<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-10327" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2019-09-27</depositionDate>
            <releaseDate>2019-10-07</releaseDate>
            <updateDate>2019-10-07</updateDate>
        </keyDates>
        <title>Processed FIB SEM images of a parasitophorous vacuole containing Toxoplasma gondii ∆CAP parasites, complemented with CAP.</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-9727-6657</authorORCID>
            <firstName>Moritz</firstName>
            <lastName>Treeck</lastName>
            <organization type="academic">The Francis Crick Institute</organization>
            <street>1 Midland Road</street>
            <townOrCity>London</townOrCity>
            <country>United Kingdom</country>
            <postOrZipCode>NW1 1AT</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-9727-6657</authorORCID>
            <firstName>Moritz</firstName>
            <lastName>Treeck</lastName>
            <organization type="academic">The Francis Crick Institute</organization>
            <street>1 Midland Road</street>
            <townOrCity>London</townOrCity>
            <country>United Kingdom</country>
            <postOrZipCode>NW1 1AT</postOrZipCode>
        </principalInvestigator>
        <principalInvestigator private="true">
            <firstName>Gary</firstName>
            <lastName>Ward</lastName>
            <organization type="academic">Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont</organization>
            <street>316 Stafford Hall, 95 Carrigan Drive</street>
            <townOrCity>Burlington</townOrCity>
            <stateOrProvince>VT</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>05405</postOrZipCode>
        </principalInvestigator>
        <principalInvestigator private="true">
            <firstName>Aoife</firstName>
            <lastName>Heaslip</lastName>
            <organization type="academic">Department of Molecular &amp; Cell Biology, University of Connecticut</organization>
            <street>91 Eagleville Road, Unit 3125</street>
            <townOrCity>Storrs</townOrCity>
            <stateOrProvince>CT</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>06269-3125</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0001-7431-7156">Hunt A</author>
            <author authorORCID="0000-0003-4608-7669">Russell MRG</author>
            <author authorORCID="0000-0002-7227-4348">Wagener J</author>
            <author>Kent R</author>
            <author>Carmeille R</author>
            <author>Peddie CJ</author>
            <author>Collinson L</author>
            <author>Heaslip A</author>
            <author>Ward GE</author>
            <author authorORCID="0000-0002-9727-6657">Treeck M</author>
        </authorsList>
        <datasetSize units="MB">583.8</datasetSize>
        <entryDOI>10.6019/EMPIAR-10327</entryDOI>
        <experimentType>FIB-SEM</experimentType>
    </admin>
    <crossReferences>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0001-7431-7156" order="1">Hunt A</author>
                    <author authorORCID="0000-0003-4608-7669" order="2">Russell MRG</author>
                    <author authorORCID="0000-0002-7227-4348" order="3">Wagener J</author>
                    <author order="4">Kent R</author>
                    <author order="5">Carmeille R</author>
                    <author order="6">Peddie CJ</author>
                    <author order="7">Collinson L</author>
                    <author order="8">Heaslip A</author>
                    <author order="9">Ward GE</author>
                    <author authorORCID="0000-0002-9727-6657" order="10">Treeck M</author>
                    <title>Differential requirements for cyclase-associated protein (CAP) in actin-dependent processes of Toxoplasma gondii</title>
                    <journal>eLife</journal>
                    <journalAbbreviation>Elife</journalAbbreviation>
                    <country></country>
                    <volume>8</volume>
                    <year>2019</year>
                    <language>English</language>
                    <externalReferences type="doi">10.7554/elife.50598</externalReferences>
                    <externalReferences type="pubmed">31577230</externalReferences>
                    <details>Image acquisition;
5 nm voxels: xy pixel set to 5 nm, FIB mill every 5 nm.
SEM: 1.5 kV with 1 nA current, 10 μs dwell time.
EsB detector grid voltage: 1200 V.
Ion beam milling: 30 kV, 700 pA.

Image processing;
Zeiss Atlas 5.2.1.25;
Gradient align
Export of cropped region of interest exported as 8 bit TIF files

Fiji;
Invert
Gaussian blur: Sigma 0.75 
Unsharp mask: Radius (Sigma) 1 pixel, Mask weight 0.6
Rotate to straighten XY (D19: no rotation)
Reslice: YZ assigned to XY plane
Scale to 10 nm isotropic voxels

IMOD;
tif2mrc</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Processed FIB SEM images of a parasitophorous vacuole containing Toxoplasma gondii ∆CAP parasites, complemented with CAP.</name>
        <directory>/data/mrc</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>1</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>SIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>1540</imageWidth>
            <pixelWidth>100.0</pixelWidth>
            <imageHeight>1254</imageHeight>
            <pixelHeight>100.0</pixelHeight>
        </dimensions>
        <details>Image acquisition;
5 nm voxels: xy pixel set to 5 nm, FIB mill every 5 nm.
SEM: 1.5 kV with 1 nA current, 10 μs dwell time.
EsB detector grid voltage: 1200 V.
Ion beam milling: 30 kV, 700 pA.

Image processing;
Zeiss Atlas 5.2.1.25;
Gradient align
Export of cropped region of interest exported as 8 bit TIF files

Fiji;
Invert
Gaussian blur: Sigma 0.75 
Unsharp mask: Radius (Sigma) 1 pixel, Mask weight 0.6
Rotate to straighten XY (D19: no rotation)
Reslice: YZ assigned to XY plane
Scale to 10 nm isotropic voxels

IMOD;
tif2mrc</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
