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&0Thesholding an Image è ’ Title Color ˇ ˇˇ ˇ ˇˇˇ ˇˇ f Tool Palette ì ‘\Transformation Table Editor é ¿flTranslate Image Ü Óö&Two Dimensional Fast Fourier Transform Ç K≤ Undo Command ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ˇ ë î– Watershed ˇˇ €zZZZZZZZZ Ç UëZoom In Command ˇ Ç VüZoom Out Command $128,0
Apple Menu
Choose About Imagine to display the version number of your copy.
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New Image Command
The New command creates a new image for you. The default is a copy of the front image, but you may also create a blank image (all zeros) or generate one of the many test patterns. By clicking on the Test Patterns button, you open a second dialog box which presents the types of patterns as icons on the left. Choose the type of pattern, two dimensional sinusoid, square wave, triangle, or ramp, and fill in the parameters in the dialog box. The periods of the pattern correspond to the width of the pattern in the horizontal and vertical directions and the phases translate the pattern by the given number of pixels to the right and down. You may also create a noise image by choosing one of the noise icons, uniform or Gaussian. With uniform noise selected, the amplitude specifies the maximum - minimum range and the offset specifies the mean value. For Gaussian, the amplitude corresponds to the standard deviation. Both routines use a high quality random noise routine rather than the Apple supplied algorithm.
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Open Image Command
Imagine opens image files in its native format as well as TIFF and PICT formats. For quantitative work, use the native format since it saves all 16 bits of the image with all the relevant scale factors and Regions Of Interest (ROIs.) To transfer images to other programs, the TIFF format, usually preferable to the PICT format, preserves some quantitative information (though not the scale factors) for further processing. Three and four dimensional images must be in Imagine's native format.
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Close Image Command
When closing an image, Imagine will ask you if you would like to save any changes: including changes to the image itself or other items such as scale factors or Regions Of Interest (ROIs.) Imagine writes the image in the original format (TIFF, PICT, native format) of the image. To write an image in another format, use the Save Copy As command.
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Save Image Command
If you would like to save any changes, including changes to the image itself or other items such as scale factors or Regions Of Interest (ROIs) before closing the image, choose Save. Imagine writes the image in the original format (TIFF, PICT, native format) of the image. To write an image in another format, use the Save Copy As command. SAVE YOUR IMAGES OFTEN!
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Save Image As Command
The Save As command allows you to save any changes, including changes to the image itself or other items such as scale factors or Regions Of Interest (ROIs) to another image file. Imagine writes the image in the original format (TIFF, PICT, native format) of the image and, if the original was a three or four dimensional image, copies the entire volume to the new file. After saving the image, the image on the screen refers to the new image file, not the previous image file, and the image title changes to reflect the change. To write an image in another format, use the Save Copy As command. SAVE YOUR IMAGES OFTEN!
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Save Copy of Image As Command
The Save Copy As command behaves much like the Save As command except you may save the image in a format other than the original format (TIFF, PICT, native format) of the image. The save dialog box will show the available image formats as icons which you may choose. After saving the image, the image on the screen does not refer to the new image file, as with Save As, but to the original image file.
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Revert Image Command
Revert restores the image to the last version saved to disk. You may preserve changes you made to the Regions Of Interest (ROIs) by answering No to the Erase All ROIs alert, otherwise Imagine will revert the ROIs also.
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Image Information Command
The Info command displays almost all the information Imagine has about your image. The scale factors determine how Imagine converts from the integer world of pixels to the real world of measurements and values. You may change the scale factors at will and give units (up to 8 characters) for each quantity. Several routines in Imagine assume you have square pixels, so it is best to use the same dimensions for the pixel height and width. You may also change the position of the slice within a volume or time series. In a volume, each slice represents the image at a different position in the volume. For a time series, each slice represents a position in time. You may choose different slice positions and points in time by changing the slice or frame number in the Info dialog. Two radio buttons in the lower left refer to the default order of the slices, by position or by time. When you change slices by clicking on the small up or down arrows in the lower left of an image window, Imagine reads the next image slice by either time or position. For example, for a X-Ray CT scan of the head you would order the slices by position, while for a movie loop, the slices should be ordered by time.
