Opening particle stacks and images
When it comes to processing EM data, you will be visually inspecting micrographs, particle stacks, and 3D volumes constantly throughout the analysis workflow.
Below is a list of common software packages that are used for visualizing 2D or 3D data. Keep in mind that each program may have different ways of displaying 2D or 3D data, depending on the type of data that you inputting:
EMAN2 is used to visualize 2D images/stacks or slices through a 3D model using the command e2display.py:
$ e2display.py [input].img
In addition to providing users with an interface with which to generate commands to run analysis routines, Relion is able to display 2D images/stacks and slices through a 3D volume.
To open a 2D image/stack or slices through a 3D volume, first open Relion via the command line:
$ relion
This will open Relion's main window. Then click 'Display' in the lower left hand corner:
On the next screen, using the file navigator to locate your 2D image/stack or 3D volume of interest. You may need to select 'All file types' from the 'Show' pull down menu if your files are .spi or .img/hed:
After clicking 'OK', you will be presented with a screen that has display options. These options allow you to magnify/bin the displayed images or change the layout of the images displayed. (Typically, values are left as the default number, but you could decrease the scale if the images have a large box size):
The resulting window will always be a series of 2D images. This could be a single image, particle stack, or 3D volume slices. In this example, it is 3D volume slices:
EMAN is used to visualize 2D images/stacks or a 3D model in projection.
This is achieved by 1) opening the main 'eman' Graphical User Interface (GUI) or 2) directly opening a stack/3D volume.
To visualize 2D images/stacks, you can open them directly using 'v2':
$ v2 [stack].img
$ v2 [image].mrc
Or by opening them using the EMAN GUI:
$ eman
Will open the window:
By clicking on Browse Files/History you will be taken to a new window:
Clicking on Matrix View will open a new window showing the stack of particles.
Notice that when you click on any image file types, EMAN will try to display the box size and stack size. For instance, in the above example, under IMAGIC Image you see 1 of 200 Images and 72 x 72 pixels because the corresponding stack is 200 particles with a box size of 72 pixels.
To visualize a 3D model in projection, simply select a 3D volume from the EMAN GUI. This will show you a 2D projection through the volume that can rotated by right clicking on the image and dragging. This will change the projection direction and change the 2D projection concomitantly.
Chimera is used to interactively visualize 3D volumes. These volumes can be in .spi or .mrc format, or a variety of other formats. To open Chimera, you can click the icon on your Desktop or simply call the command from the command line:
$ chimera
This will open UCSF Chimera. Within this software package, you can open a 3D volume by going to:
File > Open > (select 3D volume)
It will then display your volume as an isosurface, which means that the 3D information is being interpreted into a single surface at any given threshold:
