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Table of supported image formats in EMAN2

Type

Extension

Read

Write

3D

Image Stacks

Volume Stacks

Region I/O

Comments

Primary EMAN2 Format

HDF5

hdf

Y

Y

Y

Y

Y

Y

HDF5 is an international standard for scientific data (http://www.hdfgroup.org/HDF5/). It supports arbitrary metadata (header info) and is very portable. This is the standard interchange format for EMAN2. Chimera can read EMAN2 style HDF files.

Cryo-EM Formats

DM2 (Gatan)

dm2

Y

N

N

N

N

N

Proprietary Gatan format (older version)

DM3 (Gatan)

dm3

Y

N

N

N

N

Proprietary Gatan format from Digital Micrograph

DM4 (Gatan)

dm4

Y

N

Y

Y

N

Proprietary Gatan format from Digital Micrograph, used with K2 cameras

SER (FEI)

ser

Y

N

N

Y

N

Proprietary FEI format (Falcon camera ?)

EM

em

Y

Y

Y

N

Y

As produced by the EM software package

ICOS

icos

Y

Y

Y

N

Y

Old icosahedral format

Imagic

img/hed

Y

Y

Y

Y

Y

Y

This format stores header and image data in 2 separate files. Region I/O is only available for 2D. The Imagic format in EMAN2 is fully compatible with Imagic4D standard since the 2.0 release.

MRC

mrc

Y

Y

N

Y

Y

Largely compatible with CCP4. Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This behavior is partially supported in EMAN, but be aware that it is impossible to store metadata about each image in the stack when doing this, so it is not suitable as an export format for single particle work. EMAN2 supports reading of FEI MRC, which is an extended MRC format for tomography. The extra header information will be read into the header. All FEI MRC images will be 2-byte integer.

MRCS

mrcs

Y

Y

N

Y

soon?

Y

Identical to MRC format above. If the filename is .mrcs, then a 3-D volume file will automatically be treated as a stack of 2-D images. If any other extension is used, it will appear to be a single 3-D volume.

Spider Stack

spi

Y

Y

Y

Y

Y

To read the overall image header in a stacked spider file, use image_index = -1.

Spider Single

spi

Y

Y

Y

N

Y

Specify "--outtype=spidersingle" to use with e2proc2d/3d

SER

ser

Y

N

N

Y

N

Also known as TIA (Emospec) file format, used by FEI Tecnai and Titan microscope for acquiring and displaying scanned images and spectra

BDB

N/A

Y

Y

Y

Y

Y

This entry is for EMAN2's (retired) embedded database system. While it is still possible to read/write BDB's for backwards compatibility, we do not suggest any new use of this format in EMAN2 (SPARX still uses it for many operations)

Other Supported Formats

Amira

am

Y

Y

Y

N

N

A native format for the Amira visualization package

DF3

df3

Y

Y

Y

N

N

File format for POV-Ray, support 8,16,32 bit integer per pixel

FITS

fts

Y

N

Y

N

N

Widely used file format in astronomy

JPEG

jpg/jpeg

N

Y

N

N

N

Note that JPEG images use lossy compression and are NOT suitable for quantitative analysis. PNG (lossless compression) is a better alternative unless file size is of critical importance.

LST

lst

Y

Y

Y

Y

N

ASCII file contains a list of image file names and numbers. Two variants, LST and LSX. LSX is normally used in EMAN2 and has the additional restraint that all lines have the same length.

LSTFAST

lsx/lst

Y

Y

Y

Y

N

Optomized version of LST

OMAP

omap

Y

N

Y

N

N

Also called DSN6 map, 1 byte integer per pixel

PGM

pgm

Y

Y

N

N

N

Standard graphics format with 8 bit greyscale images. No compression.

PIF

pif

Y

Y

Y

Y

N

Purdue Image Format. This will read most, but not all PIF images. Recent support added for mode 40 and 46 (boxed particles). Some of the FFT formats cannot be read by EMAN2. PIF writing is normally done in FLOAT mode, which is not used very often in PIF. PIF technically permits only images with odd dimensions, EMAN does not enforce this.

