SPIDER uses NX to denote number of pixels (voxels) per row, NY to denote number of rows, and NZ to denote the number of slices or planes in a volume. A 2D image is considered to be a single slice of a volume. The first pixel in an image represents the upper left corner of the image. (Note: this is important for correct handedness when converting volumes.) All SPIDER image files consist of unformatted, direct access records. Each record contains NX 4-byte words which are stored as floating point numbers.
There are three types of SPIDER image files: Simple images/volumes. Image stack files, and Indexed image stack files.
The image data is preceeded by a header. There are LABREC records in the header, where LABREC = ceiling of (256/NX). Note that the total length of the header in SPIDER images is always >= 1024 bytes and is calculated as follows (in FORTRAN) when a new SPIDER image is created:
LENBYT = NX * 4
LABREC = 1024 / LENBYT
IF (MOD(1024,LENBYT) .NE. 0) LABREC = LABREC + 1
LABBYT = LABREC * LENBYT
Where LENBYT is the record length in bytes, and the MOD function returns the remainder of dividing 1024 by LENBYT. This variable length header is used for compatibility with FORTRAN direct access unformatted file I/O.
| Location | Name | Content | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | NZ | Number of slices (planes) in volume (=1 for an image) In some ancient 2D images this may be -1) | |||||||||||||||||||
| 2 | NY | Number of rows per slice. | |||||||||||||||||||
| 3 | IREC | Total number of records (including header records) in each image of a simple image or stacked image file. | |||||||||||||||||||
| 4 | UNUSED | Unassigned | |||||||||||||||||||
| 5 | IFORM | File type specifier.
| |||||||||||||||||||
| 6 | IMAMI | Maximum/minimum flag = 0 when the file is created, and = 1 when the maximum, minimum, average, and standard deviation have been computed and stored into this header record (see following locations). | |||||||||||||||||||
| 7 | FMAX | Maximum data value. | |||||||||||||||||||
| 8 | FMIN | Minimum data value. | |||||||||||||||||||
| 9 | AV | Average data value. | |||||||||||||||||||
| 10 | SIG | Standard deviation of data. A value of -1.0 or 0.0 indicates that SIG has not been computed. | |||||||||||||||||||
| 11 | UNUSED | No longer used. | |||||||||||||||||||
| 12 | NX | Number of pixels (samples) per line. | |||||||||||||||||||
| 13 | LABREC | Number of records in file header (label). | |||||||||||||||||||
| 14 | IANGLE | Flag that following three tilt angles are present. | |||||||||||||||||||
| 15 | PHI | Tilt angle: phi (See note #2 below). | |||||||||||||||||||
| 16 | THETA | Tilt angle: theta. | |||||||||||||||||||
| 17 | GAMMA | Tilt angle: gamma (also called psi). | |||||||||||||||||||
| 18 | XOFF | X translation. | |||||||||||||||||||
| 19 | YOFF | Y translation. | |||||||||||||||||||
| 20 | ZOFF | Z translation. | |||||||||||||||||||
| 21 | SCALE | Scale factor. | |||||||||||||||||||
| 22 | LABBYT | Total number of bytes in header. | |||||||||||||||||||
| 23 | LENBYT | Record length in bytes. | |||||||||||||||||||
| 24 | ISTACK/ MAXINDX | Position has a value of 0 in simple 2D or 3D (non-stack) files. In an "image stack" there is one overall stack header followed by a stack of images, in which each image has its own image header. A value of >0 in this position in the overall stack header indicates a stack of images. A value of <0 in this position in the overall stack header indicates an indexed stack of images and gives the maximum image number (MAXINDX) allowed in the index. | |||||||||||||||||||
| 25 | UNUSED | Unused now. Prior to release 9.0, a '-1' at this location in an overall stack indicated a valid stack and in the stacked images, a value of 1 indicated that this image was in use (existed). | |||||||||||||||||||
| 26 | MAXIM | Position is only used in the overall header for a stacked image file. There, this position contains the number of the highest image currently used in the stack. This number is updated, if necessary, when an image is added or deleted from the stack. | |||||||||||||||||||
| 27 | IMGNUM | Position is only used in a stacked image header. There, this position contains the number of the current image or zero if this image is unused. | |||||||||||||||||||
| 28 | LASTINDX | Position is only used in overall header of indexed stacks. There, this position is the highest index location currently in use. | |||||||||||||||||||
