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TiltPicker Usage » History » Version 17

Neil Voss, 04/15/2010 09:01 AM

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A copy of this page is available at:
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  http://emg.nysbc.org/projects/tiltpicker/wiki/TiltPicker_Usage
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h2. BUG TRACKING:
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 TiltPicker bugs are now tracked via the AMI redmine server, visit
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 http://emg.nysbc.org/projects/tiltpicker/
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 to file any bugs
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h2. YOUTUBE MOVIE:
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I just made a screen capture video on how to use it. It is available is low resolution on youtube:
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 http://www.youtube.com/watch?v=cw1osPBY_JM
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or you can download the full screen version from the appion.org website:
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 http://code.google.com/p/appion/downloads/list
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I recommend using VLC to watch it:
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 http://www.videolan.org/vlc/
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h2. LAUNCHING THE PROGRAM:
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To run the program, type:
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  ./ApTiltPicker.py -1 image1.mrc -2 image2.mrc -p tiltpicks.spi
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'tiltpicks.spi' is optional. I left an example in the tiltpicker folder. You must run the program in the tiltpicker folder. To run the example type:
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  ./runPicker.sh
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If all works the picker will open up and you'll have two images of ribosomes.
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h2. STEP BY STEP TUTORIAL:
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* Start TiltPicker
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** Extract TiltPicker, on command line type:	
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 tar -zxf tiltpicker-2.0.tgz
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** Go to tiltpicker directory, on command line type:
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 cd tiltpicker	
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** Display TiltPicker help, on command line type:
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 ./ApTiltPicker.py -h
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** Open TiltPicker, on command line type:	
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 ./ApTiltPicker.py -l data/rawu048b.jpg -r data/rawu049b.jpg -t 50.0	
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* Initialize picking:
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** Maximize window
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** Set correct zoom for images, if necessary
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** Center the middle bar, if necessary
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** Manually pick 5 partcle pairs from each image
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** Save picks to a file, file will then auto-save all subsequent picks
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----
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* Initialize alignment:
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** Hit the *Apply* button, circles will NOT match crosses
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** Find theta (tilt angle)
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*** Hit *Theta...* button
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*** Hit *Run*
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*** This number should match the value from Goniometer
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*** Hit *Apply* to accept this value
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** Optimize inplane rotation angles and shift
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*** *Refine* means this parameter will be optimized
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*** *Lock* means this parameter is locked and will NOT be optimized
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*** Hit *Optimize...*
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*** Hit *Run* a few times
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*** Hit *Apply*
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** Use *Mask* button to only look at overlapping regions, overlap % is shown on status bar
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** Hit *Auto Optimize*, it automatically performs theta, optimize, and mask in a single click
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** If you look at the Terminal, it will tell you how many optimization rounds were performed
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* Transfer pick particles
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** Pick a single particle in only one image.
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** Use transfer or *Xfer picks* button -- this automatically transfers the pick to the 
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* DoG pick particles
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** Measure particle size using ruler tool, zoom in to get best value
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** Run DoG picker with wrong contrast
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** Reject picks
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** Run DoG picker with correct contrast
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** Show terminal
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** Accept picks
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** Look at DoG map images
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* Clean up particle picks	
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** Use clear bad picks button	
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** Use polygon tool
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** Auto optimize
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** Use cutoff button to remove picks below a threshold
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** Add more picks
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** Save and quit
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h2. BUTTON DOCUMENTATION:
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Notes: 
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# The underlined letter on the button means that you can use the Alt button (Option on a Mac) and that letter to push the button.
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# If the button name is followed by three dots '...', it means a pop up window will be displayed for more input.
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# All buttons are also availale at the top menu
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(from left to right)
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* Apply (Alt-A) -- Displays picked particle locations from one image in the other image as circles
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* Theta... (Alt-T) -- Determine the tilt angle difference between images independent of tilt axis rotation (positive, untilted on left; negative, untilted on right)
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* Optimize... (Alt-O) -- Perform least squares refinement of all alignment parameters
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* Mask (Alt-M) -- Hide non-overlapping regions in the images (based on alignment parameters)
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* Auto Optimize (Alt-Z) -- Automatically perform above 3 steps: Theta, Optimize, and Mask in single click
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* Rm Worst Picks (Alt-W) -- Remove the worst picks by alignment error highlighted by a yellow plus (+) symbol
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* Cutoff... (Alt-C) -- Remove the worst picks by specifying an alignment error
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* Xfer picks (Alt-X) -- Transfer picks from one image to the other based on the alignment parameters
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* Rm Polygon (Alt-P) -- Remove all points located within a drawn polygon from both images, good for large pieces of crud
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* Reset... -- Reset all parameters and remove all picks, i.e., start over.
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* Dog Pick... (Alt-D) -- Run automated particle picker. Requires an estimate of the size of the particle (in pixels)
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* Quit (Alt-Q) -- Quit the program