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Help Command
After selecting the Help command, the cursor shape changes to a question mark indicating you have entered the help system. Simply click on any object (image, tool, etc...) or choose an item from the menus to see the help information associated with that particular object. To leave the help system, exit the help dialog box, if present, by clicking on the Done button and striking any key. The cursor will change back to the pointer shape.
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Import Command
Imagine has the ability to import a wide variety of image formats with the Import command. In the file open dialog, you may specify the image type (8 bit, 16 bit, etc...), the dimensions of the image, and an offset to the start of image data. Once opened, the image may be saved under Imagine's format or as PICT or TIFF. To read PICT or TIFF files use the Open command.
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Export Command
The Export command allows you to write images to files in a variety of formats. Choose the image type (8 bit, 16 bit, etc...) and an offset to begin writing image data from the save file dialog. The Ascii (spread sheet) format creates a spreadsheet compatible (tab delimited) image file which may be read and plotted in 3D by a program such as Wingz from Informix. To skip rows and columns to reduce the size of the file, choose the skip factors in the dialog.
If the Message window is in front, the Export command writes all of the data in the message window into a two column spreadsheet compatible file. The first column describes the measurement and the second column contains the values, similar to the format of the Message window on the screen.
You may also export graphs (histograms, cross sections, etc...) as spreadsheet compatible files by using the Export command when the graph window is in front and activated. This is particularly useful for preparing presentation quality graphs from image data.
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Page Setup Command
If an image window is active, Imagine adds several items to the normal Page Setup dialog to optimize the print quality of the image. You should experiment with the settings to produce the best quality images for your printer. In general, turn off options like Graphics Smoothing and Fast Bitmap Printing and use the margin and enlargement factors in the bottom section of the dialog box to ensure high quality printing. A special item for the HP PaintJet matches the colors on the screen to those on the HP PaintJet as close as possible (be sure to check the Color item.) The white and black dots which form a dithered image are not the same size, especially on laser printers. To compensate for this effect, choose the Dot Compensation option .
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Print Command
The print dialog box is the familiar Macintosh box. Simply choose the number of copies and click OK. As soon as the printer is located, a message appears regarding the number of bands sent to the printer and the total number of bands to print. You may abort the printing process at any time by holding down the Command key and typing a period '.'.
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Quit Command
When you quit, Imagine will ask if you would like to save any changes. You may answer Yes to save the image, No to discard any changes, or Cancel to abort the quit command.
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Undo Command
The Undo command reverses the last change to a Region Of Interest (ROI), Line Of Interest (LOI), or image. Before beginning an image processing task, Imagine saves a copy of the image to disk in the event that you would like to undo the modifications made to the image. To save time, you may suspend the image undo mechanism by disabling the Enable Image Undos item under the Options menu. In this suspended state, you may only undo changes to ROIs and LOIs.
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Cut Command
The Cut command does a Copy command followed by a Clear command. See the help text on Copy and Clear.
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Copy Command
Selecting a Region Of Interest (ROI) or Line Of Interest (LOI), by clicking on the ROI outline or LOI using the Arrow tool or with the Lasso tools, enables the Copy ROI or Copy Line command in the edit menu. Choosing these commands copies the object into a buffer. The copy may then be pasted into another image using the paste command. Each image has four ROIs, so you could also copy one ROI of an image to another ROI of the same image by copying the current ROI as above, changing the current ROI by clicking on the ROI indicator (a square colored box with the ROI number in the lower left corner of the image window), and pasting the copied ROI to the new current ROI.
Without any active ROI or LOI selections, or when a graph is the foremost window, the Copy command copy the front graph or image to the clipboard for pasting into other applications. In the case of graphs, both the graph data (in spreadsheet format) and the graph itself are copied to the clipboard.
If the Message window is active, the Copy command copies the entire (or a selected portion) of the Message window data to the Clipboard. You may then switch to another application, such as a spreadsheet, and paste the Message window data into a document.
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Paste Command
After copying a Region Of Interest (ROI) or Line Of Interest (LOI) using the Copy command, the Paste command inserts the copy into the active image. If the copy is a ROI, the copied ROI is combined with the current ROI.
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Clear Command
The Clear command clears any selected Region Of Interest (ROI) or Line Of Interest (LOI) (you select a ROI or LOI using the Point or Lasso tools) from the image. The delete key on the keyboard performs the same function.
If the Message window is active and you have selected one or more entries, the Clear command removes the entries from the Message window. This operation cannot be undone.
