Bsoft: Bshow

Version 1.5.4

• Home
  
• Manual
  
• Download & Install
  • Download
  • Snapshots
  • Unix install
  • VMS install
    
• Associated packages
  
  • PFT2/EM3DR2
    
  • Radon
    
• Bshow
  • Main window
  • The toolbox
  • Fitting the CTF
  • Picking particles
  • Picking filaments
  • Tomography
  • Crystallography
  • Helical processing
  • Model
    
• How to
  
  • Unix command line
    
  • VMS command line
    
  • Simple image manipulations
  • Map synthesis
    
  • CTF fitting
  • Micrograph pair alignment
  • Resolution estimation
  • Handedness determination
  • 3D particle picking
  • Sequence analysis
    
• Workflows
  
  • Single particle analysis
    
  • Tomography
    
• Distributed processing
• Programs
• Scripts
  
• Developer
  
  • Policies
    
  • Functions
    
  • Objects
    
• History
• Contributors
• References

Running Bshow

Bshow can be started from the command line with or without an image file name:

bshow
bshow file.img

On Macintosh OSX bshow has to be started in the Terminal application through an intermediate script called bshowX:

bshowX file.img

Bshow requires Tcl/Tk version 8.3 or later. On Macintosh OSX Tcl/Tk version 8.4 is required with the appropriate application (Wish Shell) and frameworks in the correct locations (see Installation

---

The main window

The main window has a menu bar, a panel for the display of 2D images and slices of 3D images, and a list of controls and information fields on the right side. (The tool panel on the left is described here.)

Menu bar:

• File:
  • Open - image file
  • Save - image file
  • Revert - resets the image to last version on disk.
    
  • Get info - opens a dialog box with image information.
  • Quit
• Image:
  • Set parameters - alternative to using the sliders (see below).
  • Modify image - changes the image in memory.
  • Fix type sign - changes between signed and unsigned integer types.
  • Center origin - shifts the origin to the center of the image.
  • Shift origin to zero - shifts the origin to the lower left back corner.
  • Crop - crops the image based on the region selected by the selection tool.
  • Pad - pads an image to a larger size.
  • Montage - lays out a montage of slices or multiple 2D images.
  • Histogram - displays a simple histogram of the image.
  • Fourier transform - calculates the Fourier transform (preserves the complex nature of the data).
  • Power spectrum - calculates a power spectrum from the image (loses the phase information).
  • Diffraction - provides some analysis of diffraction patterns.
    
• Micrograph:
  • Read parameters - reads micrograph parameters from a file (such as a STAR file).
    
  • Write parameters - writes micrograph parameters to a file (such as a STAR file).
  • Edit parameters - a text editor to display and modify parameter files.
    
  • Fit CTF - setup for fitting a CTF curve to a power spectrum.
  • Pick particles - setup for picking single particle images in a micrograph.
  • Pick filaments - setup for picking filaments in a micrograph.
  • Tomography - setup for tomographic alignment and reconstruction.
  • Crystallography - setup for analysis of crystallographic diffraction patterns.
  • Helix - setup for analysis of helical diffraction patterns.
• Model:
  • Read model - reads model of components from a file (STAR, PDB or CMM).
  • Write model - writes model of components to a file (STAR, PDB, CMM).
  • Edit model - a text editor to display and modify model files.
  • Delete all components - deletes all components and links.
  • Extract marked panels - extracts panels marked as components from a multi-level mask.
  • Help - switches to on-line help with models.
• Window (exposes existing windows):
  • Main
  • Tools
  • Magnify - shows a magnified view of the region under the mouse in 2D or 3D.
    
  • Selection - selects a region and reports the statistics.
    
  • CTF
  • Particles
  • Filaments
  • Tomography
  • Crystallography
  • Helix
  • Model
    
• About:
  • About...
  • Help - switches to on-line help with bshow.
    

Averaging mode:

With the scale below one, this mode averages all the values of the pixels neighboring a display pixel. The default is to display the nearest neighbor only.

Status bar with 3 values:

• Voxel x coordinate adjusted for scaling.
• Voxel y coordinate adjusted for scaling.
• Voxel gray scale value for the image (not the display).
  

Pixel size entry:

    Pixel size is typically used as angstrom/voxel (required for CTF calculations).

Origin:

    The origin for the current image is displayed. This can be reset using the "Image/Modify image" menu item.

Distance reporter:

    Gives the distance between mouse clicks when the distance measure toool is selected.

Sliders:

• Image number
• Slice number
• Scale - range 0.1 - 10.
• Minimum - for the image.
• Maximum - for the image.
  

Autoscale:

The image display can be quicly scaled to ± 5 standard deviation units of the average.

Range step:

The step size in the minimum and maximum sliders can be set here to allow for either fine or coarse grain control of contrast changes.  

Bernard Heymann 20071017