<entry xmlns="http://pdbe.org/empiar" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://ftp.ebi.ac.uk/pub/databases/emtest/empiar/schema/empiar.xsd" accessionCode="EMPIAR-10464" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2020-07-03</depositionDate>
            <releaseDate>2021-10-27</releaseDate>
            <updateDate>2022-02-08</updateDate>
        </keyDates>
        <title>SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-5703-2922</authorORCID>
            <firstName>Marie-Charlotte</firstName>
            <lastName>Domart</lastName>
            <organization type="academic">Francis Crick Institute, Electron Microscopy STP</organization>
            <street>1 Midland Road</street>
            <townOrCity>London</townOrCity>
            <stateOrProvince>London</stateOrProvince>
            <country>United Kingdom</country>
            <postOrZipCode>NW1 1AT</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-5703-2922</authorORCID>
            <firstName>Marie-Charlotte</firstName>
            <lastName>Domart</lastName>
            <organization type="academic">Francis Crick Institute, Electron Microscopy STP</organization>
            <street>1 Midland Road</street>
            <townOrCity>London</townOrCity>
            <stateOrProvince>London</stateOrProvince>
            <country>United Kingdom</country>
            <postOrZipCode>NW1 1AT</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author>Peddie CJ</author>
            <author authorORCID="0000-0002-5703-2922">Domart MC</author>
            <author>Collinson L</author>
        </authorsList>
        <datasetSize units="GB">553.9</datasetSize>
        <entryDOI>10.6019/EMPIAR-10464</entryDOI>
        <experimentType>CLEM</experimentType>
    </admin>
    <crossReferences>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0002-3925-8557" order="1">Yoshida N</author>
                    <author authorORCID="0000-0002-5703-2922" order="2">Domart MC</author>
                    <author order="3">Peddie CJ</author>
                    <author authorORCID="0000-0003-2458-4904" order="4">Yakimovich A</author>
                    <author order="5">Mazon-Moya MJ</author>
                    <author authorORCID="0000-0003-2921-0004" order="6">Hawkins TA</author>
                    <author order="7">Collinson L</author>
                    <author order="8">Mercer J</author>
                    <author authorORCID="0000-0002-9515-3442" order="9">Frickel EM</author>
                    <author authorORCID="0000-0002-7286-6503" order="10">Mostowy S</author>
                    <title>The zebrafish as a novel model for the &lt;i&gt;in vivo&lt;/i&gt; study of &lt;i&gt;Toxoplasma gondii&lt;/i&gt; replication and interaction with macrophages</title>
                    <journal>Disease models &amp; mechanisms</journal>
                    <journalAbbreviation>Dis Model Mech</journalAbbreviation>
                    <country></country>
                    <issue>7</issue>
                    <volume>13</volume>
                    <year>2020</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1242/dmm.043091</externalReferences>
                    <externalReferences type="pubmed">32461265</externalReferences>
                    <details>Raw data corresponding to Suppl. Fig 2, Suppl. Fig 4 and Suppl. Fig. 6 in the paper</details>
                </journalCitation>
            </universalCitation>
        </citationList>
        <relatedBioStudiesEntries>
            <bioStudiesEntry>S-BSST429</bioStudiesEntry>
        </relatedBioStudiesEntries>
    </crossReferences>
    <imageSet>
        <name>Survey SBF SEM images showing the position of the imaged ROIs at the start of each run (3 runs- #20-22)</name>
        <directory>/data/Survey_images</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>3</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>Survey images showing the position of the ROIs imaged for each run, if opened in Digital Micrograph. 
Variable pixel widths and heights. Run 20: 5000 x 5000, run 21-22: 4096 x 4096. Variable pixel widths. Run 20: 75.6nm, run 21: 87.2nm, run 22: 86.3nm</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Low magnification raw SBF SEM overview images (ROI00) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)</name>
        <directory>/data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/ROI00</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>1099</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>Low magnification overview SBF SEM images (ROI00) for runs 20-22, linked to higher magnification images in ROI01 and ROI02. Imaged at 2kV, 2us dwell, variable pressure 5Pa. 
Variable pixel widths and heights. Run 20: 7500 x 5497, run 21: 7000 x 4000, run 22: 6000 x 4000. Variable pixel widths. Run 20: 48.5nm, run 21: 54nm, run 22: 49nm.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>High magnification raw SBF SEM images (ROI01) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain over 3 runs (20-22)</name>
        <directory>/data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/ROI01</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>1099</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>High magnification images (ROI01) linked to lower magnification images in ROI00, for 3 runs (20-22). Imaged at 2kV, 2us dwell, variable pressure 5Pa.
Variable pixel widths and heights. Run 20: 16384 x 16384, run 21: 15000 x 10000, run 22: 15000 x 12000. Variable pixel widths. Run 20: 6.6nm, run 21-22: 5.8nm.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>High magnification raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain (run 20)</name>
        <directory>/data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/run20_ROI02</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>391</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>8192</imageWidth>
            <pixelWidth>69.0</pixelWidth>
            <imageHeight>8192</imageHeight>
            <pixelHeight>69.0</pixelHeight>
        </dimensions>
        <details>High magnification images (ROI02) linked to lower magnification images in ROI00 for run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>High magnification raw SBF SEM images (ROI02) of Toxoplasma Gondii tachizoites in a Zebrafish hindbrain for runs 21-22</name>
        <directory>/data/P400_SBF_SEM_F1S1_run20-22_EMPIAR-10464/run21-22_ROI02</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>705</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>High magnification images (ROI02) linked to lower magnification images in ROI00 for run 21-22. Note that it is a different ROI than ROI02-run 20. Imaged at 2kV, 2us dwell, variable pressure 5Pa. 
Variable pixel widths and heights. Run 21: 4000 x 4000, run 22: 5000 x 5000. Variable pixel widths. Run 21: 7.1nm, run 22: 6.2nm.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
