「File Formats and Other Documentation」の版間の差分
(→Image Metadata Files) |
(→Image Metadata Files) |
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|StageZ ||Z stage position in microns | |StageZ ||Z stage position in microns | ||
|- | |- | ||
− | Magnification "Film" magnification value | + | |Magnification ||"Film" magnification value |
|- | |- | ||
− | CameraLength Camera length in mm for image in diffraction mode | + | |CameraLength ||Camera length in mm for image in diffraction mode |
|- | |- | ||
− | MagIndex Magnification index | + | |MagIndex ||Magnification index |
|- | |- | ||
− | Intensity Raw intensity value between 0 and 1 | + | |Intensity ||Raw intensity value between 0 and 1 |
|- | |- | ||
− | SuperMontCoords X and Y pixel coordinates of frame in a supermontage | + | |SuperMontCoords ||X and Y pixel coordinates of frame in a supermontage |
|- | |- | ||
− | PixelSpacing Pixel spacing in Angstroms for individual image (or in 1/Angstroms for diffraction image) | + | |PixelSpacing ||Pixel spacing in Angstroms for individual image (or in 1/Angstroms for diffraction image) |
|- | |- | ||
− | ExposureDose Dose on specimen during camera exposure in electrons/sq. A | + | |ExposureDose ||Dose on specimen during camera exposure in electrons/sq. A |
|- | |- | ||
− | DoseRate Dose rate to the camera, in electrons per physical pixel per second | + | |DoseRate ||Dose rate to the camera, in electrons per physical pixel per second |
|- | |- | ||
− | SpotSize Microscope spot size | + | |SpotSize ||Microscope spot size |
|- | |- | ||
− | Defocus Relative defocus readout from microscope (microns) | + | |Defocus ||Relative defocus readout from microscope (microns) |
|- | |- | ||
− | TargetDefocus Current target for autofocus (microns) | + | |TargetDefocus ||Current target for autofocus (microns) |
|- | |- | ||
− | ImageShift X and Y image shift in basic units (close to microns) | + | |ImageShift ||X and Y image shift in basic units (close to microns) |
|- | |- | ||
− | RotationAngle Rotation of image from having tilt axis along X axis (CCW +) | + | |RotationAngle ||Rotation of image from having tilt axis along X axis (CCW +) |
|- | |- | ||
− | ExposureTime Image exposure time | + | |ExposureTime ||Image exposure time |
|- | |- | ||
− | Binning Image binning on the camera | + | |Binning ||Image binning on the camera |
|- | |- | ||
− | UsingCDS 1 if image was taken with CDS mode on | + | |UsingCDS ||1 if image was taken with CDS mode on |
|- | |- | ||
− | CameraIndex Index of the CameraProperties section for the camera used | + | |CameraIndex ||Index of the CameraProperties section for the camera used |
|- | |- | ||
− | DividedBy2 1 if image was divided by 2 | + | |DividedBy2 ||1 if image was divided by 2 |
|- | |- | ||
− | RotationAndFlip RotationAndFlip property of K2 or K3 camera | + | |RotationAndFlip ||RotationAndFlip property of K2 or K3 camera |
|- | |- | ||
− | LowDoseConSet Control set index plus 1 if image taken in Low Dose, or negative of index if not in Low Dose (index 0-6 for View, Focus, Trial, Record, Preview, Search, Mont-|- | + | |LowDoseConSet ||Control set index plus 1 if image taken in Low Dose, or negative of index if not in Low Dose (index 0-6 for View, Focus, Trial, Record, Preview, Search, Mont-|- |
map; 7 for tracking, 8 for montage) | map; 7 for tracking, 8 for montage) | ||
|- | |- | ||
− | MinMaxMean Minimum, maximum, and mean value for this image | + | |MinMaxMean ||Minimum, maximum, and mean value for this image |
|- | |- | ||
− | PriorRecordDose For an image in a tilt series taken in Low Dose mode, the cumulative dose in the Record area prior to this image, including Record and Preview images and |- | + | |PriorRecordDose ||For an image in a tilt series taken in Low Dose mode, the cumulative dose in the Record area prior to this image, including Record and Preview images and |- |
