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||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 ||		 ||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 ||
Line 9: Line 9:
||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 ||		 ||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 ||
Line 13: Line 13:
||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 ||		 ||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 ||
Line 17: Line 17:
||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||		 ||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||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 ||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 ||

Contents

  1. Table of supported image formats in EMAN2
  2. Saving EMData from Python

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. 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

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

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])

EMAN2/ImageFormats (last edited 2024-02-01 04:08:01 by SteveLudtke)