| 29 | UNUSED | Unassigned | |||||||||||||||||||
| 30 | UNUSED | Unassigned | |||||||||||||||||||
| 31 | KANGLE | Flag that additional rotation angles follow in header. 1 = one additional angle set is present, 2 = two additional angle sets. | |||||||||||||||||||
| 32 | PHI1 | Angle. | |||||||||||||||||||
| 33 | THETA1 | Angle. | |||||||||||||||||||
| 34 | PSI1 | Angle. | |||||||||||||||||||
| 35 | PHI2 | Angle. | |||||||||||||||||||
| 36 | THETA2 | Angle. | |||||||||||||||||||
| 37 | PSI2 | Angle. | |||||||||||||||||||
| 38 | PIXSIZ | Pixel size (Angstroms). | |||||||||||||||||||
| 39 | EV | Electron voltage used. | |||||||||||||||||||
| 40 | PROJ | Project number. | |||||||||||||||||||
| 41 | MIC | Micrograph number. | |||||||||||||||||||
| 42 | NUM | Micrograph window number. | |||||||||||||||||||
| 43 | GLONUM | Global image number. | |||||||||||||||||||
| 44-47 | UNUSED | Unassigned. | |||||||||||||||||||
| 48-76 | - | Reserved for XMIPP or other local transforms | |||||||||||||||||||
| 77-100 | - | Unassigned. | |||||||||||||||||||
| 101 | PSI3 | Projection angle: Psi (From 'PJ 3Q'). | |||||||||||||||||||
| 102 | THETA3 | Projection angle: Theta (From 'PJ 3Q'). | |||||||||||||||||||
| 103 | PHI3 | Projection angle: Phi (From 'PJ 3Q'). | |||||||||||||||||||
| 104 | LANGLE | If = 1 then projection angles: PSI3, THETA3 & PHI3 are present in header. | |||||||||||||||||||
| 105-211 | - | Unassigned | |||||||||||||||||||
| 212-214 | CDAT | Character *11 Creation date e.g. 27-MAY-1999 | |||||||||||||||||||
| 215-216 | CTIM | Character *8 Creation time e.g. 09:43:19 | |||||||||||||||||||
| 217-256 | CTIT | Character *160 Title |
There are three types of SPIDER image files: Simple images/volumes. Image stack files, and Indexed image stack files.
Simple image / volume with: NX x NY x NZ voxels.
Unformatted, direct access file containing a total of LABREC + NY * NZ records.
| Record No. | ---> Record No. | Contents |
|---|---|---|
| 1 | LABREC | Image/volume header |
| LABREC+1 | LABREC+NY | Slice No. 1 |
| LABREC+NY+1 | LABREC+2*NY | Slice No. 2 |
| .. | .. | Further slices |
| LABREC+NY*(NZ-1) | LABREC+NZ*NY | Slice No. NZ |
Stack of images / volumes with: NX x NY x NZ voxels in each image.
Unformatted, direct access file containing a total of LABREC + MAXIM * (LABREC + NY * NZ) records.
| Record No. | ---> Record No. | Contents |
|---|---|---|
| 1 | LABREC | Overall stack header |
| LABREC+1 | 2*LABREC | First stacked image/volume header |
| 2+LABREC+1 | 2*LABREC+NY*NZ) | Image/volume No. 1 |
| 2*LABREC+NY*NZ+1 | 3*LABREC+NY*NZ | Second stacked image/volume header |
| 3*LABREC+NY*NZ+1 | 3*LABREC+2*NY*NZ | Image/volume No. 2 |
| .. | .. | Further sets of headers & images/volumes |
| MAXIM*LABREC+(MAXIM-1)*NY*NZ+1 | (MAXIM+1)*LABREC+(MAXIM-1)*NY*NZ | Last stacked image/volume header |
| (MAXIM+1)*LABREC+(MAXIM-1)*NY*NZ+1 | (MAXIM+1)*LABREC+MAXIM*NY*NZ | Last stacked image/volume |
Indexed Stack of images / volumes with: NX x NY x NZ voxels in each image.
Unformatted, direct access file containing a total of LABREC +INDXREC + MAXIM * (LABREC + NY * NZ) records.
The image data is preceeded by an overall file header and an additional index header. There are INDXREC records in the header, where INDXREC = ceiling of (MAXINDX/NX). The user must specify a value for MAXINDX whenever an indexed stack file is originally created. (For programmers attempting to write conversion utilities, I advise them to ignore indexed stacks. They are mainly in use at only a couple of sites with specialized large data requirements.)
| Record No. | ---> Record No. | Contents |
|---|---|---|
| 1 | LABREC | Overall stack header |
| LABREC+1 | LABREC+INDXREC | Overall index header |
| INDXREC+LABREC+1 | INDXREC+2*LABREC | First stacked image/volume header |
| INDXREC+2+LABREC+1 | INDXREC+2*LABREC+NY*NZ) | Image/volume No. 1 |
| INDXREC+2*LABREC+NY*NZ+1 | INDXREC+3*LABREC+NY*NZ | Second stacked image/volume header |
| INDXREC+3*LABREC+NY*NZ+1 | INDXREC+3*LABREC+2*NY*NZ | Image/volume No. 2 |
| .. | .. | Further sets of headers & images/volumes |
| INDXREC+MAXIM*LABREC+(MAXIM-1)*NY*NZ+1 | INDXREC+(MAXIM+1)*LABREC+(MAXIM-1)*NY*NZ | Last stacked image/volume header |
| INDXREC+(MAXIM+1)*LABREC+(MAXIM-1)*NY*NZ+1 | INDXREC+(MAXIM+1)*LABREC+MAXIM*NY*NZ | Last stacked image/volume |
Source: image_doc.html Last update: 30 Oct. 2013 ArDean Leith