PNG

png

Y

Y

N

N

N

Excellent format for presentations. Lossless data compression, 8 bit or 16 bit per pixel

SAL

hdr/img

Y

N

N

N

N

Scans-A-Lot. Old proprietary scanner format. Separate header and data file

SITUS

situs

Y

Y

Y

N

N

Situs-specific ASCII format on a cubic lattice. Used by Situs programs

TIFF

tiff/tif

Y

Y

N

N

N

Good format for use with programs like photoshop. Some variants are good for quantitative analysis, but JPEG compression should be avoided.

V4L

v4l

Y

N

N

N

N

Used by some video-capture boards in Linux. Acquires images from the V4L2 interface in real-time(video4linux).

VTK

vtk

Y

Y

Y

N

N

Native format from Visualization Toolkit

XPLOR

xplor

Y

Y

Y

N

N

8 bytes integer, 12.5E float ASCII format

File format conversions

  • Most EMAN2 programs will read and write any of the formats above directly without conversion.
  • e2proc2d.py and e2proc3d.py provide options for saving in specific formats with specific data modes.

  • The Save as button in the e2display.py and e2projectmanager.py browsers can be used to save into an arbitrary format.

Special issues for MRC/CCP4 files

MRC/CCP4 format supports a single 1-D, 2-D or 3-D image, with an associated header. At some point in time, someone decided it would be a good idea to store sets of 2-D particle images as "stacks" in 3-D. That is, a set of NZ identically sized NX x NY images are stacked to make a single 3-D pseudo-volume image. The problem is that the original format was not designed for this, and historically there was no consistent way a program could tell if an MRC file contains a true volume (like a 3-D reconstruction) or a stack of 2-D images. While a number of developers have recently agreed upon a standard way of doing this in future, the last 30 years of files floating around in the community don't have this information stored in a consistent way. As of EMAN2.1, stack files should use the ".mrcs" extension and single volumes should use the ".mrc" extension. ".mrc" files will always be read as if they contain a single image, and ".mrcs" files can never be 3-D. This may evolve in the future as the new standards become more refined.

Additionally, there are options in the e2proc2d.py command which will treat single volume files as stacks of images without the .mrcs extension (again, if you just use the .mrcs extension, these methods should not be required) :

  • --threed2twod - reads an MRC-style stack file and outputs to a 'normal' set of 2-D images (used by all other file formats supporting multiple images)

  • --twod2threed - reads a set of 2-D images and outputs an MRC-style stack

  • --threed2threed - reads an MRC-style stack file and outputs to another MRC-style stack file

These options can also be used with other file formats.

Reading and Writing images in Python (for programmers)

The main image object in EMAN2 is called EMData(). EMData objects represent an image in an arbitrary file format in the computer's memory, with arbitrary associated tag-based metadata.

Simple Image Reading/Writing

The specification for reading/writing images is:

   1 # note that optional arguments [ ] below require all previous arguments to be specified
   2 
   3 # Read multiple images at once, class-method
   4 imagelist=EMData.read_images(filename,[image#_list],[header_only])
   5 
   6 # Read a single image
   7 img=EMData()
   8 img.read_image(filename,[image#],[header_only],[Region])
   9 # or
  10 img=EMData(filename,[image#],[header_only])
  11 
  12 
  13 # write a single image
  14 EMData.write_image(filename,image#,[filetype],[header_only],[Region],[Datatype])

Where filename, is the name of the file containing the image data, in any supported format, image# is the zero-indexed image number within the file, image#_list is a python list or tuple of image numbers, header_only is a boolean flag indicating that only the header should be read/written from/to the file, Region is a Region(x0,y0,xsize,ysize) or Region(x0,y0,z0,xsize,ysize,zsize) object.

