<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-10215" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2018-10-03</depositionDate>
            <releaseDate>2019-04-05</releaseDate>
            <updateDate>2020-02-24</updateDate>
        </keyDates>
        <title>Rabbit muscle aldolase single particle cryoEM</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0001-8634-2279</authorORCID>
            <firstName>Alex</firstName>
            <lastName>Noble</lastName>
            <organization type="academic">New York Structural Biology Center</organization>
            <street>89 Convent Avenue</street>
            <townOrCity>New York</townOrCity>
            <stateOrProvince>NY</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>10027</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <firstName>Bepler</firstName>
            <lastName>Tristan</lastName>
            <organization type="academic">Computational and Systems Biology, Massachusetts Institute of Technology</organization>
            <street>32 Vassar St</street>
            <townOrCity>Cambridge</townOrCity>
            <stateOrProvince>Massachusetts</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>02139</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author>Bepler T</author>
            <author>Morin A</author>
            <author>Rapp M</author>
            <author>Brasch J</author>
            <author authorORCID="0000-0001-9943-8819">Shapiro L</author>
            <author authorORCID="0000-0001-8634-2279">Noble AJ</author>
            <author authorORCID="0000-0002-2724-7228">Berger B</author>
        </authorsList>
        <datasetSize units="TB">1.4</datasetSize>
        <entryDOI>10.6019/EMPIAR-10215</entryDOI>
        <experimentType>EMDB</experimentType>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-20529</emdbEntry>
            <emdbEntry>EMD-20531</emdbEntry>
            <emdbEntry>EMD-20532</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author order="1">Bepler T</author>
                    <author order="2">Morin A</author>
                    <author order="3">Rapp M</author>
                    <author order="4">Brasch J</author>
                    <author authorORCID="0000-0001-9943-8819" order="5">Shapiro L</author>
                    <author authorORCID="0000-0001-8634-2279" order="6">Noble AJ</author>
                    <author authorORCID="0000-0002-2724-7228" order="7">Berger B</author>
                    <title>Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs</title>
                    <journal>Nature methods</journal>
                    <journalAbbreviation>Nat. Methods</journalAbbreviation>
                    <country></country>
                    <issue>11</issue>
                    <volume>16</volume>
                    <firstPage>1153</firstPage>
                    <lastPage>1160</lastPage>
                    <year>2019</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1038/s41592-019-0575-8</externalReferences>
                    <externalReferences type="pubmed">31591578</externalReferences>
                    <details>Raw frames, micrographs aligned with MotionCor2, particle picks, and particle stacks are included.</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Micrographs along with all other magnification images from the collection</name>
        <directory>/data/leginon</directory>
        <category>micrographs - single frame</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>1061</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>3710</imageWidth>
            <pixelWidth>0.832</pixelWidth>
            <imageHeight>3838</imageHeight>
            <pixelHeight>0.832</pixelHeight>
        </dimensions>
        <details>Frame aligned with MotionCor2.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Micrograph frames</name>
        <directory>/data/frames</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>1061</numImagesOrTiltSeries>
        <framesPerImage>30</framesPerImage>
        <voxelType>UNSIGNED 16 BIT INTEGER</voxelType>
        <dimensions>
            <imageWidth>7420</imageWidth>
            <pixelWidth>0.416</pixelWidth>
            <imageHeight>7676</imageHeight>
            <pixelHeight>0.416</pixelHeight>
        </dimensions>
        <details>Super-res frames and references. Includes picks for Topaz and Topaz-published.</details>
        <segmentationList/>
        <micrographsFilePattern>data/frames/rawdata/*.mrc.*</micrographsFilePattern>
        <pickedParticlesFilePattern>data/particle picks/</pickedParticlesFilePattern>
        <pickedParticlesDirectory>data/particle picks/</pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>CryoEM structures in the paper</name>
        <directory>/data/all_structures_in_paper</directory>
        <category>picked particles - single frame - unprocessed</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>9</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>variable</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>variable</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details>All structures for EMPIAR-10025, EMPIAR-10028, NYSBC-aldo with Topaz, published, and Topaz-published picks as described in the manuscript titled: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Includes most Topaz particle picks and stacks for EMPIAR-10025, EMPIAR-10028, NYSBC-aldo with Topaz, published, and Topaz-published picks as described in the manuscript titled: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs</details>
        <segmentationList/>
        <micrographsFilePattern>data/all_particle_stacks_in_paper</micrographsFilePattern>
        <pickedParticlesFilePattern>data/all_particle_stacks_in_paper/</pickedParticlesFilePattern>
        <pickedParticlesDirectory>data/all_particle_stacks_in_paper/</pickedParticlesDirectory>
    </imageSet>
</entry>
