GC Image (LCxLC Edition) Users' Guide

Image Viewer

LC Image allows users to visualize, process, analyze, and report on LCxLC images with the ultimate goal of identifying and quantifying chemicals in sample solutions. This chapter provides an overview of the LC Image main interface. Subsequent chapters describe specific operations in more detail.

The main interface of LC Image is the Image Viewer, pictured in Figure 1. The Image Viewer has (from top to bottom):

• the title bar, which displays the name of the image;
• the menu bar, which provides menu access to operations, tools, settings, and help resources;
• tool bars, with buttons for commonly used operations, tools, and cursor modes;
• the Viewport, which displays the region-of-interest of the image with axes; and
• the status bar, which displays the position of the cursor and the value of the pixel at the cursor location.

Figure 1: The Image Viewer has a title bar, menu bar, tool bars, image display with axes, and status bar.

Menu Structure

The Image Viewer has seven top-level menus.

• File - Operations on files.
  • Open Image - Open an image file in LC Image format.
  • Save Image - Save the image to its file in LC Image format.
  • Save As - Save the image to a specified file in LC Image format.
  • Close Image - Close the image.
  • Recent Images - Open an image from a list of recently used files.
  • Import Image - Import an image from a file in a format other than LC Image format.
  • Export Image - Export an image to a file in a format other than LC Image format.
    • Export Image as Picture - Export an image as a picture format: JPEG, PNG, PNM, TIFF or Bitmap.
    • Export Image as CSV - Export an image data into a (one-dimensional or two-dimensional) CSV (Comma delimited) file.
    • Export Image as Text MS -Export the spectra of all samples or selected blobs in an image into a text file.
    • Export Image as mzXML - Export the spectra of all samples in an image into a mzXML file.
  • Export Method - Export a method folder containing the method files.
  • Import Image Model - Import an image model from a LC Image Model file.
  • Export Image Model - Export an image model to LC Image Model file.
  • Save Blob Table - Save the table of blob peaks.
  • Save Blob Set Table - Save the table of blob sets.
  • Save Summary Report - Save Summary Report.
  • Save Filter Report - Save Filter Report
  • Save Template - Save the template in the open image.
  • Save Journal - Save viewable journal of actions.
  • Save Script - Save runnable script of actions.
  • Import Graphics - Import graphics from a file.
  • Export Graphics - Export graphics to a file.
  • Print Image - Print the image.
  • Exit - Exit the program.
• Edit - Edit operations on the image and blob table.
  • Undo - Undo the previous operation.
  • List Operations - Display operations list.
  • Undo All - Undo all previous operations.
  • Run Script - Execute operations from a script file.
  • Copy Viewport - Copy the current viewport image to the clipboard.
  • Edit Blobs - Edit selected blob(s).
  • Cut Metadata - Cut metadata from the selected blob.
  • Copy Metadata - Copy metadata from the selected blob.
  • Paste Metadata - Paste metadata to the selected blob.
  • Cluster Blobs - Partition selected blob(s) into clusters.
  • Exclude Blobs in Shape - Exclude blob(s) in selected graphic Shape.
  • Local Blob Detection - Perform local blob detection on selected graphic Shape or selected blob.
  • Deconvolve/Unmix - Deconvolve/unmix the selected blob(s).
  • Cycle Internal Standard - Cycle the internal standard of the selected blob.
  • Find Blobs - Find and select blob(s).
  • CLIC Expression - Build CLIC expression.
  • Auto Text - Create a text object from image attributes automatically.
  • Auto Mesh - Create a mesh for the entire image automatically.
  • Select All - Select all objects based on the current palette mode.
• View - Tools for image and data visualization.
  • Image Attributes - View information about the image file.
  • Colorize - Control colorization of the image.
  • Set Viewport - Resize or reposition the viewport on the image.
  • Navigator - Control the region-of-interest (ROI) in the Viewport.
  • 1D View - Show a one-dimensional view with slices of the image.
  • Text View - Show a text view of data values.
  • 3D View - Show a projected three-dimensional intensity-surface view.
  • MS Cube - Show LCxLC-MS data in a 3D space.
  • Multi-Projections - Show one-dimensional slices and projections.
  • Visualize Data - Visualize attributes of the image data.
