Appion

h1. View Stacks

This option takes the user to the stack summary page, which is also accessible from the "X Complete" link under the "Stack" submenu in the Appion SideBar.

h2. Description and Options Available:

A.  The stack description can be edited by clicking on the "edit" button.

B.  The raw stack particles can be viewed in an independent web browser window by clicking on the "stackname" link.  The new window contains options for stack manipulation such as excluding certain particles or creating templates for alignment and particle selection.

C.  Clicking on the "selection run name" link opens a summary page for the particle picking runs that were used to create this stack.  The new window contains options for downloading particle data to your local machine, viewing selection run histograms, and a summary of the input parameters used during particle picking.

D.  Clicking on the ".hed" or ".img" disk image links next to the stack file name opens a window for downloading stack particles to your local machine.

E.  Several options (mean and stdev filter, center particles, sort junk, create substack) exist for filtering particle stacks and are discussed below.

!http://emg.nysbc.org/attachments/320/Picture_52.png!

h2. E.1 Filter by Mean/STdev:  Filter particle stack by mean and stdev values

# Check run name, output directory location, and write a description for this filtering run.

# Input min and max values for the x-axis (mean particle intensity) and the y-axis (stdev).

# Click "Test selected points" to refresh the graph with a trapezoid that defines the particles to keep.

!http://emg.nysbc.org/attachments/321/Picture_54.png!

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