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Yorodumi- EMDB-8174: CryoET of U2OS Cells and Associated Manual Segmentation of Mitoch... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8174 | ||||||||||||||||||
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Title | CryoET of U2OS Cells and Associated Manual Segmentation of Mitochondria | ||||||||||||||||||
Map data | U2OS Cells | ||||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||||||||
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_8174.map.gz | 12.6 MB | EMDB map data format | |
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Header (meta data) | emd-8174-v30.xml emd-8174.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_8174.png | 105.6 KB | ||
Masks | emd_8174_msk_1.map emd_8174_msk_2.map emd_8174_msk_3.map emd_8174_msk_4.map | 32.7 MB 32.7 MB 32.7 MB 32.7 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8174 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8174.map.gz / Format: CCP4 / Size: 16.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | U2OS Cells | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_8174_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_8174_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #3
File | emd_8174_msk_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #4
File | emd_8174_msk_4.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mitochondria from U2OS Cells
Entire | Name: Mitochondria from U2OS Cells |
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Components |
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-Supramolecule #1: Mitochondria from U2OS Cells
Supramolecule | Name: Mitochondria from U2OS Cells / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: Bone |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS |
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Grid | Model: Quantifoil SiO2 R1/4 / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
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 |
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 / Cs: 2.0 mm / 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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