File Formats and Other Documentation
提供: Eospedia
目次
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。
Global Data
| 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) |
Section Data
| 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 | 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) | |
| 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 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. |
Direct Electron Specific Section Data
| DE12-ServerSoftwareVersion | Server software version |
| DE12-PreexposureTime(s) | Pre-exposure time |
| DE12-TotalNumberOfFrames | Total number of frames in acquisition |
| DE12-FramesPerSecond | Frame rate in frames per second |
| DE12-SensorModuleSerialNumber | Serial number of sensor |
| DE12-SensorReadoutDelay(ms) | Delay before starting to read out sensor during exposure |
| DE12-IgnoredFramesInSummedImage | Number of frames ignored in a summed image |
Additional Data in MontSection
| Additional Data in MontSection | |
| FullMontSize | Full size of montage in X and Y if all pieces are present |
| BufISXY | Image shift associated with overview buffer |
| ProbeMode | 1 for microporbe, 0 for nanoprobe |
| MoveStage | 1 if for a stage montage |
| ConSetUsed | Control set used for the montage (0 = View, 3 = Record, 5 = Search, 6 = MontMap |
| MontBacklash | The nominal backlash for this montage, or 0 0 if using an anchor at the center |
| ValidBacklash | The nominal backlash for this montage, or 0 0 if using an anchor at the center or doing a zigzag pattern |
| DriftSettling | Drift settling in control set used |
| CameraModes | Shutter mode and read mode |
| FocusOffset | Focus offset for low dose View or Search, assigned to map item DefocusOffset if a map is made |
| NetViewShifts | Image shift offsets for low dose View or Search |
| ViewBeamShifts | Beam shift offsets for low dose View or Search |
| 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 | |
| RegisteredToID | Integer | 0 | mRegisteredToID | For an imported map, ID of map that it was registered to for transforming | |
| SuperMontXY | Two Integers | -1,-1 | SuperMontX/Y | Camera coordinate of a montage in supermontage | |
| OrigReg | Integer | Regis | mOriginalReg | Original registration (default is Registration) | |
| DrawnID | Integer | 0 | mDrawnOnMapID | ID of map point/polygon was drawn on | |
| BklshXY | Two Floats | 0,0 | mBacklashX/Y | Backlash when a montage was taken or associated with item | |
| SamePosId | Integer | 0 | mAtSamePosID | Items with this matching were taken at same raw stage position | |
| RawStageXY | wo Floats | -10000,-10000 | mRawStageX/Y | Raw stage position before adjustments | |
| Acquire | Integer | 0 | mAcquire | Flag for acquiring | |
| PieceOn | Integer | -1 | mPieceDrawnOn | Index of montage piece item was drawn on (piece_#_in_X * #_of_pieces_in_Y + piece_#_in_Y), or index of nearest piece if item is on a missing piece, in which case XYinPc will not be written to file. | |
| XYinPc | Two Floats | -1,-1 | mX/YinPiece | X,Y coordinates in the montage piece, in right-handed pixels of stored montage | |
| MapFile | String | Req if Map | mMapFile | Full or relative path of map file (see Read & Open) | |
| MapID | Integer | Req if Map | mMapID | Unique ID (all items get one, not just maps) | |
| FocusAxisPos Float | -1.e8 | mFocusAxisPos | Stored position of Focus area on inter-area axis | ||
| LDAxisAngle | Two integers | 0,0 | mRotateFocusAxis, mFocusAxisAngle | First value: 1 to rotate inter-area axis from tilt axis, 0 not to; second value: angle of rotation | |
| FocusOffsets | Two Floats | 0,0 | mFocusX/Yoffset | Offset of focus subarea in X and Y in unbinned pixels (Y inverted) | |
| HoleArray | Two integers | 0,0 | mNumX/Yholes | # of positions in X and Y for multiple Record | |
| SkipHoles | List of integers | none | mSkipHolePos | Pairs of X,Y indexes for positions to skip from that array specified in HoleArray. Positions are numbered from 0 at lower-left in stage coordinates | |
| TargetDefocus | Float | -1.e8 | mTargetDefocus | Target defocus for Acquire or tilt series item | |
