<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-13391" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2026-02-27</depositionDate>
            <releaseDate>2026-07-27</releaseDate>
            <updateDate>2026-07-27</updateDate>
        </keyDates>
        <title>Cryo-ET dataset on lamellae of Dictyostelium discoideum cells acquired with various tilt-increments</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, Department of Molecular Sociology</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="0000-0002-0615-572X">Tuijtel MW</author>
            <author authorORCID="0000-0002-7397-1321">Beck M</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody>Chan Zuckerberg Initiative</fundingBody>
                <code>2021-234666</code>
                <country>United States</country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">707.5</datasetSize>
        <entryDOI>10.6019/EMPIAR-13391</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>cell</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-57021</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0002-0615-572X" order="1">Tuijtel MW</author>
                    <author authorORCID="0000-0002-5279-8806" order="2">Majtner M</author>
                    <author authorORCID="0000-0002-5457-4478" order="3">Turoňová B</author>
                    <author authorORCID="0000-0002-7397-1321" order="4">Beck M</author>
                    <title>Optimising the tilt-increment for in situ cryo-electron tomography</title>
                    <journal>eLife</journal>
                    <journalAbbreviation></journalAbbreviation>
                    <country></country>
                    <language>English</language>
                    <externalReferences type="doi">10.7554/eLife.111639.1</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 1-degree tilt increment</name>
        <directory>/data/Data_1degree</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>63</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>Tilt-series were aimed to collect 121 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_1deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_1degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_1degree_threshold5.star and TM_1degree_threshold6.star. Ribosome particle locations after M refinment are provided in M_1degree_particles.star.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 2-degree tilt increment</name>
        <directory>/data/Data_2degree</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>119</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>Tilt-series were aimed to collect 61 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_2deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_2degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_2degree_threshold5.star and TM_2degree_threshold6.star. Ribosome particle locations after M refinment are provided in M_2degree_particles.star.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 3-degree tilt increment</name>
        <directory>/data/Data_3degree</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>120</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>Tilt-series were aimed to collect 41 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_3deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_3degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_3degree_threshold5.star and TM_3degree_threshold5.5.star. Ribosome particle locations after M refinment are provided in M_3degree_particles.star.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 5-degree tilt increment</name>
        <directory>/data/Data_5degree</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>122</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>Tilt-series were aimed to collect 25 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_5deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_5degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_5degree_threshold5.star. Ribosome particle locations after M refinment are provided in M_5degree_particles.star.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Tilt-series on lamellae of Dictyostelium discoideum cells acquired with a 10-degree tilt increment</name>
        <directory>/data/Data_10degree</directory>
        <category>tilt series</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>89</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>Tilt-series were aimed to collect 13 tilts, for some, fewer tilts were acquired. Tilt-series are sorted according to ascending tilt angle apart from -60 to +60 from lamella pre-tilt (8deg). mdoc files with metadata provided by SerialEM are also provided.
Tilt images that were discarded during processing are specified in "tilt_clean_10deg.txt".
Alignment results from IMOD are provided as TS_XXXX.xf files.
Tomograms that were used for STA are marked in tomo_list_10degree.txt.
Coordinates to raw ribosome particle picks by template matching are provided in TM_10degree_threshold3.75.star. Ribosome particle locations after M refinment are provided in M_10degree_particles.star.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