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Zoom In Command
To magnify the image by a factor of 2, choose Zoom In. If the entire window will not fit on the screen, the window will be resized with scroll bars. The Zoom Out command reduces the image by a factor of 2, but not less than the original size.
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Zoom Out Command
To magnify the image by a factor of 2, choose Zoom In. If the entire window will not fit on the screen, the window will be resized with scroll bars. The Zoom Out command reduces the image by a factor of 2, but not less than the original size.
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Fill Inside ROI Command
The Fill Inside ROI command fills the region of the image which lies inside the current Region Of Interest (ROI) with a constant value. To set up for the fill command, make sure the image is on the top of the Imagine Stack. (If you do not know about the Imagine Stack, click on Done and click on the four lines in the bottom of the Imagine tool palette at the left of the screen.) If it is not, make sure the image is the front window and choose Push Image from the Push sub-menu of the Edit menu, or clicking on the title bar of the image. Next you must push the value to fill the image by choosing Push Number from the Push sub-menu of the Edit menu or simply begin to type a number: Imagine will pop up a dialog box for you to type in your number. Click OK and Imagine will put the number on the top of the Imagine stack. Now you are ready to choose the Fill Inside ROI command. The stack type calculations may seem awkward at first, but they are very fast and efficient. The stack is modeled after the Reverse Polish Notation (RPN) calculators popularized by Hewlett-Packard. If you are used to such a calculator, you will find Imagine intuitive and efficient.
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Fill Outside ROI Command
The Fill Outside ROI command fills the region of the image which lies outside the current Region Of Interest (ROI) with a constant value. To set up for the fill command, make sure the image is on the top of the Imagine Stack. (If you do not know about the Imagine Stack, click on Done and click on the four lines in the bottom of the Imagine tool palette at the left of the screen.) If it is not, make sure the image is the front window and choose Push Image from the Push sub-menu of the Edit menu, or clicking on the title bar of the image. Next you must push the value to fill the image by choosing Push Number from the Push sub-menu of the Edit menu or simply begin to type a number: Imagine will pop up a dialog box for you to type in your number. Click OK and Imagine will put the number on the top of the Imagine stack. Now you are ready to choose the Fill Outside ROI command. The stack type calculations may seem awkward at first, but they are fast and efficient. The stack is modeled after the Reverse Polish Notation (RPN) calculators popularized by Hewlett-Packard. If you are used to such a calculator, you will find Imagine intuitive and efficient.
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Flip ROI Command
The Flip ROI command flips the ROI around the center image column. If you would like to draw just half of a symmetric ROI,
1) Draw one half of the ROI
2) Copy the ROI using the Copy command
3) Flip the ROI with the Reflect ROI command
4) Adjust the position of the ROI, if necessary
5) Paste the copied ROI
You would then have a ROI composed of both the original and reflected versions. You may also flip only a portion of a ROI by selecting only the sub-region with one of the Lasso tools and choosing the Flip ROI command.
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Inlay Calibration Stripe
Adding a known calibration stripe to an image helps maintain the quantitative quality of an image despite distortions such as filming and non-quantitative file formats. Before adding the stripe, draw a ROI (using the rectangle tool) where you would like to place the calibration stripe, then choose the Inlay Calibration Stripe command. The dialog allows you to choose the minimum and maximum value of the stripe (the defaults are the minimum and maximum values of the image) and the number of discrete steps (use a large number for a continuous scale.) Choose the orientation and click OK. Note that the stripe becomes an actual part of the image and cannot be removed later.
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Tool Palette
Click on individual objects in the tool palette for a complete description of their functions and uses.
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Point Tool
Use the Point Tool to select, drag, and resize Regions Of Interest (ROIs) and Lines Of Interest (LOIs.) To select a ROI, click on the outline. Imagine responds by drawing a box around the entire ROI. You may then resize the ROI by dragging the handles of the box. If while dragging, you decide that you did not want to change the ROI, drag the mouse outside of the window and the ROI will return to its original form. You could also choose the Undo command to restore the ROI to its original form.
To move a ROI, click on the outline of the ROI and drag it to its new location. As with resizing, if you drag outside of the window, the ROI returns to its original location.
To reorient a LOI, click on one of the endpoints and drag it to a new location. If you click near the center of the LOI, the drag moves the entire line without changing the slope.
