Table of supported image formats in EMAN2

Type	Extension	Read	Write	3D	stack	Comments
MRC	mrc	Y	Y	Y	N
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
HDF5	hdf	Y	Y	Y	Y	can write different size image into same stack
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
LST	lst	Y	Y	Y	Y	ASCII file contains a list of image file names
PIF	pif	Y	Y	Y	Y	images in PIF stack are homogenous
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		N	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	lossy data compression
FITS	fts	Y	N	Y	N	common file format in astronomy
LSTFAST	lsx/lst	Y	Y	Y	Y	ASCII file contains a list of image file names

Saving EMData from Python

If you want to be prompted to supply a image name using a standard dialog use this approach

   1 # save a single image
   2 a = test_image()
   3 from emsave import save_data
   4 save_data(a)
   5 
   6 # save a list of images as a stack
   7 b = test_image(2)
   8 save_data([a,b])

-  ⇤ ← Revision 6 as of 2009-04-21 21:25:50 → 
  Size: 1453
  Editor: gtang
  Comment:
+   ← Revision 7 as of 2009-04-21 22:51:44 → ⇥
  Size: 1835
  Editor: gtang
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-||Spider ||spi ||Y ||Y || ||Y || ||
||Imagic ||img/hed ||Y ||Y || ||Y ||seperate header and data file||
||HDF5 ||hdf ||Y ||Y ||Y ||Y ||can write different size image into same stack||
||DM3 ||dm3 || ||N || || || ||
||TIFF ||tiff/tif || || || || || ||
||PGM ||pgm || || ||N||N||8 bits per pixel||
||LST ||lst ||Y||Y||Y||Y||ASCII file contains a list of image file names||
||PIF ||pif || || || ||Y||images in PIF stack are homogenous||
||VTK || || || ||Y||N|| ||
||PNG ||png || || || || ||lossless data compression||
||SAL ||hdr/img||Y||N||N||N||seperate header and data file||
||ICOS || || || ||Y||N|| ||
||EMIM || || || || || || ||
||Gatan2 || ||Y||N||N||N|| ||
||Amira || ||N||Y||Y||N|| ||
||XPLOR || || || ||Y||N||8 bytes integer, 12.5E float format||
||EM ||em || || ||Y||N|| ||
||V4L || ||Y||N|| || || ||
||JPEG ||jpg/jpeg ||N||Y|| ||N||lossy data compression||
||FITS || ||Y||N||Y|| ||common file format in astronomy||
||LSTFAST || || || || || || ||
+||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 ||
||HDF5 ||hdf ||Y ||Y ||Y ||Y ||can write different size image into same stack ||
||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 ||
||LST ||lst ||Y ||Y ||Y ||Y ||ASCII file contains a list of image file names ||
||PIF ||pif ||Y||Y||Y||Y ||images in PIF stack are homogenous ||
||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 || ||N ||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 ||lossy data compression ||
||FITS ||fts||Y ||N ||Y ||N||common file format in astronomy ||
||LSTFAST ||lsx/lst||Y||Y||Y||Y||ASCII file contains a list of image file names||