• New Model: Clear current model and creates a new one.
• Open Model: Load a new model file.
• Reload Model: Reload the current model from file.
• Save Model: Save model file to current file name.
• Save Model as...: Save model file, and prompts for a name.
• Write Model as -->: Write model to one of the following formats.
  • Imod – native model format.
  • Wimp – Used on BL3DEMC VAX machine.
  • NFF
  • Synu – San Diego format.
• Movie/Montage...: Open window to control range and interval of movies and to select movie and montage (higher-resolution) snapshots.
• Set Snap Dir...: Set a directory to put snapshots into. The same directory will be used for model snapshots. The default directory is the current working directory that the program was started from. This entry will open a directory chooser in the current browser directory, which may be different. Setting a snap directory does not change the current browser directory.
• Gray TIF Snaps: This entry is a checkable option; when it is checked, TIFF snapshots of all image windows will be saved as 8-bit gray scale. The option is saved with the user preferences.
• Memory to TIF: Save entire color image from memory to TIFF file.
• Extract File...: Extract portion of current image file selected by the rubber band in the top Zap window, using the Trimvol command that would be produced with the I button in that window. If there is no rubber band in a Zap Window, it extracts the whole area shown in the top Zap window. Rotation around X is included if the image is loaded flipped. A single slice is extracted if the Lo and Hi fields are empty; otherwise those fields specify the range in Z. If there is a rubber band in the top Slicer window, the program will instead use Rotatevol to extract the portion of the file selected by the rubber band. The depth limits of the range must be set with the Lo and Hi buttons.
• Process File...: Apply current operation(s) in the Image Processing dialog to the current image file if possible. If there is no Zap window with a rubber band, the whole file will be processed. Otherwise, the subarea in the rubber band will be processed, but the Lo and Hi limits must be set to process more than one slice.
• Save Info Text...: Save the contents of the text box at the bottom of the Info window to a file.
• Quit: Exit program.

• Model -->
  • Header...:  Settings.
    • Whether model will be drawn or not [t]
    • The Z scale for viewing the model
    • The resolution (spacing between points)
    • The pixel size in real units (nm, um, mm)
  • Offsets...: Shift model data in X, Y, and Z.
  • Clean: Delete all objects that have no points.
• Object -->
  • New: Create a new object.
  • Delete: Delete current object or all selected objects.
  • Type...: Edit Object type.
  • Color...: Opens requester for changing object color.
  • Move...: Move all contours in object to a different object; or, for an objects with a saved isosurface and no contours, move the mesh data into another object of the same kind.
  • Select by #... Enter a list of object numbers (consisting of comma-separated ranges) to select. All contours in each object will be added to the selection and displayed thicker in the Zap window.
  • Combine: Combine all selected objects into one object. This can be used to combine objects with saved isosurfaces, but all objects being combined must be of the same kind (regular versus saved isosurface).
  • Info: Print information on object by running imodinfo with -o option.
  • Clean: Delete empty contours from object. The operation cannot be undone if it removes more than 100 contours.
  • Break by Z: Break all contours in object into separate ones by Z.
  • Fill in Z: For every contour in an open object, add point at each Z level skipped by existing points.
  • Flatten: Flatten all contours in object to lie in single Z plane.
  • Sort by Dist: For all contours in the object, sorts points by interpoint distance so that sucessive points are as near to each other as possible.
  • Renumber...: Move the current object to a new object number.
• Surface -->
  • New: Create a new contour on a new surface. [N]
  • Go To...: Go to a different surface.
  • Move...: Move contours to new surfaces within object.
  • Delete: Delete all contours in the current surface.  [Ctrl+Shift+D]
  • Sort: Sort all contours in an open or closed contour object by their surface numbers and by their Z values within each surface. If there are multiple times, contours will be sorted first by time, then by surface and Z value within each time. Note that this operation cannot be undone.
• Contour -->
  • New: Create a new contour. [n]
  • Delete: Delete current contour or all selected contours. [D]
  • Move...: Move current contour to a new object #.
  • Copy...: Copy contours to new object or new Z level.
  • Sort: Sort all contours in an open or closed contour object by their Z values. If there are multiple times, contours will be sorted first by time, then by Z value within each time. Note that this operation cannot be undone.
    –––––––
  • Break...: Break a contour into two contours.
  • Join...: Join two contours together.
  • Break by Z: Break a closed contour into separate ones by Z.
  • Fill in Z: If current contour is in an open object, add point at each Z level skipped by existing points.
  • Loopback: Add duplicate points in reverse to make a complex cap.
  • Invert: Invert the order of points in the current contour.
    –––––––
  • Info: Print area and length of current contour.
  • Auto...: Open window for making new contours using threshold.
  • Type...: Select a surface, time index or label for a contour.
• Point -->
  • Delete: Delete Current point. [Delete]
  • Size...: Set size of individual points.
  • Distance: Show distance between model points.
  • Value: Show current voxel value.
  • Sort by Z: Sort points in contour by their Z values.
  • Sort by dist: Sort points in contour by interpoint distance so that sucessive points are as near to each other as possible.
• Image -->
  • Flip/Rotate: Exchange Y and Z dimensions of the image data by rotating around X
  • Process...: Process images by filtering.
  • Reload...: Reload image data with current contrast.
  • Fill Cache: Fill the image cache if there is one.
  • Cache Filler...: Open window to control cache filling.
• Fine grain...: Open window to set fine grained display properties.
• Angles...: Open window to save and restore slicer angles.
• Scale bar...: Open window to draw scale bars in windows.
• Save Dock: Save the current list of dialogs docked to the Information Window and their open/closed state in settings.
• Reopen Dock: Reopen and restack dialogs to recreate the previously saved state. Ones that were already open will be inserted at the saved position in the stack; open dialogs that were not in the saved list will go to the end of the stack.
• Options...: Open window to set program preferences.

• ZaP: Open a Zoom and Pan modeling window. [z]
• Multi-Z: Open a Multi-Z window for displaying successive slices in an array of small panels.
• XYZ: Open an XYZ slice viewing window.
• Slicer: Open window showing a sliced view of the image data. [\]
• Linked Slicers: Open one slicer per image file, each locked to one file, with a single slice control toolbar to control them all.
• Model View: Open a 3dmod model view (3dmodv) window. [v]
• Pixel View: View pixel values in a grid.
• Graph: Open the Image Graph window. [G]
• Locator: Open window showing subarea of active zap window.
• Isosurface: Open model view window with isosurface display of image data. [U]
• Tumbler: Open 3-D projection window.

• Bead Fixer: Open a window for doing basic operations on a fiducial model.
• Line Track: Open window to allow automated tracking along a line (e.g., membrane) between marked points, and from one slice to the next.
• Bead Helper: Open Andrew Noske's plugin with tools to help fix large fiducial models.
• Drawing Tools: Open Andrew Noske's plugin with some modeling tools, including a tool to draw or modify a contour with a circular cursor.

Help Index