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Yorodumi- EMDB-8173: CryoET of MEF Cells and Associated Manual Segmentation of Microtu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8173 | ||||||||||||||||||
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Title | CryoET of MEF Cells and Associated Manual Segmentation of Microtubule and Actin | ||||||||||||||||||
Map data | Mouse Embryonic Fibroblast Cells | ||||||||||||||||||
Sample |
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Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||
Authors | Hecksel CW / Darrow MC / Dai W / Galaz-Montoya JG / Chin JA / Mitchell PG / Chen S / Jakana J / Schmid MF / Chiu W | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Microsc Microanal / Year: 2016 Title: Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms. Authors: Corey W Hecksel / Michele C Darrow / Wei Dai / Jesús G Galaz-Montoya / Jessica A Chin / Patrick G Mitchell / Shurui Chen / Jemba Jakana / Michael F Schmid / Wah Chiu / Abstract: Although acknowledged to be variable and subjective, manual annotation of cryo-electron tomography data is commonly used to answer structural questions and to create a "ground truth" for evaluation ...Although acknowledged to be variable and subjective, manual annotation of cryo-electron tomography data is commonly used to answer structural questions and to create a "ground truth" for evaluation of automated segmentation algorithms. Validation of such annotation is lacking, but is critical for understanding the reproducibility of manual annotations. Here, we used voxel-based similarity scores for a variety of specimens, ranging in complexity and segmented by several annotators, to quantify the variation among their annotations. In addition, we have identified procedures for merging annotations to reduce variability, thereby increasing the reliability of manual annotation. Based on our analyses, we find that it is necessary to combine multiple manual annotations to increase the confidence level for answering structural questions. We also make recommendations to guide algorithm development for automated annotation of features of interest. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8173.map.gz | 25.9 MB | EMDB map data format | |
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Header (meta data) | emd-8173-v30.xml emd-8173.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_8173.png | 134.9 KB | ||
Masks | emd_8173_msk_1.map emd_8173_msk_10.map emd_8173_msk_11.map emd_8173_msk_12.map emd_8173_msk_13.map emd_8173_msk_14.map emd_8173_msk_2.map emd_8173_msk_3.map emd_8173_msk_4.map emd_8173_msk_5.map emd_8173_msk_6.map emd_8173_msk_7.map emd_8173_msk_8.map emd_8173_msk_9.map | 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB 56.8 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8173 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8173 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8173.map.gz / Format: CCP4 / Size: 28.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mouse Embryonic Fibroblast Cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 18.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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-Sample components
-Entire : Microtubule and Actin from Mouse Embryonic Fibroblast Cells
Entire | Name: Microtubule and Actin from Mouse Embryonic Fibroblast Cells |
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Components |
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-Supramolecule #1: Microtubule and Actin from Mouse Embryonic Fibroblast Cells
Supramolecule | Name: Microtubule and Actin from Mouse Embryonic Fibroblast Cells type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) / Tissue: embryonic fibroblast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: PBS | |||||||||||||||||||||
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 21 K / Instrument: LEICA EM GP / Details: Plunged into liquid ethane (LEICA EM GP). | |||||||||||||||||||||
Details | Intact mammalian cells | |||||||||||||||||||||
Cryo protectant | Ringer's Solution | |||||||||||||||||||||
Sectioning | Other: NO SECTIONING | |||||||||||||||||||||
Fiducial marker | Manufacturer: EMS / Diameter: 15 nm |
-Electron microscopy
Microscope | JEOL 2100 |
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Temperature | Min: 98.0 K / Max: 98.0 K |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 2.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 12000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD Details: Final reconstruction was binned by two before segmentation. Number images used: 27 |
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