<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-12161" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2024-02-14</depositionDate>
            <releaseDate>2024-09-26</releaseDate>
            <updateDate>2025-04-11</updateDate>
        </keyDates>
        <title>SBF SEM images of a notoroid in transverse orientation (Fig S24)</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-5703-2922</authorORCID>
            <firstName>Marie-Charlotte</firstName>
            <lastName>Domart</lastName>
            <organization type="academic">The Francis Crick Institute, Electron Microscopy STP</organization>
            <street>1 Midland Road</street>
            <townOrCity>London</townOrCity>
            <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">The Francis Crick Institute, Electron Microscopy STP</organization>
            <street>Midland road</street>
            <townOrCity>London</townOrCity>
            <country>United Kingdom</country>
            <postOrZipCode>NW1 1AT</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0002-5703-2922">Marie-Charlotte Domart MCD</author>
            <author>Lucy M Collinson LMC</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody></fundingBody>
                <code></code>
                <country></country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">11.5</datasetSize>
        <entryDOI>10.6019/EMPIAR-12161</entryDOI>
        <experimentType>SBF-SEM</experimentType>
        <scale>tissue</scale>
    </admin>
    <crossReferences>
        <citationList>
            <universalCitation>
                <journalCitation published="false" preprint="true">
                    <author order="1">Tiago Rito TR</author>
                    <author order="2">Ashley R.G. Libby ARGL</author>
                    <author order="3">Madeleine Demuth MD</author>
                    <author authorORCID="0000-0002-5703-2922" order="4">Marie-Charlotte Domart MCD</author>
                    <author order="5">Jake Cornwall-Scoones JCS</author>
                    <author order="6">James Briscoe JB</author>
                    <title>Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation</title>
                    <journal></journal>
                    <journalAbbreviation></journalAbbreviation>
                    <country></country>
                    <externalReferences type="doi">10.1038/s41586-024-08332-w</externalReferences>
                    <details>The data in this entry are the ones shown in Fig 6m and Fig S24 of the paper</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Low magnification raw SBF SEM overview images (ROI00) of notoroid in transverse orientation</name>
        <directory>/data/FigS24/ROI00</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
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        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>7000</imageWidth>
            <pixelWidth>610.0</pixelWidth>
            <imageHeight>7000</imageHeight>
            <pixelHeight>610.0</pixelHeight>
        </dimensions>
        <details>Low magnification overview SBF SEM images (ROI00), linked to higher magnification images in ROI01 and ROI02 below. Imaged at 1.8kV, 2us dwell, with FCC with a 30um aperture. 50nm slices.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>High magnification raw SBF SEM images (ROI01) of notochord in notoroid in transverse orientation</name>
        <directory>/data/FigS24/ROI01</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
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        <dimensions>
            <imageWidth>7000</imageWidth>
            <pixelWidth>88.0</pixelWidth>
            <imageHeight>7000</imageHeight>
            <pixelHeight>88.0</pixelHeight>
        </dimensions>
        <details>High magnification images (ROI01) linked to lower magnification images in ROI00. Imaged at 1.8kV, 2us dwell, with FCC with a 30um aperture. 50nm slices.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>High magnification raw SBF SEM images (ROI02) of notochord in notoroid in transverse orientation</name>
        <directory>/data/FigS24/ROI02</directory>
        <category>micrographs - single frame</category>
        <headerFormat>DM4</headerFormat>
        <dataFormat>DM4</dataFormat>
        <numImagesOrTiltSeries>50</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>7000</imageWidth>
            <pixelWidth>83.0</pixelWidth>
            <imageHeight>7000</imageHeight>
            <pixelHeight>83.0</pixelHeight>
        </dimensions>
        <details>High magnification images (ROI02) linked to lower magnification images in ROI00. Imaged at 1.8kV, 2us dwell, with FCC with a 30um aperture. 50nm slices.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Survey image showing the relative position of each of the ROIs above</name>
        <directory>/data/Survey-image</directory>
        <category>micrographs - single frame</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>1</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>Survey image used to setup the multi ROI run in Digital Micrograph. Shows the position of each ROI.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