|- | |- | ||
− | View | + | |View i||mages taken in tasks |
|- | |- | ||
− | XedgeDxy Edge displacement in X and Y for montage piece to the right of this piece | + | |XedgeDxy ||Edge displacement in X and Y for montage piece to the right of this piece |
|- | |- | ||
− | YedgeDxy Edge displacement in X and Y for piece above this piece | + | |YedgeDxy ||Edge displacement in X and Y for piece above this piece |
|- | |- | ||
− | XedgeDxyVS Edge displacement for piece to right, computed with very sloppy option | + | |XedgeDxyVS ||Edge displacement for piece to right, computed with very sloppy option |
|- | |- | ||
− | YedgeDxyVS Edge displacement for piece above, computed with very sloppy option | + | |YedgeDxyVS ||Edge displacement for piece above, computed with very sloppy option |
|- | |- | ||
− | StageOffsets When aligning montage pieces with image shift, this is the effective stage position (actual position plus the stage equivalent to the image shift adjustment) |minus the nominal stage position of the piece. | + | |StageOffsets ||When aligning montage pieces with image shift, this is the effective stage position (actual position plus the stage equivalent to the image shift adjustment) |minus the nominal stage position of the piece. |
|- | |- | ||
− | AlignedPieceCoords Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option off. | + | |AlignedPieceCoords ||Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option off. |
|- | |- | ||
− | AlignedPieceCoordsVS Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option on. | + | |AlignedPieceCoordsVS ||Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option on. |
|- | |- | ||
− | SubFramePath Directory or file in which subframes of exposure were stored | + | |SubFramePath ||Directory or file in which subframes of exposure were stored |
|- | |- | ||
− | NumSubFrames Number of subframes stored | + | |NumSubFrames ||Number of subframes stored |
|- | |- | ||
− | FrameDosesAndNumbers Dose per frame in electrons per square Angstrom followed by number of frames at that dose; variable-sized frame sums will have multiple pairs of such values | + | |FrameDosesAndNumbers ||Dose per frame in electrons per square Angstrom followed by number of frames at that dose; variable-sized frame sums will have multiple pairs of such values |
|- | |- | ||
− | DateTime Time and date of image acquisition; the format of the date is dd-Mon-yy regardless of locale. | + | |DateTime ||Time and date of image acquisition; the format of the date is dd-Mon-yy regardless of locale. |
|- | |- | ||
− | NavigatorLabel Label of Navigator item, added if Acquire at Items is being run and a tilt series is not | + | |NavigatorLabel ||Label of Navigator item, added if Acquire at Items is being run and a tilt series is not |
|- | |- | ||
− | FilterSlitAndLoss Energy filter slit width and energy loss if slit is in, 0 0 otherwise | + | |FilterSlitAndLoss ||Energy filter slit width and energy loss if slit is in, 0 0 otherwise |
|- | |- | ||
− | ChannelName Detector name for a STEM image | + | |ChannelName ||Detector name for a STEM image |
|- | |- | ||
− | MultishotHoleAndPosition Hole identifier and position within hole when taking multiple record images; peripheral positions are numbered from 1 and the center is numbered 0. For a regular pattern, hole identifiers are a pair of numbers relative to the center of the pattern; for a custom pattern, they are simply numbers starting at 1. | + | |MultishotHoleAndPosition ||Hole identifier and position within hole when taking multiple record images; peripheral positions are numbered from 1 and the center is numbered 0. For a regular pattern, hole identifiers are a pair of numbers relative to the center of the pattern; for a custom pattern, they are simply numbers starting at 1. |
