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Local Z Projector example dataset and parameters 03

Laure Mancini; Nicolas Dray; Laure Bally-Cuif; Jean-Yves Tinevez


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  <identifier identifierType="DOI">10.5281/zenodo.4629231</identifier>
  <creators>
    <creator>
      <creatorName>Laure Mancini</creatorName>
      <affiliation>Institut Pasteur</affiliation>
    </creator>
    <creator>
      <creatorName>Nicolas Dray</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2632-6004</nameIdentifier>
      <affiliation>Institut Pasteur</affiliation>
    </creator>
    <creator>
      <creatorName>Laure Bally-Cuif</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6611-6274</nameIdentifier>
      <affiliation>Institut Pasteur</affiliation>
    </creator>
    <creator>
      <creatorName>Jean-Yves Tinevez</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0998-4718</nameIdentifier>
      <affiliation>Institut Pasteur</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Local Z Projector example dataset and parameters 03</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-03-23</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4629231</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4629230</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Adult zebrafish brain, imaged on a laser-scanning confocal microscope.&lt;/p&gt;

&lt;p&gt;Brains were dissected in 1X solution of phosphate buffered saline (PBS - Fisher Bioreagents) and directly transferred to a 4% paraformaldehyde solution in PBS for fixation. They were fixed for 2 to 4 hours at room temperature (RT) under permanent agitation. After four washing steps in PBS, brains were dehydrated through 5 minutes series of 25%, 50% and 75% methanol diluted in 0.1% tween-20 (Sigma Life Science &amp;ndash; P9416) PBS solution and kept in 100% methanol (Sigma-Aldrich, 322415) at -20&amp;deg;C. The whole-mount immunohistochemistry (IHC) started by the rehydration of the telencephali. Then, the brains were subjected to an antigen retrieval step using Histo-VT One (Nacalai Tesque) for an hour at 65&amp;deg;C. Brains were rinsed in a 0.1% DMSO and 0.1% Triton X-100 (Sigma Life Science&amp;ndash; 1002135493) PBS 1X solution (PBT) and then blocked with 4% normal goat serum in PBT (blocking buffer) 4 hours at RT. The blocking buffer was later replaced by the primary antibodies solution, and the brains were kept overnight at 4&amp;deg;C on a rocking platform. The next day, brains were rinsed over 24 hours at room temperature with PBT and incubated in a solution of secondary antibodies diluted in PBT overnight, in the dark, and at 4&amp;deg;C on a rocking platform. After several washes, the telencephali were mounted in PBS on slides using a 0.7 mm-thick holder. The primary antibody anti-ZO1 was used at 1:200 (Mouse monoclonal IgG1 anti-ZO1, Thermo Fisher, cat. #33-9100, RRID: AB_2533147) and the secondary antibody anti IgG was used at 1:1000 (Goat anti-Mouse IgG (H+L) Alexa633 conjugated, Thermo Fisher, cat. #A-21052, RRID : AB_2535719).&lt;/p&gt;

&lt;p&gt;Images of whole-mounted immunostained telencephali were acquired on confocal microscope (LSM700, Carl Zeiss A.G), using a 40X oil objective. We acquired images with a z-step of 0.65 &amp;micro;m. We averaged each line four times with an image resolution of 1024 &amp;times;1024 pixels with a bit-depth of 12-bits. We recorded mosaics with a 15% overlap to image an entire hemisphere per fish.&lt;/p&gt;

&lt;p&gt;See the accompanying paper:&amp;nbsp;&lt;em&gt;DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href="https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2"&gt;https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2&lt;/a&gt;&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/322936/">322936</awardNumber>
      <awardTitle>Dynamics and Homeostasis of Germinal Zones in the Adult Vertebrate Brain</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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