ジャーナル: Biol Imaging / 年: 2023 タイトル: Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow. 著者: Neville B-Y Yee / Elaine M L Ho / Win Tun / Jake L R Smith / Maud Dumoux / Michael Grange / Michele C Darrow / Mark Basham / 要旨: Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex ...Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With the advancement in technology, microscopes are currently capable of producing images amounting to terabytes of data per day, posing great challenges for scientists as the speed of processing of the images cannot keep up with the ever-higher throughput of the microscopes. Therefore, automation is an essential and natural pathway on which image processing-from individual micrographs to full tomograms-is developing. In this paper, we present Ot2Rec, an open-source pipelining tool which aims to enable scientists to build their own processing workflows in a flexible and automatic manner. The basic building blocks of Ot2Rec are plugins which follow a unified application programming interface structure, making it simple for scientists to contribute to Ot2Rec by adding features which are not already available. In this paper, we also present three case studies of image processing using Ot2Rec, through which we demonstrate the speedup of using a semi-automatic workflow over a manual one, the possibility of writing and using custom (prototype) plugins, and the flexibility of Ot2Rec which enables the mix-and-match of plugins. We also demonstrate, in the Supplementary Material, a built-in reporting feature in Ot2Rec which aggregates the metadata from all process being run, and output them in the Jupyter Notebook and/or HTML formats for quick review of image processing quality. Ot2Rec can be found at https://github.com/rosalindfranklininstitute/ot2rec.
ダウンロード / ファイル: emd_17767.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
IMOD weighted back-projection reconstruction of tilt series from Position 09 using Ot2Rec.
ボクセルのサイズ
X=Y=Z: 14.96 Å
密度
最小 - 最大
-493.020230000000026 - 491.525539999999978
平均 (標準偏差)
11.63147 (±63.113579999999999)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
-256
サイズ
512
512
512
Spacing
512
512
512
セル
A=B=C: 7659.52 Å α=β=γ: 90.0 °
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添付データ
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試料の構成要素
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全体 : JEG-3 human choriocarcinoma cell line
全体
名称: JEG-3 human choriocarcinoma cell line
要素
細胞: JEG-3 human choriocarcinoma cell line
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超分子 #1: JEG-3 human choriocarcinoma cell line
超分子
名称: JEG-3 human choriocarcinoma cell line / タイプ: cell / ID: 1 / 親要素: 0
由来(天然)
生物種: Homo sapiens (ヒト)
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実験情報
-
構造解析
手法
クライオ電子顕微鏡法
解析
電子線トモグラフィー法
試料の集合状態
cell
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試料調製
緩衝液
pH: 7.4
グリッド
モデル: Quantifoil R2/2 / メッシュ: 200
凍結
凍結剤: ETHANE / チャンバー内湿度: 80 % / 装置: LEICA EM GP
切片作成
集束イオンビーム - 装置: OTHER / 集束イオンビーム - イオン: OTHER / 集束イオンビーム - 電圧: 30 / 集束イオンビーム - 電流: 0.3 / 集束イオンビーム - 時間: 1.0E-14 / 集束イオンビーム - 温度: 105 K / 集束イオンビーム - Initial thickness: 1000 / 集束イオンビーム - 最終 厚さ: 200 集束イオンビーム - 詳細: Note: initial thickness and duration of FIB milling was not recorded.. The value given for _em_focused_ion_beam.instrument is ThermoFisher Scios. This is not in a ...集束イオンビーム - 詳細: Note: initial thickness and duration of FIB milling was not recorded.. The value given for _em_focused_ion_beam.instrument is ThermoFisher Scios. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.
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電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
撮影
フィルム・検出器のモデル: TFS FALCON 4i (4k x 4k) 平均電子線量: 1.48 e/Å2