| FileToOpen | String | none | mFileToOpen | Name of file to open for Acquire or tilt series item | |
| TSParamIndex | Integer | -1 | mTSParamIndex | Index of into parameter array for tilt series | |
| MontParamIndex | Integer | -1 | mMontParamIndex | Index into array of parameters for montages to open | |
| FilePropIndex | Integer | -1 | mFilePropIndex | Index into array of file options for file to open | |
| MapMontage | Integer | Req if Map | mMapMontage | Flag that map is a montage | |
| MapSection | Integer | Req if Map | mMapSection | Section number in file | |
| MapBinning | Integer | Req if Map | mMapBinning | Binning at which map was taken, or of initial overview map image for montage | |
| MapMagInd | Integer | Req if Map | mMapMagInd | Magnification index of map, or of non-map image a point or polygon was drawn on | |
| MapCamera | Integer | Req if Map | mMapCamera Camera index | ||
| MapScaleMat | Four Floats | Req if Map | mMapScaleMat | Stage to pixel scale matrix for drawing, based on pixels of initial map image. For
montage, needs to be adjusted by ratio of currently loaded map width/height to initial map width/height | |
| MapWidthHeight | Two Integers | Req if Map mMapWidth/Height | Size of initial map image at which scale matrix was defined | ||
| MapMinMaxScale | Two Floats | 0,0 | mMapMin/MaxScale | Min and max scale values of image when map was defined | |
| MapFramesXY | Two Integers | 0,0 | mMapFramesX/Y | Number of montage frames when acquired | |
| MontBinning | Integer | 0 | mMontBinning | Actual binning of montage used to make the map | |
| MapExposure | Float | 0. | mMapExposure | Exposure time for original map images | |
| MapSettling | Float | 0. | mMapSettling | Drift settling | |
| ShutterMode | Integer | -1 mShutterMode | Shutter mode | ||
| K2ReadMode | Integer | 0 mK2ReadMode | Read mode for K2/K3 camera | ||
| MapSpotSize | Integer | 0 | mMapSpotSize | Spot size at which map was taken | |
| MapIntensity | Double | 0 | mMapIntensity | Intensity at which map was taken | |
| MapSlitIn | Integer | 0 | mMapSlitIn | Filter slit state when map was taken | |
| MapSlitWidth | Float | -1. | mMapSlitWidth | Filter slit width when map was taken | |
| RotOnLoad | Integer | 0 | mRotOnLoad | Flag to rotate when load | |
| RealignedID | Integer | 0 | mRealignedID | ID of lower mag map with nearby realign error | |
| RealignErrXY | Two Floats | 0,0 | mRealignErrX/Y | Final stage error of that realign operation | |
| RealignReg | Integer 0 | mRealignReg | Original registration of that realign | ||
| ImageType | Integer | 0 | mImageType | Map file type 0-3 for MRC, IMOD, TIFF, IDOC | |
| MontUseStage | Integer | -1 | mMontUseStage | 1 if montage was taken with stage, 0 if not, -1 if unknown | |
| DefocusOffset | Float | 0. | mDefocusOffset | Defocus offset for map based on View images | |
| K2ReadMode | Integer | 0 | mK2ReadMode | Read mode for K2/K3 camera | |
| MapLDConSet | Integer | -1 | mMapLowDoseConSet | Set # (0-4) used for map taken in low dose | |
| MapTiltAngle | Float | -10000. | mMapTiltAngle | Tilt angle at which map was taken | |
| PtsX | NumPts | Floats | Req | mPtX | X stage cordinates of points |
| PtsY | NumPts | Floats | Req | mPtY | Y stage cordinates of points |
| UserValueN | String | none | mUserValueMap | Arbitrary value set by script; N is # (currently1-8) | |
| BaseMarkerShift - a section containing a stored shift from Shift to Marker (names are from BaseMarkerShift structure). | |||||
| FromMag | Integer | fromMagInd | Mag index of map item was marked on | ||
| ToMag | Integer | toMagInd | Mag index of image with marker point | ||
| ShiftX | Float | shiftX | X component of shift in microns | ||
| ShiftY | Float | shiftY | Y component of shift in microns | ||
| T|SParam - a section containing tilt series parameters. See TiltSeriesParam.h in the source code for a description of each item. | |||||
| MontParam - a section containg montage parameters. See MontageParam.h in the source code for a description of each item. | |||||
| FileOptions - a section containing properties for opening a file. See FileOptions.h in the source code in case this has descriptions. | |||||
