Differences between revisions 3 and 30 (spanning 27 versions)

e2spt_boxer

This program is used for interactive tomographic single particle picking (locating and extracting subtomograms).

For a more extensive description of the e2spt_boxer interface and its usage, as well as background on Single Particle Tomography and proposed 'exercises' to learn how to do SPT in EMAN2, download the e2spt Users' Guide from the EMAN2 TUTORIALS page:

http://blake.bcm.edu/emanwiki/EMAN2/Tutorials

To see the entire list of command line options for e2spt_boxer, and an explanation of what they're for, type e2spt_boxer.py -h at the command line.

OPTIONS

-B	--boxsize	int	Box size in pixels
	--inmemory	bool	This will read the entire tomogram into memory. Much faster, but you must have enough ram !
	--yshort	bool	This means you have a file where y is the short axis
	--apix	float	Override the A/pix value stored in the tomogram header
-h	--help	bool	show this help message and exit
-v	--verbose	int	verbose level [0-9], higner number means higher level of verboseness

USAGE

e2spt_boxer.py tomogram.rec --inmemory

If you don't provide the --inmemory option, the data will be read from disk, opposed to being read from memory (which is faster).

Provide the --yshort option if the shortest dimension of your tomogram (the "ice thickness") is along the y axis (for example, 4096 x 500 x 4096).

e2spt_boxer consists of _3 GUI windows_.

1) The MAIN window opens immediately when you run e2spt_boxer.py from the command line.

2) The PARTICLE LIST window opens when you click anywhere in the slice views of the MAIN window to select a subvolume.

3) Same thing for the SINGLE PARTICLE VIEW window.

MAIN e2spt_boxer window

This window consists of three orthogonal views or slices through the tomogram, parallel to the XY, XZ and YZ planes, and a small options panel on the bottom left corner.

The yellow cross that comes up when you click on any of the views indicates the position of the cutting planes.

You can "scroll" through the slices in the largest projection (XY, looking at the tomogram from the "top") with the scroll bar on the bottom right corner, or by scrolling with the middle mouse button while pressing and holding SHIFT.

Select particles with left click, and delete them with SHIFT + left click.

You can "tweak" the center of any of the blue boxes that come up when you do left click by dragging it in any of the 3 slice views.

PARTICLE LIST window

SINGLE PARTICLE VIEW window

SAVING the COORDINATES FILE and the BOXED SUB-VOLUMES The file menu is located at the top left corner of your screen if you're a Mac user, and at the top left corner of the Main boxer window if you're using Windows or Linux.

Click on the File menu to save a text file with the coordinates of the sub-volumes selected (choose Save Box Coord).

To save the sub-volumes as individual files (numbered from 0 to N), choose Save Boxed Data.

To save the sub-volumes as a single stack file choose Save Boxes as Stack, which means you would only see one file listed in the directory where you save the stack, but it actually contains ALL the sub-volumes you’ve extracted (and EMAN2 can tell).

Note: You have to EXPLICITLY supply the format for the files you save. Use .hdf for boxed particles saved as separate files, or as a stack.

-  ⇤ ← Revision 3 as of 2011-03-22 19:15:24 → 
  Size: 965
  Editor: jgalaz
  Comment:
+   ← Revision 30 as of 2018-04-03 16:42:40 → ⇥
  Size: 3652
  Editor: jgalaz
  Comment: changed e2tomoboxer to e2spt_tomoboxer
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= e2tomoboxer =
+= e2spt_boxer =
 Line 5:
-'''Options'''
+For a more extensive description of the e2spt_boxer interface and its usage, as well as background on Single Particle Tomography and proposed 'exercises' to learn how to do SPT in EMAN2, download the __'' '''e2spt Users' Guide''' ''__ from the EMAN2 TUTORIALS page:
 http://blake.bcm.edu/emanwiki/EMAN2/Tutorials

To see the entire list of command line options for '''e2spt_boxer''', and an explanation of what they're for, type ''e2spt_boxer.py -h'' at the command line.

==== OPTIONS ====
-Line 13:
+Line 18:
-'''USAGE'''
+=== USAGE ===
{{{
e2spt_boxer.py tomogram.rec --inmemory 
}}}
If you don't provide the ''--inmemory'' option, the data will be read from disk, opposed to being read from memory (which is faster).
-Line 15:
+Line 24:
-e2tomoboxer.py tomogram.rec --yshort --inmemory
+Provide the ''--yshort'' option if the shortest dimension of your tomogram (the "ice thickness") is along the y axis (for example, 4096 x 500 x 4096).
-Line 17:
+Line 26:
-If you don't provide the "inmemory" option, the data will be read from disk, opposed to being read from memory (which is faster).
+e2spt_boxer consists of _3 GUI windows_.
-Line 19:
+Line 28:
-Provide the "yshort" option if the shortest dimension of your tomogram (the "ice thickness") is along the y axis (for example, 4096 x 500 x 4096).
+) The __''MAIN'' window__ opens immediately when you run ''e2spt_boxer.py'' from the command line.

2) The __''PARTICLE LIST'' window__ opens when you click anywhere in the slice views of the MAIN window to select a subvolume.

3) Same thing for the __''SINGLE PARTICLE VIEW'' window__.

'''MAIN e2spt_boxer window'''

This window consists of three orthogonal views or slices through the tomogram, parallel to the XY, XZ and YZ planes, and a small options panel on the bottom left corner.


{{attachment:main.png}}


The yellow cross that comes up when you click on any of the views indicates the position of the cutting planes.

You can "scroll" through the slices in the largest projection (XY, looking at the tomogram from the "top") with the scroll bar on the bottom right corner, or by scrolling with the middle mouse button while pressing and holding SHIFT.

Select particles with left click, and delete them with SHIFT + left click.

You can "tweak" the center of any of the blue boxes that come up when you do left click by dragging it in any of the 3 slice views.

''' PARTICLE LIST window'''

{{attachment:particle_list.png}}

'''SINGLE PARTICLE VIEW window'''

{{attachment:single_particle_view.png}}


'''SAVING the COORDINATES FILE and the BOXED SUB-VOLUMES'''
The file menu is located at the top left corner of your screen if you're a Mac user, and at the top left corner of the Main boxer window if you're using Windows or Linux.

{{attachment:file_menu.png}}

Click on the __''File menu''__ to save a text file with the coordinates of the sub-volumes selected (choose '''Save Box Coord'''). 

To save the sub-volumes as individual files (numbered from 0 to N), choose '''Save Boxed Data'''. 

To save the sub-volumes as a single stack file choose '''Save Boxes as Stack''', which means you would only see one file listed in the directory where you save the stack, but it actually contains ALL the sub-volumes you’ve extracted (and EMAN2 can tell).

Note: You have to EXPLICITLY supply the format for the files you save. Use .hdf for boxed particles saved as separate files, or as a stack.