Appion

h1. Align tilt series

Currently, there are three working methods for automated or semi-automated alignment:

# using the correlation-based image alignment from Imod packages as implemented in eTomo "Rough Alignment".

# using iterative geometry-refinement/reconstruction method from proTomo.

# using the phase-correlated image alignment determined during Leginon data collection (Available as the initial alignment when using proTomo method.

!http://emg.nysbc.org/attachments/267/Picture_62.png!

h2. General Workflow:

# Select the tiltseries to align.

# Check the runname and enter a description.

# Use the radio button to select Protomo Refinement or IMOD shift-only alignment.

# To submit the job to the cluster click the "Align Tilt Series" button.  Alternatively, click on "Just Show Command" to obtain a command that can be pasted into a UNIX shell.

!http://emg.nysbc.org/attachments/263/Picture_55.png!

# If your job has been submitted to the cluster, a page will appear with a link "Check status of job", which allows tracking of the job via its log-file. This link is also accessible from the "1 running" option under the "Aliogn tilt series" submenu in the appion sidebar.

# Now click on the "1 Complete" link under the "Align tilt series" submenu. This opens a summary of all tilt series alignment runs that have been completed for this dataset.

!http://emg.nysbc.org/attachments/266/Picture_61.png!

# Clicking on the "alignrun id" opens a summary page for the alignment cycles that were run.

# Clicking on the "refine cycle" number opens a report page for that cycle including input parameters and directory paths.  Clicking on "Alignment Movie" opens a new web-browser with a movie of the aligned tilt series.

# The same alignment cycle can be repeated by clicking "Repeat Last Aligner Iteration" or another initiated by clicking "Setup Next Aligner Iteration" (See Step 11 below).

# In order to [[Create full tomogram|calculate a tomogram]] from the aligned tiltseries, click on the "Create full tomogram" link in the Tomography menu on the Appion Sidebar.

!http://emg.nysbc.org/attachments/272/Picture_70.png!

# If you selected "Repeat Last Aligner Iteration or "Setup Next Aligner Iteration" in step 9:  Enter the tilt image that protomo should use as a starting point for refinement during this next round; default is to use zero degree image.  Note that once you've entered this image number, the corresponding image is surrounded by a blue circle in the tilt-series graph.  If the previous refinement run was good for only a subset of the tiltseries, then under the "Reset alignment outside the range.." caption, enter a range for the sub-set of images for which the refinement was good.  A box will appear in the graph above, showing the subset of images for which the previous alignment parameters will be kept; the remaining images will retain their alignment parameters for the run before last.  Note that a dropdown menu is available in case the alignment parameters to apply are from a run other than the previous.  Default is to include all images and to use the last iteration.

# Enter a description of this run.  For example "repetition of alignrun id 5".

# Click "Align Tilt Series" to submit to the cluster.  Alternatively, click "Just Show Command," to copy and paste the command into a unix shell.

!http://emg.nysbc.org/attachments/295/Picture_5.png!

# If your job has been submitted to the cluster, a page will appear with a link "Check status of job", which allows tracking of the job via its log-file. This link is also accessible from the "1 running" option under the "Aliogn tilt series" submenu in the appion sidebar.

# Now click on the "1 Complete" link under the "Align tilt series" submenu. This opens a summary of all tilt series alignment runs that have been completed for this dataset, including the latest refinement runs.  Either proceed with more refinement as outlined in steps 9-14, or continue to [[Create full tomogram|calculate a tomogram]] from the aligned tiltseries.

h2. Notes, Comments, and Suggestions:

[[tomo alignment appiondata|appiondata tables involved in this process]]

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[[Tomography|< Tomography]] | [[Create full tomogram|Create Full Tomogram >]]

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