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||Type || Extension || Read || Write || 3D || stack || Comments || ||MRC || mrc || Y || Y || Y || N || || ||Spider || spi || Y || Y || || Y || || ||Imagic || img/hed || Y || Y || || Y || || ||HDF || hdf || Y || Y || Y || Y || || ||DM3 || dm3|| || Y || || || || ||TIFF || tiff/tif || || || || || || ||PGM || pgm || || || || || || ||LST || lst || Y || || || || || ||PIF || pif || || || || || || ||VTK || || || || || || || ||PNG || png || || || || || || ||SAL || || || || || || || ||ICOS || || || || || || || ||EMIM || || || || || || || ||Gatan2 || || || || || || || ||Amira || || || || || || || ||XPLOR || || || || || || || ||EM || em || || || || || || ||V4L || || || || || || || ||JPEG || jpg/jpeg || || || || || || ||FITS || || || || || || || ||LSTFAST || || || || || || || |
<<TableOfContents>> = Table of supported image formats in EMAN2 = ||Type ||Extension ||Read ||Write ||3D ||stack ||Comments || ||HDF5 ||hdf ||Y ||Y ||Y ||Y ||This is the only format supporting the full metadata model used in EMAN2. That is, this is the only format you can export data from the database into and preserve all of the information about each image. Technically it can also support different sized images in the same stack, though this behavior is not normally used. || ||MRC ||mrc ||Y ||Y ||Y ||N || 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.|| ||Spider ||spi ||Y ||Y ||Y ||Y ||To read the overall image header in a stacked spider file, use image_index = -1. || ||Imagic ||img/hed ||Y ||Y ||Y ||Y ||seperate header and data file, cannot store multiple 3D images in one file || ||DM3 ||dm3 ||Y ||N ||N ||N || || ||TIFF ||tiff/tif ||Y ||Y ||N ||N ||8bit or 16bit per pixel || ||PGM ||pgm ||Y ||Y ||N ||N ||8 bits per pixel || ||PIF ||pif ||Y ||Y ||Y ||Y ||images in PIF stack are homogenous. PIF doesn't currently work. || ||VTK ||vtk ||Y ||Y ||Y ||N || || ||PNG ||png ||Y ||Y ||N ||N ||lossless data compression, 8 bit or 16 bit per pixel || ||SAL ||hdr/img ||Y ||N ||N ||N ||seperate header and data file || ||ICOS ||icos ||Y ||Y ||Y ||N || || ||EMIM ||emim ||Y ||N ||Y ||Y ||images in stack are homogenous || ||Gatan2 ||dm2 ||Y ||N ||N ||N || || ||Amira ||am ||Y ||Y ||Y ||N || || ||XPLOR ||xplor ||Y ||Y ||Y ||N ||8 bytes integer, 12.5E float format || ||EM ||em ||Y ||Y ||Y ||N || || ||V4L ||v4l ||Y ||N ||N ||N ||Acquires images from the V4L2 interface in real-time(video4linux). || ||JPEG ||jpg/jpeg ||N ||Y ||N ||N ||lossy data compression || ||FITS ||fts ||Y ||N ||Y ||N ||common file format in astronomy || ||LST ||lst ||Y ||Y ||Y ||Y ||ASCII file contains a list of image file names and numbers. Used in EMAN1 to avoid large files. Not commonly used in EMAN2|| ||LSTFAST ||lsx/lst ||Y ||Y ||Y ||Y ||Optomized version of LST|| = Saving EMData from Python = If you want to be prompted to supply a image name using a standard dialog use this approach {{{#!python # save a single image a = test_image() from emsave import save_data save_data(a) # save a list of images as a stack b = test_image(2) save_data([a,b]) }}} |
Table of supported image formats in EMAN2
Type |
Extension |
Read |
Write |
3D |
stack |
Comments |
HDF5 |
hdf |
Y |
Y |
Y |
Y |
This is the only format supporting the full metadata model used in EMAN2. That is, this is the only format you can export data from the database into and preserve all of the information about each image. Technically it can also support different sized images in the same stack, though this behavior is not normally used. |
MRC |
mrc |
Y |
Y |
Y |
N |
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. |
Spider |
spi |
Y |
Y |
Y |
Y |
To read the overall image header in a stacked spider file, use image_index = -1. |
Imagic |
img/hed |
Y |
Y |
Y |
Y |
seperate header and data file, cannot store multiple 3D images in one file |
DM3 |
dm3 |
Y |
N |
N |
N |
|
TIFF |
tiff/tif |
Y |
Y |
N |
N |
8bit or 16bit per pixel |
PGM |
pgm |
Y |
Y |
N |
N |
8 bits per pixel |
PIF |
pif |
Y |
Y |
Y |
Y |
images in PIF stack are homogenous. PIF doesn't currently work. |
VTK |
vtk |
Y |
Y |
Y |
N |
|
PNG |
png |
Y |
Y |
N |
N |
lossless data compression, 8 bit or 16 bit per pixel |
SAL |
hdr/img |
Y |
N |
N |
N |
seperate header and data file |
ICOS |
icos |
Y |
Y |
Y |
N |
|
EMIM |
emim |
Y |
N |
Y |
Y |
images in stack are homogenous |
Gatan2 |
dm2 |
Y |
N |
N |
N |
|
Amira |
am |
Y |
Y |
Y |
N |
|
XPLOR |
xplor |
Y |
Y |
Y |
N |
8 bytes integer, 12.5E float format |
EM |
em |
Y |
Y |
Y |
N |
|
V4L |
v4l |
Y |
N |
N |
N |
Acquires images from the V4L2 interface in real-time(video4linux). |
JPEG |
jpg/jpeg |
N |
Y |
N |
N |
lossy data compression |
FITS |
fts |
Y |
N |
Y |
N |
common file format in astronomy |
LST |
lst |
Y |
Y |
Y |
Y |
ASCII file contains a list of image file names and numbers. Used in EMAN1 to avoid large files. Not commonly used in EMAN2 |
LSTFAST |
lsx/lst |
Y |
Y |
Y |
Y |
Optomized version of LST |
Saving EMData from Python
If you want to be prompted to supply a image name using a standard dialog use this approach