Appion

h1. Manual Masking

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[[Crud Finding|< Crud Finding]]

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Manual masking is used to mask out regions of cruds on micrographs such that particles picked in the masked out regions will not be used in subsequent processing (e.g. stack creation).

h2. To launch:

# The user selects the option of:

> # Assess run of the same name (default)

> # Combined run with existing assessment run

> # Assess run under a new name 

# After that, the user clicks on either "show command" or "run manual masking", which will then show the command

# The user will need to launch the program from a terminal

# The interface of manual masking is similar to manual picker or tilt picker, except that instead of picking particles, the user will draw polygons to define the mask

# After that, the user proceeds on to the next image

h2. Output:

# The masking results can be used as a filter when making a stack of particles

# The user chooses the desired masking session to apply for filtering out unwanted particle picks