Filetype can be : IMAGE_UNKNOWN, IMAGE_AMIRA, IMAGE_IMAGIC, IMAGE_PIF, IMAGE_SPIDER, IMAGE_VTK, IMAGE_DM3, IMAGE_GATAN2, IMAGE_LST, IMAGE_PNG, IMAGE_TIFF, IMAGE_XPLOR, IMAGE_DM4, IMAGE_HDF, IMAGE_MRC, IMAGE_SAL, IMAGE_EM, IMAGE_ICOS, IMAGE_PGM, IMAGE_SINGLE_SPIDER, IMAGE_V4L. If IMAGE_UNKNOWN is used on write, then the file extension will be used to determine the filetype. Note that since MRC format does not distinguish between 3-D volumes and stacks of 2-D images, the '.mrcs' extension MUST be used for stack files, and the '.mrc' extension MUST be used for non-stack volume data.

Datatype can be: EM_CHAR, EM_FLOAT, EM_INT, EM_UINT, EM_USHORT, EM_DOUBLE, EM_FLOAT_COMPLEX, EM_SHORT, EM_UCHAR, EM_USHORT_COMPLEX, EM_SHORT_COMPLEX. While SHORT_COMPLEX types are defined, they should never be actually used. FLOAT_COMPLEX is only really usable for HDF files. Strongly suggest not reading/writing complex images, and simply recomputing the FFT instead. Not all file formats support all data types!

If no image#_list is specified to read_images, then ALL images in the file will be read in.

   1 # Create a new EMData object and initializes it with the first image in "myimage.hdf".
   2 # This will work with any supported file format, not just HDF
   3 img=EMData("myimage.hdf")
   4 
   5 # Replace the data in EMdata object 'img' with the 3rd image from "myimage.hdf" (the first is #0)
   6 img.read_image("myimage.hdf",2)
   7 
   8 # Write an EMData object to disk as the 3rd image in "image.hdf"
   9 img.write_image("image.hdf",2)
  10 
  11 # Read all of the images from the SPIDER stack file (also works with single image files) "test.spi"
  12 # lst will become a list of EMData objects
  13 lst=EMData.read_images("test.spi")
  14 
  15 # Count the number of images available in a stack file
  16 n=EMUtil.get_image_count("myimage.hdf")
  17 
  18 # Create a new EMData object with ONLY HEADER INFORMATION from the 5th image
  19 # in the "myimage.hdf" stack file. Any image processing operations on this object
  20 # will cause EMAN2 to crash, because it doesn't have data loaded for the actual image.
  21 # This can be useful when all you need is the header information from a bunch of images.
  22 hdr=EMData("myimage.hdf",4,True)

Region I/O

Region I/O permits reading or writing sub-images/volumes from within a file. It is not supported for all file formats. This is useful when processing huge files (like full 4k tomograms) on machines with limited RAM. For region reading, it is possible to specify a Region extending outside the actual image dimensions, though this generally isn't a good idea. For region writing, the region must be completely inside image bounds.

   1 # Read a subimage with origin (1,1,1) and size 8x8x8
   2 img = EMData
   3 region = Region(1,1,1,8,8,8)
   4 img.read_image("3dimage.hdf",0,False,region)

Storage type

Internally EMAN2 stores all images as 32-bit (single precision) floating point. Many file formats also support other storage modes. The various formats are defined in a dictionary imported from EMAN2.py: file_mode_map. There is also a file_mode_range dictionary which contains the numeric limits for each type. If you set the header values renfer_min and render_max in each image before writing, this will control how the float data is scaled to the specified mode. ie - if render_min is 0 and render_max is 1.0, then the 0-1 range in the internal image will be mapped to the full available scale of (integer mode) output formats. Note also that not all file formats support all modes.

Here are some examples of how to write in alternative formats:

img = EMData(128,128)
img.write('float-image.mrc')  #by default, image will be write as float
img.write_image('short-image.mrc', 0, IMAGE_MRC, False, None, EM_SHORT) #write mrc file in short (16bit)
img.write_image('byte-image.mrc', 0, IMAGE_MRC, False, None, EM_UCHAR) #write mrc file in byte (8bit)
img.write_image('byte-image.spi', 0, IMAGE_UNKNOWN, False, None, EM_FLOAT) #write mrc file in byte (8bit)

EMAN2ImageFormats (last edited 2019-03-16 23:32:39 by SteveLudtke)