The ROI Centering option in the Option menu affects the way a ROI or LOI changes when you resize it. With the centering enabled, Imagine resizes the ROI or LOI so that the center remains fixed at its original location.
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Measurement Tool
When you would like to measure the distance between two points in an image, choose the Measurement Tool, and click on the first point. Notice that the measurement windowpane in the lower section of the tool palette changes from x to dx and from y to dy. As you drag the mouse, while holding down the button, the values of dx and dy reflect the distance from the original point.
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Square Lasso Tool
You may wish to process or analyze only a portion of your image. Normally to accomplish this task, you would draw a Region Of Interest (ROI) using the Square, Oval, or Freehand tool to define the region you would like to operate on. Then by holding down the Option key (or by setting the ROI Option Lock option of the Option menu) while choosing the processing task, such as a histogram analysis, tells Imagine to process only the portion of the image within the ROI. If you wish to process only a portion of the ROI, the Square and Free Hand Lasso Tools can be used to select only a sub-region of the ROI. After using one of the Lasso Tools, Imagine indicates the sub-region by a revolving boundary. You may also delete a sub-region from the ROI using the Clear command from the Edit menu, or move only the sub-region to a new location by choosing the Point Tool, clicking on the boundary of the sub-region, and dragging it to a new location.
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Free Hand Lasso Tool
You may wish to process or analyze only a portion of your image. Normally to accomplish this task, you would draw a Region Of Interest (ROI) using the Square, Oval, or Freehand tool to define the region you would like to operate on. Then by holding down the Option key (or by setting the ROI Option Lock option of the Option menu) while choosing the processing task, such as a histogram analysis, tells Imagine to process only the portion of the image within the ROI. If you wish to process only a portion of the ROI, the Square and Free Hand Lasso Tools can be used to select only a sub-region of the ROI. After using one of the Lasso Tools, Imagine indicates the sub-region by a revolving boundary. You may also delete a sub-region from the ROI using the Clear command from the Edit menu, or move only the sub-region to a new location by choosing the Point Tool, clicking on the boundary of the sub-region, and dragging it to a new location.
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Eraser Tool
After drawing a Region Of Interest (ROI), the Eraser Tool helps you to make both major and minor changes to the shape of the ROI. Choose one of the smaller eraser shapes from the Eraser Shapes dialog box of the Option menu to begin with; they are easier to use than the large shapes. Run the Eraser along the boundary of the ROI to see how it nudges the boundary to exclude the eraser. With a little bit of practise, it is easy to make fast subtle refinements to the boundary.
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Loupe Tool
Rather than zooming the entire image, if you would like to see a single small detail choose the Loupe Tool. The cursor will change to the shape of a magnifying glass as you pass it over the image. Press the button and Imagine will zoom a small area of the image for you to help clarify details. You may drag the mouse over the image to quickly examine many small details without zooming the entire image.
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Hand Tool
The Hand Tool works like its equivalent in a paint program. If the image does not fit entirely in the window, the scroll bars appear along the edges of the window. You may use the scroll bars to pan along the image, or choose the Hand Tool and drag the image by clicking anywhere on the image and dragging it to a new location. Though it performs the same function, the Hand Tool may be more intuitive for you than the scroll bars.
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Dropper Tool
The Dropper Tool takes the value of an image at a specific point and places this value on the top of the Imagine stack.
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Square ROI Tool
The three Region Of Interest (ROI) Tools allow you to draw various shapes for composing ROIs. ROIs specify specific regions of the image that you wish to process or analyze separately from the rest of the image. Imagine allows this type of ROI selective processing for almost every operation. The ROI Tools work just like their counterparts in a drawing or painting program. Use them in any combination to create an outline of the ROI. If you are confused as to exactly which area of the image lies within the ROI, turn on the Paint ROIs option in the Option menu. Imagine will paint the region of the image within the ROI.
Each image has four ROIs, only one active at a given time. To change from the current ROI to the next, click on the small colored square at the lower left of the image window, called the ROI indicator. The number changes to the number of the next ROI and the next ROI replaces the previous ROI. You may choose ROI selective processing in one of two ways. Holding down the Option key while choosing a processing task from the menu tells Imagine to process only the area of the image within the current ROI. The ROI Option Lock option of the Option menu enables ROI selective processing without using the Option key.