  • Analyze Blobs - Visualize and analyze attributes of the blobs.
  • Compare Images - Compare differences between two images
  • Blob Table - View the table of blob peaks.
  • Blob Set Table - View the table of blob peak sets.
  • Template Table - View the table of template objects.
  • Template Match Results - View the recently applied template match results.
• Filter - Operations and filters on the image and blob table.
  • Shift Phase - Shift the second-column phase of the image.
  • Correct Baseline - Remove the baseline offset from the image.
  • Skip Correct Baseline - Process image without removing the baseline offset from the image.
  • Arithmetic Operations - Perform arithmetic operations on pixels.
  • Detect Blobs - Detect blob peaks in the image.
  • Load Template - Load a template to the image.
  • Match Template - Match a template to the image.
  • Apply Template - Apply a template to the image.
  • Clear Template Match - Clear all template matches from the image.
  • Update Template - Update template according to template matching result.
  • Transform Template - Alter the current template.
  • Search Library - Search library to identify blobs
• Configure - Customize settings.
  • Configure Settings - Specify the settings for various operations, including:
    • System - Configure themes and memory usage.
    • Axes - Configure the axes units, axes labels, and Import Image settings.
    • Legend - Configure the legends to be displayed on the image.
    • Multi-Channel - Configure the multi-channel image display settings.
    • Search Library - Configure the library lookup settings.
    • Baseline Correction - Configure the baseline correction algorithm.
    • Blob Detection - Configure the blob detection algorithm.
    • Blob Statistics - Configure the blob statistics parameters.
    • Blob Mouse-Overs - Configure data shown on mouse-over.
    • Blob Display - Configure the blob display settings.
    • Graphics Display - Configure the graphics display settings.
    • Structure Display - Configure chemical structure display settings.
    • Text Display - Configure text object display settings
    • 3D View - Configure the three-dimensional view settings.
    • Template - Configure the template display and automated features.
    • Template Matching - Configure the template matching algorithm.
  • Configure Blob Table - Specify the blob features in the blob table. For a list of the blob features, see the white paper: Blob Metadata and Statistics in LC Image.
  • Configure Blob Set Table - Specify the blob set features in the blob set table.
  • Configure Amount Table - Specify the reference for the Composition/Amount table.
  • Configure Calibration Table - Specify the reference for the Calibration Table and the calibration function parameters.
  • Configure LRI Table - Create or edit calibration tables for calculating Linear Retention Time Indices.
  • Configure Mass Calibration - Configure the settings and model for ToF-to-Mass calibration.
  • Compound Library - View or edit the Compound Library.
• Windows - Window arrangements
  • Cascade - Cascade current window(s).
  • Tile Horizontal - Tile the window(s) horizontally.
  • Tile Vertical - Tile the window(s) vertically.
  • Reset TIC Window - Dock the TIC window in its default position.
  • Set the current window from a list of available windows.
• Help - Help utilities.
  • Users' Guide - Display the GC Image (LCxLC Edition) Users' Guide.
  • Incident Report - Submit an incident report to GC Image, LLC.
  • Memory Monitor - Monitor the system memory.
  • About LC Image - Display version and license information.

Menu Tool Bar

The Image Viewer toolbar has buttons for some commonly used operations, tools, and cursor modes. Each tool bar button has an identifying icon and a tool tip describing the action is displayed when the cursor lingers over a button. The top menu is configured as follows.

File actions
Button	Action
	Import an image.
	Open an image.
	Close the image.
	Save the image.
	Print the image.
Edit actions
Button	Action
	Undo previous operation.
	Find blobs.
	Build CLIC expression.
	Edit blobs.
View actions
Button	Action
	Colorize.
	Scale Viewport.
	Reset Display.
	Switch to Previous Display Configuration
	Switch to Next Display Configuration
	Show Navigator.
	Show 1D view.
	Show text view.
	Show 3D perspective.
	Show blob table.
	Show blob set table.
	Show template table.
	Compare images
Filter actions
Button	Action
	Shift phase.
	Correct baseline.
	Perform arithmetic operations.
	Detect blobs.
	Search library.

