<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-13031" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2025-10-06</depositionDate>
            <releaseDate>2025-10-29</releaseDate>
            <updateDate>2025-10-29</updateDate>
        </keyDates>
        <title>Systematic membrane thickness variation across cellular organelles revealed by cryo-ET</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-7397-1321</authorORCID>
            <firstName>Martin</firstName>
            <lastName>Beck</lastName>
            <organization type="academic">Max Planck Institute of Biophysics</organization>
            <street>Max-von-Laue-Straße 3</street>
            <townOrCity>Frankfurt am Main</townOrCity>
            <stateOrProvince>Hessen</stateOrProvince>
            <country>Germany</country>
            <postOrZipCode>60438</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-7397-1321</authorORCID>
            <firstName>Martin</firstName>
            <lastName>Beck</lastName>
            <organization type="academic">Max Planck Institute of Biophysics</organization>
            <street>Max-von-Laue-Straße 3</street>
            <townOrCity>Frankfurt am Main</townOrCity>
            <stateOrProvince>Hessen</stateOrProvince>
            <country>Germany</country>
            <postOrZipCode>60438</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0001-6077-7338">Glushkova D</author>
            <author authorORCID="0009-0005-1690-9125">Boehm S</author>
            <author authorORCID="0000-0002-7397-1321">Beck M</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>Max Planck Society</fundingBody>
                <code>NA</code>
                <country>Germany</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">97.9</datasetSize>
        <entryDOI>10.6019/EMPIAR-13031</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>cell</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-55308</emdbEntry>
            <emdbEntry>EMD-55310</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="false" preprint="false">
                    <author authorORCID="0000-0001-6077-7338" order="1">Glushkova D</author>
                    <author authorORCID="0009-0005-1690-9125" order="2">Boehm S</author>
                    <author authorORCID="0000-0002-7397-1321" order="3">Beck M</author>
                    <title>Systematic membrane thickness variation across cellular organelles revealed by cryo-ET</title>
                    <journal>Journal of Cell Biology</journal>
                    <journalAbbreviation>JCB</journalAbbreviation>
                    <country></country>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>cryoCARE-denoised bin4 tomograms of HEK293 cells</name>
        <directory>/data/cryoCARE</directory>
        <category>reconstructed volumes</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>15</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>1024</imageWidth>
            <pixelWidth>7.884</pixelWidth>
            <imageHeight>1024</imageHeight>
            <pixelHeight>7.884</pixelHeight>
        </dimensions>
        <details>CryoCARE denoised bin4 tomograms of HEK293 cells. Denoising was performed on even and odd frames. Tomograms were reconstructed using weighted back-projection (WBP) implemented in AreTomo2.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Processed tilt series with alignment files for HEK293 cells</name>
        <directory>/data/TiltSeries</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>15</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>SIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>4096</imageWidth>
            <pixelWidth>1.971</pixelWidth>
            <imageHeight>4096</imageHeight>
            <pixelHeight>1.971</pixelHeight>
        </dimensions>
        <details>Aligned, sorted, and cleaned tilt series (prior to and after dose-filtering), organized in separate folders. Each tilt series folder includes acquisition metadata (.mrc.mdoc), tilt angles (.rawtlt), and GCTF CTF estimation output (.star) files. An AreTomo subfolder within each tilt series contains AreTomo2 alignment (.aln) and IMOD transform (.xf) files used for weighted back-projection reconstruction.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
