexible-acousto-optic/10.1117/1.JBO.24.10.106504.full?tab=ArticleLinkCited
- identifier: Paper
  name: Improving the characterization of ex vivo human brain optical properties using
    high numerical aperture optical coherence tomography by spatially constraining
    the confocal parameters
  relation: dcite:IsPublishedIn
  repository: Neurophotonics
  schemaKey: Resource
  url: https://pubmed.ncbi.nlm.nih.gov/33094126/
- identifier: Paper
  name: 'as-PSOCT: Volumetric microscopic imaging of human brain architecture and
    connectivity'
  relation: dcite:IsPublishedIn
  repository: Neuroimage
  schemaKey: Resource
  url: https://pubmed.ncbi.nlm.nih.gov/29017866/
- identifier: Proceedings
  name: Measuring myelin content and cell density in human brain with Optical Coherence
    Tomography
  relation: dcite:IsPartOf
  repository: Optical Techniques in Neurosurgery, Neurophotonics, and Optogenetics
  schemaKey: Resource
  url: https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11629/116291J/Measuring-myelin-content-and-cell-density-in-the-human-brain/10.1117/12.2578489.short
- identifier: Proceedings
  name: Fast volumetric mapping of human brain slices
  relation: dcite:IsPublishedIn
  repository: bioRxiv
  schemaKey: Resource
  url: https://www.biorxiv.org/content/10.1101/2020.10.27.357186v1
- identifier: Proceedings
  name: A novel algorithm to optimize generalized gamma distributed multiplicative
    noise with implications on speckle removal from OCT images
  relation: dcite:IsPublishedIn
  repository: bioRxiv
  schemaKey: Resource
  url: https://www.biorxiv.org/content/10.1101/2020.10.07.329227v1
- identifier: Paper
  name: 'Large-scale, cell-resolution volumetric analysis allows layer-specific investigation
    of human brain cytoarchitecture (MAGIC: A label-free fluorescence method for 3D
    high-resolution reconstruction of myelinated fibers in large volumes)'
  relation: dcite:IsPublishedIn
  repository: Biomedical Optics Express
  schemaKey: Resource
  url: https://www.biorxiv.org/content/10.1101/2020.08.06.219444v1
- identifier: Paper
  name: Segmentation of supragranular and infragranular layers in ultra-high-resolution
    7T ex vivo MRI of the human cerebral cortex
  relation: dcite:IsPublishedIn
  repository: Cerebral Cortex
  resourceType: dcite:JournalArticle
  schemaKey: Resource
  url: https://academic.oup.com/cercor/article-abstract/34/9/bhae362/7755370?login=false
repository: https://dandiarchive.org
schemaKey: Dandiset
schemaVersion: 0.6.0
studyTarget:
- 'Our consortium will develop and utilize an imaging infrastructure to create a human
  brain cell census and instantiate it in a coordinate system that will enable an
  immediate impact of all in vivo MRI studies of the human brain. Our imaging pipeline
  begins with 150 μm isotropic ex vivo structural MRIs and 500 μm 90 direction diffusion
  MRI. 4x4x2 cm tissue blocks will then be imaged with serial sectioning polarization
  sensitive optical coherence tomography (PS-OCT) to obtain 20 μm isotropic resolution
  images of cyto- and myelo-architectural features and fiber tractography. Registration
  with the MRI is preserved because imaging is performed before sectioning. Serial
  sections with 150 μm thickness are cut from the block face, cleared, and subsequently
  imaged by selective plane imaging microscopy (SPIM) with 1 μm isotropic resolution,
  and with multiplexed histological staining of multiple molecular markers. Segmentation
  of common features amongst the SPIM, OCT, and MRI, permits registration of the cellular
  information from SPIM back to the MRI coordinate system with OCT serving as an important
  intermediary permitting registration of SPIM with MRI with micrometer resolution.
  Our aims are designed to establish our imaging workflow and build a cell census
  atlas for language regions in human frontal cortex, resulting in a clear path forward
  for obtaining the cell census for the entire human brain. '
url: https://dandiarchive.org/dandiset/000026/draft
version: draft
wasGeneratedBy:
- identifier: fischl_mri_proj
  name: Brain Initiative Cell Census Network (BICCN)
  schemaKey: Project
  used: []
  wasAssociatedWith: []