The bottom toolbar of the Image Viewer has a palette with buttons that control the cursor mode for the Viewport. Like the other toolbar buttons, the palette buttons have identifying icons and informative tool-tips. The bottom toolbar also has several action buttons.

Palette
Button	Cursor Mode
	View.
	Enable text mode.
	Enable chemical structure mode.
	Select graphic.
	Edit graphic vertices.
	Delineate selected graphics with polyline.
	Remove shared edge of mesh to merge panels.
	Draw point.
	Draw polyline.
	Draw rectangle.
	Draw polygon.
	Select blob(s) by point.
	Select blob(s) by polyline.
	Select blob(s) by rectangle.
	Select blob(s) by polygon.
	Draw blob free hand.
	Draw blob with oval tool.
	Draw blob with rectangle tool.
	Show point multi-spectrum.
	Show peak multi-spectrum.
	Show blob multi-spectrum.
	Select template object.
	Edit template graphic vertices.
	Delineate selected template graphics with polyline.
	Remove shared edge of template mesh to merge panels.
	Draw template point.
	Draw template polyline.
	Draw template rectangle.
	Draw template polygon.
	Draw template peak.
	Draw template text.
	Draw template chemical structure.
Template Actions
Button	Action
	Add to template.
	Load template.
	Match template.
	Apply template.
Object Actions
Button	Action
	Cut blob metadata.
	Copy blob metadata.
	Paste blob metadata.
	Cycle internal standard.
	Delete object(s).
	Clear Metadata

Note: The following cursor mode sets are each selectable within a single button via pull-down menus.

• Graphic modes: select graphic, split graphics, merge mesh panels, edit graphic vertices, draw point, draw polyline, draw rectangle, draw polygon.
• Blob modes: select by point, select by polyline, select by rectangle, select by polygon, draw blob by hand, draw blob with oval tool, draw blob with rectangle tool.
• Multi-spectrum modes: point ms, peak ms, blob ms.
• Template modes: select template object, split template graphics, merge template mesh panels, edit template graphic vertices, draw template point, draw template polyline, draw template rectangle, draw template polygon, draw template text, draw template chemical structure.

Keyboard Short-Cuts and Hot-Keys

• Menu short-cuts use the <Alt>-key plus another character to quickly select menu choices. For example, <Alt>-key plus F O selects "File->Open Image". The menu shortcuts are noted with underlines in the menu choices.
• Action and palette hot-keys use the <Ctl>-key plus another character to quickly invoke operations or change the palette mode. These hot-keys only work while Image Viewer is focused (an image is selected).

  Keystroke(s)	Action
  <Ctl>+O	Open image
  <Ctl>+S	Save image
  <Ctl>+I	Import image
  <Ctl>+Z	Undo previous operation
  <Ctl>+A	Select All (depending on palette mode)
  <Ctl>+X	Cut blob metadata
  <Ctl>+C	Copy blob metadata
  <Ctl>+P	Paste blob metadata
  <Ctl>+1	View palette mode
  <Ctl>+2	Text palette mode
  <Ctl>+3	Chemical structure palette mode
  <Ctl>+4	Graphics palette mode
  <Ctl>+5	Blob palette mode
  <Ctl>+6	Multi-channel palette mode
  <Ctl>+7	Template palette mode

• Several other keystrokes have special functions.

  Keystroke(s)	Action
  <F2>	Copy image view or 3D view (view must be previously selected by mouse click in view pane).
  <F3>	Find blobs (in blob palette mode).
  <Del>	Delete or exclude selected object(s) (depending on palette mode).
  t or T	Toggle blob display configuration.
  c or C	Toggle selected images color maps.
  <Arrows>	Pan or scroll the image.
  <PgUp> and <PgDn>	Scroll the image with large steps.
  <Tab>	Select next overlapping peak (in blob palette mode).
  m or M	Toggle template display to show matched template view and normal template view or both.

Contents Previous: Installation and Start-Up Next: File Input and Output

GC Image (LCxLC Edition)™ Users' Guide © 2001–2011 by GC Image, LLC, and the University of Nebraska.