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Oval ROI Tool
The three Region Of Interest (ROI) Tools allow you to draw various shapes for composing ROIs. ROIs specify specific regions of the image that you wish to process or analyze separately from the rest of the image. Imagine allows this type of ROI selective processing for almost every operation. The ROI Tools work just like their counterparts in a drawing or painting program. Use them in any combination to create an outline of the ROI. If you are confused as to exactly which area of the image lies within the ROI, turn on the Paint ROIs option in the Option menu. Imagine will paint the region of the image within the ROI.
Each image has four ROIs, only one active at a given time. To change from the current ROI to the next, click on the small colored square at the lower left of the image window, called the ROI indicator. The number changes to the number of the next ROI and the next ROI replaces the previous ROI. You may choose ROI selective processing in one of two ways. Holding down the Option key while choosing a processing task from the menu tells Imagine to process only the area of the image within the current ROI. The ROI Option Lock option of the Option menu enables ROI selective processing without using the Option key.
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Free Hand ROI Tool
The three Region Of Interest (ROI) Tools allow you to draw various shapes for composing ROIs. ROIs specify specific regions of the image that you wish to process or analyze separately from the rest of the image. Imagine allows this type of ROI selective processing for almost every operation. The ROI Tools work just like their counterparts in a drawing or painting program. Use them in any combination to create an outline of the ROI. If you are confused as to exactly which area of the image lies within the ROI, turn on the Paint ROIs option in the Option menu. Imagine will paint the region of the image within the ROI.
Each image has four ROIs, only one active at a given time. To change from the current ROI to the next, click on the small colored square at the lower left of the image window, called the ROI indicator. The number changes to the number of the next ROI and the next ROI replaces the previous ROI. You may choose ROI selective processing in one of two ways. Holding down the Option key while choosing a processing task from the menu tells Imagine to process only the area of the image within the current ROI. The ROI Option Lock option of the Option menu enables ROI selective processing without using the Option key.
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Line Tool
Several of the Imagine processing tasks, principally Cross Section from the Analysis menu, require a Line Of Interest (LOI.) To create a LOI, choose the Line Tool, click on a starting point in the image, and drag to the ending point of the line. Release the button and Imagine will draw the LOI. You may reorient a LOI with the Point Tool by clicking on one of the endpoints and dragging it to a new location. If you click near the center of the LOI, the drag moves the entire line without changing the slope.
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Invert Color Scale Button
Inverting the color scale inverts the colors of the image. For a gray scale color scale, the inverted image appears like the negative of the original. The inversion only affects the colors on the screen, not the image itself.
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Default Color Scale Button
Click the Default button sets the brightness and contrast to the default settings determined by Imagine.
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Adjust Color Scale Button
To change the brightness and contrast of the image on the screen, click on the Adjust button and move the mouse. The cursor will disappear. Moving the mouse up and down changes the brightness, while moving to the side changes the contrast. To change only the brightness, hold down the shift key while moving the mouse. After you have finished, click the mouse once more and the cursor will return. The changes in brightness and contrast affect only the colors on the screen, not the image itself.
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Pop Stack Button
The Pop stack button removes the entry from the current top of stack and moves all lower entries up. If the new top of stack is an image, Imagine brings that image window to the front.
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Last X Button
The Last X button works just like Last X on Reverse Polish Notation (RPN) calculators (after which Imagine was modeled.) The last entry popped off the stack, by you or by Imagine, is replaced on the stack. Though not absolutely necessary, the Last X button can help speed up your processing by avoiding reentry of many numbers on the stack.
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Imagine Stack
All of the processing in Imagine revolves around the Imagine stack. To process images and numbers, you first place them on the stack. Imagine works much like the Reverse Polish Notation (RPN) calculators popularized by Hewlett-Packard, so if you understand RPN, you understand the Imagine stack. The stack holds four entries, displayed on four lines at the bottom of the tool palette, which may be either image, number, or empty entries.
Before diving into image processing with the Imagine stack, begin with the basics: pushing and popping numbers and images on the stack. The stack is like a stack of books, you can only add an item to the top (pushing an item) or remove the item from the top (popping an item.) To push on image on the stack, bring the image window to the front of the desktop by clicking on it. If the image is already in front, choose Push Image from the Push sub-menu of the Edit menu. The easiest way to push a number is to simply type the number in, Imagine quickly responds with a dialog box to receive your entry. You could also choose the Push Number from the Push sub-menu of the Edit menu. It is worth the time to look at the Push sub-menu of the Edit menu. For example, suppose you would like to threshold the image to the mean of the image. You could use the Image Statistics command from the Analysis menu to find the mean value of the image and then type in the mean to push it on the stack, but the Push sub-menu has a command, Push Mean, which quickly finds the mean of the image and pushes it on the stack, all in one operation. To pop an item from the stack, click on the Pop button next to the stack.
