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| = Welcome to the EMAN1/2 Wiki = | = Welcome to the EMAN Wiki = |
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| This site now contains the official documentation for the EMAN1 and EMAN2 projects. Some of this ever-changing documentation may migrate into the static documentation included with the EMAN1 and EMAN2 distributions. But this is likely to be the best source for up-to-date information on both packages. In true wiki style, all EMAN users are encouraged to contribute their own experience by directly editing this documentation. Most of the docs are editable by any user that has registered an account on the server. |
Most of the docs are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account. |
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| * [[EMAN2|EMAN2.1]] We still maintain legacy docs for EMAN1, though it is no longer supported. Best practices in the field have changed considerably since the last update to EMAN1, and we can no longer recommend it for single particle reconstructions due to the lack of "gold standard" resolution measures, and other necessary validations. Unlike EMAN2.0x, EMAN2.1 has abandoned the problematical BDB system, and has many other improvements to make it as easy to use for both beginners as well as advanced users, and we strongly encourage users to upgrade. |
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| * [[EMAN2]] === Which link to follow ? === In most cases, the EMAN2 link. While still fully functional, EMAN1 is no longer actively developed. EMAN2 is capable of replacing virtually every aspect of processing that might have been done previously in EMAN1, and in most cases with more accuracy and less effort. |
Welcome to the EMAN Wiki
Most of the docs are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account.
The new Wiki documentation is here:
We still maintain legacy docs for EMAN1, though it is no longer supported. Best practices in the field have changed considerably since the last update to EMAN1, and we can no longer recommend it for single particle reconstructions due to the lack of "gold standard" resolution measures, and other necessary validations. Unlike EMAN2.0x, EMAN2.1 has abandoned the problematical BDB system, and has many other improvements to make it as easy to use for both beginners as well as advanced users, and we strongly encourage users to upgrade.
What is EMAN ?
EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community, though it is beginning to be used in other fields as well. EMAN has a particular focus on performing a task known as single particle reconstruction. In this method, images of nanoscale molecules and molecular assemblies embedded in vitreous (glassy) ice are collected on a transmission electron microscope, then processed using EMAN to produce a complete 3-D recosntruction at resolutions now approaching atomic resolution. For low resolution structures (~2 nm), this may require ~8 hours of computer processing and a few thousand particles. For structures aimed at ~0.5 nm or better resolution, hundreds of thousands of particles and hundreds of thousands of CPU-hours (on large computational clusters) may be required. Indeed, EMAN is often used in supercomputing facilities as a test application for large-scale computing.
Scientific image processing is distinguished from typical 'Photoshop' image processing in that it is analytical in nature. Images processed in EMAN are floating point greyscale images. That is, the pixel values in the images are represented as real numbers, not as small integers (typical GIF/JPG/PNG images are limited to integral values from 0-255 for each pixel). Processing often includes complex image processing operations in Fourier or Wavelet space. EMAN was first released in 1999, and has been under continuous development since. It consists of a C++ library of hundreds of different image/volume processing algorithms with bindings into the popular Python scripting language. In new EMAN development, all user-level programs (of which there are over 200 in EMAN 1.8) are developed in Python, allowing the knowledgable end-user to make modifications without having to download or compile any of the C++ source code.