NewCASE Manual.

Contents.

• 1. Introduction
• 2. Project Structure
• 3. Project Window
  • 2.1 Project menu
  • 2.2 Left side pannel
  • 2.3 Middle pannel
  • 2.4 Right side pannel
  • 2.5 Directory tabs
  • 2.6 Other windows related to project
• 4. Micrograph Window
  • 3.1 File selection
  • 3.2 Ethan parameters
  • 3.3 Zoom and Pan controls
  • 3.4 Micrograph Toolbox
• 5. Mosaic Window
  • 4.1 File selection
  • 4.2 Maps and Delete boxes
  • 4.3 Particle Control buttons
  • 4.4 Delete button

  1. Introduction

  NewCASE is a frontend for ethan. Ethan is a program that identifies circular particles of certain size in a micrograph and extracts into separate files of given size. All ethan parameters are given at command like. To facilitate the use of ethan we have created NewCASE, a graphical user interface. NewCASE augments ethan with few other functions, like projects, that allows work to be stopped, saved and continued later. Ethan and NewCASE accept MRC and PGM file formats as input. Output is written in MRC format.

  Quick reference cards [1| 2| 3]

  2. Project structure.

  Project consists of groups. Groups contain micrographs with similar parameters, approximate virus size, and cutout box. A group can have zero or more micrograph files. A project can have several groups, each of which should have their own parameters. Once a group is created and all member micrographs are added, parameters for this group are set. This can be done either by visualizing the micrograph or from previous knowledge. Then a group is processed, during the processing individual virus files are extracted from the micrographs. Individual virus files can be examined and deleted if judged not fit. It is helpful to think of a project as of a tree, where groups are branches of project, micrographs are branches of groups and finally individual virus files are branches of micrographs.

  3. Project Window.

  Project menu.

  New Clears all fields and variables of the project, it is used before starting a project from scratch. Open... Open menu item opens a file chooser, where a previously saved NewCASE project file should be selected. Once this is done a project tree is loaded from project file. (.cse) Save Saves the project to file. Use this when a project already has a name. Save as ... First prompts for a name and path for the project file then writes it. Use this function when saving a project for the first time, or when a copy of a project with a different name is desired. Configure ethan Brings up ethan configuration window. Autosave Checkbox. If this function is turned on (checkbox it ticked) NewCASE will save the project automatically at certain critical points. If this function is not turned on, user should decide when exactly does he want to save the project, usually, NewCASE will ask before exiting whether to save the project. Exit Exits the program. If Autosave function is off, user is prompted to save the project.

  Left side panel. (Functions related to unprocessed groups only.)

  Middle panel. (Functions related to both processed and unprocessed groups.)

  Large '+' button Prompts user for Group name then adds group to to the project. This button is alway active. Small '+' button Adds a micrograph file to selected group. This button is only active when a group is selected. This button will open window with a list of data (.mrc .pgm) files that are located in current data directory. Small '-' button This button removes a single selected micrograph file. It is only active when a such file is selected.

  Process '->' button Processes a selected unprocessed group and moves it from unprocessed tree to processed. This function can only be used when an unprocessed group is selected ethan parameters (particle radius and box size) for this group are set the group contains at least 1 micrograph Visualize 'eye' button Opens up a micrograph window to visualize a micrograph. This function can only be used when a micrograph file is selected in either processed or unprocessed tree. Large '-' button Removes a group, from either of two trees, when removing a processed group, all output files are deleted. This function can only be used when a group is selected.

  Right side panel.

  Mosaic view button opens up a mosaic window with all output virus files created by ethan from selected input file. This function can only be used when a micrograph file from a processed group is selected.

  Directory tabs.

  
  • Project directory is the directory where project file is saved. It is also the root of whole directory structure created by NewCASE for a project. It is advised that each project is placed in a separate directory. Project directory can only be changed before the project is saved for the very first time. It is changed by clicking on "browse" button on the right of project tab.
  • Data directory is a directory from which input micrograph data files are read. This directory can be located anywhere in the file system and needs only to be open for reading. This however does not restrict the project to one data directory, this setting can be changed at any time during the project life cycle.

    Other windows related to project

    New Group window

    When large '+' button is pressed it opens up this window, where a name for a new group can be put in. There is only one basic restriction to this operation, it is not allowed to have two groups with same name. Ant printable characters can be used, including spaces in the name of a group.
    

    Select data files window

    When small '+' button is pressed it opens up this window. It lists all data (.mrc and .pgm) files that are located in current data directory. One or more (with shift key) files can be selected, when 'OK' is hit selected files enter a group which was previously selected in unprocessed tree box. 'Select All' button will select all listed files. Same file should not be included in a group more then once.
    

