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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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{
  "description": "<p>Adult zebrafish brain, imaged on a laser-scanning confocal microscope.</p>\n\n<p>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 &ndash; P9416) PBS solution and kept in 100% methanol (Sigma-Aldrich, 322415) at -20&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&deg;C. Brains were rinsed in a 0.1% DMSO and 0.1% Triton X-100 (Sigma Life Science&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&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&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).</p>\n\n<p>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 &micro;m. We averaged each line four times with an image resolution of 1024 &times;1024 pixels with a bit-depth of 12-bits. We recorded mosaics with a 15% overlap to image an entire hemisphere per fish.</p>\n\n<p>See the accompanying paper:&nbsp;<em>DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.</em></p>\n\n<p><a href=\"https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2\">https://www.biorxiv.org/content/10.1101/2021.01.15.426809v2</a></p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Institut Pasteur", 
      "@type": "Person", 
      "name": "Laure Mancini"
    }, 
    {
      "affiliation": "Institut Pasteur", 
      "@id": "https://orcid.org/0000-0002-2632-6004", 
      "@type": "Person", 
      "name": "Nicolas Dray"
    }, 
    {
      "affiliation": "Institut Pasteur", 
      "@id": "https://orcid.org/0000-0001-6611-6274", 
      "@type": "Person", 
      "name": "Laure Bally-Cuif"
    }, 
    {
      "affiliation": "Institut Pasteur", 
      "@id": "https://orcid.org/0000-0002-0998-4718", 
      "@type": "Person", 
      "name": "Jean-Yves Tinevez"
    }
  ], 
  "url": "https://zenodo.org/record/4629231", 
  "datePublished": "2021-03-23", 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/b9955a84-5eb2-4d4a-bbc5-e6f86eec9419/LZP-dataset-3.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.4629231", 
  "@id": "https://doi.org/10.5281/zenodo.4629231", 
  "@type": "Dataset", 
  "name": "Local Z Projector example dataset and parameters 03"
}
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