The vast majority of the Imagine routines use only three basic stack configurations. The simplest are the tasks which process a single image. Examples would be the unary math operations like Change Sign, Absolute Value, and the Analysis menu commands such as Spectrum and Histogram. The filtering operations (Convolutions, Sobel Enhancement,...) also use only a single image. To set up the Imagine stack for these processes, simply put the image on the top of the stack. Typically, this only involves clicking on the image to bring in to the front of the desktop.
Another class of routines require a single numerical parameter. An example is the Threshold routine which replaces all of the pixels of the image which are above a threshold with one value, and all the pixels below the threshold with another value. Imagine must know the value of the threshold. You pass the threshold by placing it on the stack on top of the image you wish to process. Explicitly, place the image on the stack and then place the threshold (a number) on the stack. When Imagine has finished processing the image, it will remove (pop) the threshold from the stack, leaving the image on the top of the Imagine stack. All of the Imagine routines which involve an image and a constant value (adding a constant to an image, thresholding, filling the Region Of Interest (ROI) with a constant,...) use the stack configuration where a number is placed on top of an image.
The routines which involve two images, such as adding two images together, require two images placed one on top of the other on the Imagine stack. The order of their placement determines the order of the operation (important for subtraction and division) and which image receives the result. As rule, the image pushed first receives the result, consistent with stack approach. As to the order of operation, the top image corresponds to the right term of an expression. To subtract image A from image B, place B on the stack and then place A on top of B. B will then receive the result B-A. After processing the two images, Imagine will pop the top image from the stack and bring the second image, which received the result, to the top of the stack and its window to the front of the desktop.
Complex image operations treat a pair of images, one real and the other imaginary, as a single complex pair. The imaginary image is always placed below (pushed first) the real image on the stack. For example, to add two complex images,
- place the imaginary image of the image pair A on the stack
- place the real image of the image pair A on the stack
- place the imaginary image of the image pair B on the stack
- place the real image of the image pair B on the stack
- choose the complex Add command from the Complex sub-menu. Imagine will remove the real and imaginary images of the image pair B from the stack and place the real part of the result in the real image of image pair A and the imaginary part of the result in the imaginary image of image pair A.
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Color Scale
The color scale determines how the image appears on the screen. You may alter the color scale by choosing a different type from the Color Scale sub-menu of the Option menu or changing the brightness or contrast using the Adjust button.
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Color Band
You may add a band of color to the color scale by choosing Add Band from the Color Scale sub-menu of the Option menu. Choose the width and placement of the band as well as its color (the default is red) from the dialog box. When the band is added to the color scale, the regions of the image which lie within the band will appear in the band color. You may change the location of the band by using the scroll bar next to the color scale.
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Brightness and Contrast Windowpane
This brightness and contrast windowpane displays the values of the brightness and contrast of the color scale in units of the front image on the desktop.
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Slice Position and Time Windowpane
This slice position and time windowpane contains the slice position and time of the current slice of the image volume. Imagine accepts 3 and 4 dimensional images in its native format. See the help text of the Info command of the File menu.
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Pointer Position and Value Windowpane
This pointer position and value windowpane displays the coordinates of the mouse with respect to the origin of the image (upper left corner) in image units. The value of the image at this point is also displayed below the coordinates.
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Square Lasso Addition Tool
The Square Lasso Addition Tool works like the Square Lasso Tool, EXCEPT that Imagine adds the new lassoed region to any current lasso region. The Addition Tools help to create disjoint lasso regions or to add small regions missed in the first lasso attempt. Also see help information on the Square Lasso Tool, Free Hand Lasso Tool, and Free Hand Lasso Addition Tool.
$1,26
Free Hand Lasso Addition Tool
The Free Hand Lasso Addition Tool works like the Free Hand Lasso Tool, EXCEPT that Imagine adds the new lassoed region to any current lasso region. The Addition Tools help to create disjoint lasso regions or to add small regions missed in the first lasso attempt. Also see help information on the Square Lasso Tool, Free Hand Lasso Tool, and Square Lasso Addition Tool.