    4. Micrograph window

    When a micrograph is selected and visualize button is clicked micrograph window opens. Initially this window shows the whole micrograph, scaled to fit. This window can be used to explore the micrograph, select ethan settings and test run ethan.

    File selection

    This tab is designed to show clearly which part of the project a user is working with. Group output shows the name of current group and it cannot be changed in this window. In order to change the group, close micrograph window, select a file form desired group and click visualize button.
    File chooser shows which micrograph is currently on display. It can be used to select a different file from the same group. For example user might set ethan parameters with one micrograph, and test run ethan on a different file with these same parameters.

    Ethan parameters

    Two ethan parameters, radius and box size are shown here. They are set using the toolbox. Once radius has been set ethan can be test ran by clicking the button in this tab. When this button is clicked for the first time for a given micrograph, ethan is ran. It finds the particles in the micrograph, and shows them on as red circles. It is possible to see how well ethan works with different radius parameter. Test run is a toggle button, to remove red circles that show found particles click the button up. When user clicks this button down again, ethan is not run, results of previous run are used to draw particles.

    Zoom and Pan controls

    Often micrographs are fairly large in size, so in order to see the whole micrograph in a window it has to be scaled down to fit the size of the window. In this view it might be difficult to set particle radius precisely because particles appear much smaller because of down-scaling. In order to examine micrograph closely and set radius more precisely it is possible to zoom in to a desired area. Two buttons in this tab, set zoom value. 1:1 button sets screen resolution to that of the image, so each one pixel on the screen actually corresponds to exactly one pixel in the micrograph. Fit to screen is the other button and it is used to shrink the image to fit the window. When only a part of the image is displayed, user may want to see what the micrograph looks like in the regions neighbouring to the one being displayed. The for arrow buttons are used to scroll micrographs.

    Micrograph Toolbox

    The toolbox buttons don't do anything by themselves, they just set mouse mode. With mode set, clicks on the image will perform different functions.
    Looking glass '+' mode button sets custom zoom mode. Once this button is down, select upper left corner (by pressing and holding left mouse button) of the area of the micrograph that you want to see closer, then drag the mouse (with left button down) and and release the mouse button to set the bottom right corner of the area. After that the area is enlarged to fit current display. It may happen that the resolution of the enlarged image is greater that that of the micrograph, in this case only upper left corner is used, and current display is filled with image at resolution of the micrograph. The screen resolution can never be higher then micrograph resolution.
    Diameter select mode button is used to set ethan parameter. When in diameter select mode first click (and hold) on the particle boundary, then as mouse is dragged a circle will appear, move the mouse so that this circle covers the particle completely then release the mouse button. As radius of this circle changes it will be shown in ethan parameter tab.
    Cutout box select mode is used to determine the size of the final particle files that ethan has to extract from micrograph. It is advisable that box size is at least twice the radius. The box size is identified by clicking and dragging mouse across one particle so as to ensure that box covers the whole particle . Notice that this box is always a square, so the right bottom corner will not always be under mouse pointer, the size of the square is limited the smallest difference (x or y) between a point where left mouse button was pressed and current location of mouse pointer. To finalize the box mouse button is released.
    

    Close button closes micrograph window and passes particle radius and cutout box size (if they were set) to the group.

    5. Mosaic window

    Mosaic window displays results of running ethan, that is individual particles extracted from micrographs from one group. Sometimes ethan will pick a broken particle, or an object with similar size and shape that is not a particle. To catch these false positives user must examine every particle, the program lets user delete such files.

    File selection

    This tab has very similar in functionality to file selection tab in micrograph window. Group text output shows name of the current group, and the file chooser changes the source micrograph.
    

    Maps and delete boxes

    All found particles are shown as buttons in the Map box. Particles scheduled for deletion are moved to delete box, this is done to make sure that none of the good files are deleted. It gives user a chance to look over all particles that will be deleted.
    

    Particle control buttons

    Using these two buttons particle files can be moved between maps and delete boxes. First user has to select the particles that need to be moved, this is done by clicking on each them. After that the selected particles can be moved by pressing one of the arrow buttons. If particles are moved from map to delete box then right '->' arrow should be pressed. If particles are returned from delete box to maps box then left '<-' arrow buttonī should be pressed.
    

    Delete button

    Delete button removes all particles currently in the delete box and also all files they represent. Since a name of the file consists of its serial number, certain filename manipulation are done to keep the list continuous.