em2em: 3DEM Conversion Program

Description | Download | Manual

Description

Program to convert images (2-D images and 3-D volumes) from/to formats typically used in 3-D electron microscopy (3DEM).

FORMATS CURRENTLY SUPPORTED:

BROOKHAVEN STEM A format used to store STEM images (Import only)
CCP4 Crystallography community format
DATA ONLY Raw images, no header available
DIG. MICROGRAPH 2 Gatan's dm2 format
EM MPI für Biochemie, Martinsried, Germany
FEI MRC FEI's MRC files with extended header
FEI MRCS FEI's MRCS files (stacked MRC file)
FEI Raw Image FEI's raw image format
FORMATTED ASCII formatted files
IMAGIC Image Science, Berlin, Germany
JPEG Coloured/grey scale to grey scale images
KONTRON Kontron image format
MDPP NYU-MC, Ross Smith
MEDIPIX Raw MEDIPIX image format
MRC MRC/LMB, Richard Henderson & Tony Crowther, others
OFFSET Skip a specified number of (header) bytes
PIF Purdue Ariality, Tim Baker
PGM Portable greymap format (P2 and P5)
POSTSCRIPT Adobe Postscript (export only)
RAWIV/VOLUMETRIC The rawiv data format is used to represent3D volumetric data of scalar fields defined on a regular grid
RGB_TIFF The red/green/blue parts of a coloured TIFF image are imported/exported as single (greyscale) images
SHF GATAN's simple header file format
SITUS The map format of Willy Wrigger's docking program Situs
SPIDER Albany, Joachim Frank
SUPRIM J.P. Schroeter and P. Bretaudiere, Also used in PHOELIX (B. Carragher, M. Whittaker & R. Milligan)
TIA (EMISPEC) The EMISPEC format used bei FEI (TECNAI/TITAN)
TIFF Tagged image format
TVIPS Image formats used by the TVIPS (Tietz Video and Image Processing Systems) company, Germany. (The two formats used are EM and TIFF with a specific tag)
X-PLOR A system for X-ray crystallography and NMR (Import only)

CORRECTION FOR BYTE SWAP:

Images from different workstations and operating systems can be converted automatically, i.e.

UNIX / Linux
Mac OS X
MS Windows

CONVERSION OF SERIES OF IMAGES:

Stacks of image files can be converted in one step


EASE OF USE:

All questions and options are asked by em2em before the conversion starts.

There is a GUI windows application of em2em. and a line-by-line version running in a terminal window.


INTERACTIVE HELP:

"Help" or "?" is a legitimate answer to every question asked by the em2em. This option provides context sensitive help. The program also suggest default answers


Interested?

Groups running IMAGIC or having signed a Shared Resources agreement will find em2em within their IMAGIC system. The commands are EM2EM or IMPORT-EXPORT.

If you do not use IMAGIC you can download your FREE em2em copy here.

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