SPIDER Data File Header Locations

Location	Name	Content
1	NZ	# of slices (planes) in volume (=1 for an image) Previously called: NSLICE. In some legacy 2D images this may be -1
2	NY	# of rows per slice. Previously called: NROW.
3	IREC	Total # of records (including header records) in each image of a simple image or stacked image file.
4	UNUSED	Unassigned
5	IFORM	File type specifier. 1 R 2D image. 3 R 3D volume. -11 FO 2D Fourier, mixed radix odd -12 FE 2D Fourier, mixed radix even -21 FO 3D Fourier, mixed radix odd -22 FE 3D Fourier, mixed radix even
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	Obsolete, no longer used.
12	NX	# of pixels (samples) per line. Previously called: NSAM.
13	LABREC	# 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 # 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	-	Used 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	11 Character creation date e.g. 27-MAY-1999
215-216	CTIM	8 Character creation time e.g. 09:43:19
217-256	CTIT	160 Character title

Page updated: 13 Nov. 2019     ArDean Leith