|- | |- | ||
− | CameraPixelSize For diffraction image, the size of the image pixel on the camera in microns, namely the physical chip pixel size times the binning | + | |CameraPixelSize ||For diffraction image, the size of the image pixel on the camera in microns, namely the physical chip pixel size times the binning. |
− | + | ||
− | + | ||
|- | |- | ||
+ | |Voltage ||High voltage in kV for diffraction image. | ||
+ | |} | ||
+ | |||
+ | {| | ||
+ | |+ | ||
Direct Electron Specific Section Data | Direct Electron Specific Section Data | ||
|- | |- | ||
− | DE12-ServerSoftwareVersion Server software version | + | |DE12-ServerSoftwareVersion Server software version |
|- | |- | ||
DE12-PreexposureTime(s) Pre-exposure time | DE12-PreexposureTime(s) Pre-exposure time |
2022年12月30日 (金) 05:19時点における版
Image Metadata Files
SerialEMは、画像のメタデータをIMOD "autodoc" フォーマットでテキストファイルに保存する。 この形式は、キーワードと値のペアをセクションと呼ばれるブロックに整理したものである。 このセクションには、さまざまな種類のデータが含まれているが、 SerialEMのファイルでは、基本的に1種類のセクションしか使用しない。 セクションは、大括弧付きのキーと値のペアで始まります。
[セクションタイプ = 名前]
ここで、セクションの「名前」または値は通常,ユニークに設定するが、 IMOD autodocリーダーではそうである必要はない。
セクションヘッダ以下の行は、次のような形式で表現される。
キー = 値
そのセクションに関連するデータを提供する。 さらに、キーと値のペアは、セクション・ヘッダの前のファイルの最初に記載することもでき、これらはグローバル値として参照される。
すべての値はオートドキュメントファイルにテキスト文字列として保存されるが、特定の種類の情報を期待するソフトウェアは、これらの文字列を1つまたは複数の浮動小数点または整数値に変換することがよくある。
IMOD ライブラリ libcfshr の autodoc モジュールには、1 つ、2 つ、3 つ、または多数の浮動小数点または整数値をファイルの指定セクションに格納または取得するための関数が含まれている。 autodoc形式がSerialEMに選ばれた理由は、このライブラリがすぐに利用できること、このような関数を利用すると便利なこと、IMODのautodoc読込み機能との互換性があること、などである。
SerialEMが生成する画像関連autodocファイルには2種類ある。
1) ".mdoc "ファイルは、MRCファイルに関するデータを提供し、画像ファイルと同じ名前ですが、拡張子が".mdoc "になっています。 セクションタイプは "ZValue "で、各セクションの名前はファイル内の画像のZ値で、0から順に番号が付けられている。
2) 一連の単一画像TIFFファイルをMRCファイルと同様に扱うための情報を提供する".idoc "ファイル。 ここでのセクションタイプは "Image "で、各セクションの名称はTIFFファイルの名称である。
グローバルデータは、MRCファイルのヘッダーにある情報の一部を複製したものである。 また、MRCファイルのタイトルは "T "型のセクションヘッダに格納されます。
SerialEMが使用するIMODライブラリは、HDFファイルのメタデータにアクセスするために同じ内部オートドック構造を使用する。 したがって、これらのメタデータ情報をすべてautodoc形式のテキストファイルに抽出することは、次のようなコマンドで簡単にできる。
extracttilts -attr filename.hdf filename.hdf.mdoc
のようなコマンドで、これらのメタデータ情報をオートドック形式のテキストファイルに抽出することができる。
DataMode | MRC file mode |
ImageSize | X and Y size of images |
Montage | 1 if the file is a montage |
ImageSeries | 1 for an .idoc file describing a series of single-image files |
ImageFile | In a .mdoc file, contains the name of the image file |
PixelSpacing | Pixel spacing in Angstroms that would be in MRC header (or in 1/Angstroms for diffraction images) |
TiltAngle | Tilt angle in degrees |
PieceCoordinates | Pixel coordinates in X and Y and section Z value for montage piece |
StagePosition | X and Y stage position in microns |
StageZ | Z stage position in microns |
Magnification | "Film" magnification value |
CameraLength | Camera length in mm for image in diffraction mode |
MagIndex | Magnification index |
Intensity | Raw intensity value between 0 and 1 |
SuperMontCoords | X and Y pixel coordinates of frame in a supermontage |
PixelSpacing | Pixel spacing in Angstroms for individual image (or in 1/Angstroms for diffraction image) |
ExposureDose | Dose on specimen during camera exposure in electrons/sq. A |
DoseRate | Dose rate to the camera, in electrons per physical pixel per second |
SpotSize | Microscope spot size |
Defocus | Relative defocus readout from microscope (microns) |
TargetDefocus | Current target for autofocus (microns) |
ImageShift | X and Y image shift in basic units (close to microns) |
RotationAngle | Rotation of image from having tilt axis along X axis (CCW +) |
ExposureTime | Image exposure time |
Binning | Image binning on the camera |
UsingCDS | 1 if image was taken with CDS mode on |
CameraIndex | Index of the CameraProperties section for the camera used |
DividedBy2 | 1 if image was divided by 2 |