$1,27
The Threshold Toggle
The Threshold Toggle switches between two states: normal and thresholding. In the thresholding state, the constrast is forced and maintained at 0. Upon returning to the normal state, the color manager returns the contrast to its previous value. The recommended technique of thresholding images:
- Click on the Threshold Toggle to reduce the contrast
- Click on the Adjust Button
- Move the mouse to find the desired brightness
- Click again to free the mouse
- Choose Push Brightness from the Push submenu
- Choose the Threshold command from the Arithmetic menu
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Add Brightness Stripe to Color Scale
You may add a band of color to the color scale by choosing Add Band from the Color Scale sub-menu of the Option menu. Choose the width and placement of the band as well as its color (the default is red) from the dialog box. When the band is added to the color scale, the regions of the image which lie within the band will appear in the band color. You may change the location of the band by using the scroll bar next to the color scale. You may change the parameters of the brightness stripe by choosing the Add Brightness Stripe command again.
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Remove Brightness Stripe from Color Scale
This command removes the brightness stripe from the color scale.
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Change the Color Scale
You may choose any of the color scales listed in the Color Scale sub-menu. Advanced users may want to try using the Color Scale Compiler in the Imagine utilities to create their own color scales.
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Push Brightness
This item pushes the current brightness value, shown in the brightness-contrast windowpane of the tool palette, on the stack. Also see help on the Thresholding Toggle in the tools window.
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Push Contrast
This item pushes the current contrast value, shown in the brightness-contrast windowpane of the tool palette, on the stack.
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Push Brightness Stripe Level
This item behaves much like the Push Brightness command except it pushes the level of the brightness stripe. This type of operation is also useful for thresholding and clipping image values.
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Push Brightness Stripe Width
Pushes the value of the brightness stripe width on the stack.
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Push Mean
Pushes the mean (average) of the image on the stack. If you hold down the Option key while choosing Mean or if the ROI Option Lock is enabled, Imagine pushes the mean of the area of the image contained in the current Region Of Interest (ROI.)
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Push Min
Pushes the minimum of the image on the stack. If you hold down the Option key while choosing Min if the ROI Option Lock is enabled, Imagine pushes the minimum of the area of the image contained in the current Region Of Interest (ROI.)
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Push Max
Pushes the maximum of the image on the stack. If you hold down the Option key while choosing Max if the ROI Option Lock is enabled, Imagine pushes the maximum of the area of the image contained in the current Region Of Interest (ROI.)
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Push Standard Deviation
Pushes the standard deviation of the image on the stack. If you hold down the Option key while choosing Standard Deviation if the ROI Option Lock is enabled, Imagine pushes the standard deviation of the area of the image contained in the current Region Of Interest (ROI.)
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Push Number
In response to this item, Imagine opens a dialog box to accept a numerical entry. After you close the dialog box, the number is pushed onto the Imagine stack.
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Push Image
Pushes the image in front on the desktop on the stack.
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Flip Image Horizontally
Choosing this item flips the image about a horizontal axis, exchanging the top and bottom. Regions Of Interest (ROIs) and the Line Of Interest (LOI) are not changed.
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Flip Image Vertically
Choosing this item flips the image about a vertical axis, exchanging the right and left. Regions Of Interest (ROIs) and the Line Of Interest (LOI) are not changed.
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Expand Image
Imagine asks you the amount of expansion in the horizontal and vertical directions, from 0 to 100%. Choose the Resize option if you wish to increase the image boundaries to accommodate the expanded image. Notice that the boundaries of 3 and 4D images cannot be resized since the size of the slice would no longer match the size of the other slices of the volume. The Pixel Recalculation option, causes Imagine to recompute the pixel dimensions after expansion so that distance measurements match each other before and after the change . The Regions Of Interest (ROIs) and the Line Of Interest (LOI) are resized to match the change in the image.
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Shrink Image
Imagine asks you the amount of reduction in the horizontal and vertical directions, from 0 to 100%. Choose the Resize option if you wish to decrease the image boundaries to enclose the reduced image. Notice that the boundaries of 3 and 4D images cannot be resized since the size of the slice would no longer match the size of the other slices of the volume. The Pixel Recalculation option, causes Imagine to recompute the pixel dimensions after reduction so that distance measurements match each other before and after the change. The Regions Of Interest (ROIs) and the Line Of Interest (LOI) are resized to match the change in the image.
