JWeb

Contents

1. INTRODUCTION
2. OVERVIEW
3. OPERATIONS
4. WHATS NEW
5. INSTALLATION ON LINUX
6. FAQ for SPIDER and Web

INTRODUCTION

OVERVIEW

1) operations permitted on a single image
2) operations permitted on a set of images
3) operations permitted on a volume

In most cases, in a JWeb GUI, when a desired option is selected by clicking on a check box or clicking on a radio button, the relevant sub-options are enabled and the rest are disabled.

OPERATIONS

• Image Operations

  • File

    Saves file in the following formats (Saves the gray scale value) :

    • SPIDER
    • RAW
    • BMP
    • JPEG
    • PNG
    • PNM
    • TIFF

  • EDIT

    Manipulates the image using following sub-menus:

    • TRANSLATE : moves the image in X and Y direction
    • RESIZE : changes the display size of the image
    • CONTRAST : changes the contrast of the image
    • WINDOW : can window an image using options, (1) Interactive, (2) Fixed Size, and (3) Specified Co-ordinate

  • ANALYSIS

    Analyses and manipulates the image using following sub-menus:

    • PIXEL : outputs (1) Screen Value, (2) File Value. Can draw markers. Information about the pixel value and X,Y position of the marker can be written to a SPIDER document file.
    • ANNOTATE : Reads a SPIDER document file and draws markers at the positions read from the document file.
    • MARKER : Draws markers on an image and writes the positional infomation on to a SPIDER document file. Used for marker picking for Tomography purposes.
    • HISTOGRAM : Displays histogram of the image.
    • DISTANCE : Sets of distances from connecting points OR sets of distances from a single point on the image can be measured. Relevant information can be saved onto a document file.
    • MASK : A mask can be created interactively by using this menu.

• Image Series Operations
  • MONTAGE

    Displays a series of image as montage. The image series can be treated as a volume by clicking on the "Treat as Volume" check box (The images are treated as Z-slices of the volume).

  • SLIDE

    Shows individual images in a single image window. Images are updated by moving a slider in the GUI. The image series can be treated as a volume by clicking on the "Treat as Volume" check box (The images are treated as Z-slices of the volume).

  • MOVIE

    Shows a movie of the images in "one-way" or "two-way" mode. Delay time can be set using a slider. The image series can be treated as a volume by clicking on the "Treat as Volume" check box (The images are treated as Z-slices of the volume).

  • CATEGORIZE

    Mostly used to pick particles for single particle reconstruction work. There are two ways one can pick particles. 1) Pick Individual Particles - By clicking on individual images to select particles, 2) Pick A Set of Particles - By clicking on the first and last image of a stretch of good particles. .

  • MARKERS

    Mostly used to pick markers for tomographic reconstruction work. Markers on a series of images are picked and the co-ordinates are saved onto a SPIDER document file. Deleting, moving and renumbering of markers can be easily accomplished.

• Volume Operations
  • MONTAGE

    Displays slices of the volume as montage.

  • SLICER

    Displays individual slices on a single image window. Slices are updated by moving a slider in the GUI.

  • MOVIE

    Shows movie of the slices in "one-way" or "two-way" mode. Delay time can be set using a slider.

  • SURFACE

    Constructs and displays surface of a volume. Threshold, contribution from depth versus surface reflectivity and Eulerian rotation angles can be set in the GUI. Euler angle convention used are same as used in SPIDER. A movie option can be selected to display and save a sequence of frames at different thresholds or at different rotation angles.

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  Source: jweb.html     Last update: 01/25/17     Bimal Rath