RotationAndFlip | RotationAndFlip property of K2 or K3 camera |
LowDoseConSet | -
map; 7 for tracking, 8 for montage) |
MinMaxMean | Minimum, maximum, and mean value for this image |
PriorRecordDose | - |
View i | mages taken in tasks |
XedgeDxy | Edge displacement in X and Y for montage piece to the right of this piece |
YedgeDxy | Edge displacement in X and Y for piece above this piece |
XedgeDxyVS | Edge displacement for piece to right, computed with very sloppy option |
YedgeDxyVS | Edge displacement for piece above, computed with very sloppy option |
StageOffsets | minus the nominal stage position of the piece. |
AlignedPieceCoords | Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option off. |
AlignedPieceCoordsVS | Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option on. |
SubFramePath | Directory or file in which subframes of exposure were stored |
NumSubFrames | Number of subframes stored |
FrameDosesAndNumbers | Dose per frame in electrons per square Angstrom followed by number of frames at that dose; variable-sized frame sums will have multiple pairs of such values |
DateTime | Time and date of image acquisition; the format of the date is dd-Mon-yy regardless of locale. |
NavigatorLabel | Label of Navigator item, added if Acquire at Items is being run and a tilt series is not |
FilterSlitAndLoss | Energy filter slit width and energy loss if slit is in, 0 0 otherwise |
ChannelName | Detector name for a STEM image |
MultishotHoleAndPosition | Hole identifier and position within hole when taking multiple record images; peripheral positions are numbered from 1 and the center is numbered 0. For a regular pattern, hole identifiers are a pair of numbers relative to the center of the pattern; for a custom pattern, they are simply numbers starting at 1. |
CameraPixelSize | For diffraction image, the size of the image pixel on the camera in microns, namely the physical chip pixel size times the binning. |
Voltage | High voltage in kV for diffraction image. |
DE12-ServerSoftwareVersion Server software version | |
ViewBeamTilts | Incremental beam tilts for low dose View or Search |
ViewDefocus | Focus offset for low dose View or Search, assigned to image buffer when reading in |
Alpha | Alpha value on JEOL |
FilterState | 0/1 if slit is out/in, and slit width |
SerialEM Navigator Fileに関する説明になります。
下記の翻訳に なります。 [https://bio3d.colorado.edu/SerialEM/stableHlp/html/about_formats.htm#navigator ]
SerialEM 3.6では、Navigatorの出力が1項目につき1行のタブ区切り形式からオートドック形式に変更され、代わりにXMLとして出力するオプションが追加されている。
XMLやautodocファイルは、以前のバージョンのタブ区切りファイルと同様に、読み挙げることができる。
グローバル・データは2行あります。
AdocVersion = x.xx LastSavedAs = xy.nav
という2行のグローバルデータがあり、2行目は最後に保存したときのファイルの完全な絶対パスとファイル名である。
次に、各項目は'Item'タイプのセクションにあり、そのラベル文字列を値として持つ。
次の表は、セクションに出現するすべてのキー、期待される値の種類、それが必須かどうか、必須でない場合はどのようなデフォルト値が設定されるかを示したものである。
Key | Type of value | Default value, or Required | CMapDrawItem member(s) | Description |
---|---|---|---|---|
Color | Integer | Req | mColor | Color index (0-5) |
StageXYZ | Three Floats | Req (unless external) | mStageX/Y/Z | Stage position adjusted for current mag |
NumPts | Integer | Req | mNumPoints | Number of points |
Corner | Integer | 0 | mCorner | Flag for corner point |
Draw | Integer | 1 | mDraw | Flag to draw |
RegPt | Integer | 0 | mRegPoint | Registration point number |
Regis | Integer | Req | mRegistration | Registration at which item exists |
Type | Integer | Req | mType | Type: 0-2 for point, polygon, map |
Note | String | blank | mNote | Note string |
GroupID | Integer | 0 | mGroupID | ID of group thatitem belongs to |
PolyID | Integer | 0 | mPolygonID | ID of polygon used to define supermontage |
FitToPolygonID | Integer | 0 | mFitToPolygonID ID of polygon that this montage map was fit to | |
Imported | Integer | 0 | mImported | Indicator of an imported map or point drawn on one |