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Translate Image
Imagine prompts you for the amount of translation (positive is to the right and down) in either number of pixels or distance according to the image units. The Regions Of Interest (ROIs) and the Line Of Interest (LOI) are resized to match the change in the image.
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Crop Image
Choosing the Crop command crops the image to the current window size. Notice that 3 and 4D images cannot be cropped since the size of the slice would no longer match the size of the other slices of the volume.
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Rotate Image
Rotates the image by a given number of degrees using bilinear interpolation.
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The Windows Menu
The first entry of the Windows menu is always the message window. To remove the message window temporarily out of your way on the desktop, click on its close button. You may later bring back the window by choosing its name from the Windows menu.
The names of any open images or graphs also appear in the Windows menu. To bring any of these to the front of the desktop, choose its name from the menu.
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Image Statistics
This item computes the mean, minimum, maximum, standard deviation, and area of the image and displays the results in the message window, along with the name of the image. If you hold down the Option key while choosing Standard Deviation if the ROI Option Lock is enabled, these statistics are computed only for the area of the image contained in the current Region Of Interest (ROI.)
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Cross Section Statistics
This item computes the mean, minimum, maximum, standard deviation, and area of the image along a line defined by the Line Of Interest and displays the results in the message window, along with the name of the image. If you do not know how to draw a LOI, click on Done and then click on the Line tool in the tool palette.
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Cross Section
This item computes the cross section of the image along a line defined by the Line Of Interest and displays the results in a graph window which you may later export to a spreadsheet or presentation graphics program using the Export command from the File menu. If you do not know how to draw a LOI, click on Done and then click on the Line tool in the tool palette.
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Column Average Plot
This command computes the average pixel value for each image column either for the entire image or a Region Of Interest (ROI) if the ROI Option Lock (under the Option menu) is on or the Option key held down while choose the Column Average Plot from the Analysis menu. The value are true averages, even for irregularly shaped regions.
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Histogram
To compute the histogram of the image (the number of pixels at each pixel value), choose the Histogram command. Imagine will display the results in a graph window which you may later export to a spreadsheet or presentation graphics program using the Export command from the File menu. If you hold down the Option key while choosing Histogram or if the ROI Option Lock is enabled, the histogram is computed only for the area of the image contained in the current Region Of Interest (ROI.)
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Spectrum
To compute the spectrum of the image (the number of pixels at each pixel value), choose the Histogram command. Imagine will display the results in a new image window. If you hold down the Option key while choosing Spectrum or if the ROI Option Lock is enabled, the spectrum is computed only for the area of the image contained in the current Region Of Interest (ROI.)
$136,8
Cine
The Cine command will display slices of a 3 or 4D image in rapid succession. Imagine will ask whether you would like to view the slices by position or by time, and, after you have made your choice, will load the relevant data. This can consume very large amounts of memory! Once the slices have been loaded, a small box resembling the controls of a tape recorder appears in the upper left of your screen. You may use these controls to cycle through the images one by one, or play them through in rapid succession. The position of the scroll bar indicator determines the number of images per second to display.
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Moment Analysis
The moment commands compute the first, second central, third central, as well as the skewness of an image or the portion of an image contained in a Region Of Interest (ROI.) To understand moments, imagine that the image is an object and the brightness of a pixel corresponds to the mass of the object at that one point. The first moment gives the centroid of the image, or in terms of the object, the center of gravity. The higher order moments are central moments and computed relative to the centroid. The second moment gives some indication of how spread out the object is. A point gives a much smaller second moment than a disk of the same mass. The skewness measures the symmetry of the object, perfect even symmetry gives zero for skewness.
You may measure the moments of just part of an image by drawing a ROI and enabling ROI selective processing with the ROI Option Lock toggle of the Options menu or by holding the Option key down while choosing a moment analysis command. Be aware that the shape of the ROI has a great impact on its moment.
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Title Color
You may choose any color you like for the title of an image. The standard six colors appear in the menu. To choose another color, pick Chooser from the menu and Imagine will bring up the Color Chooser dialog box to pick any color you wish.
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ROI Color
You may choose any color you like for the Regions Of Interest (ROIs) of an image. The standard six colors appear in the menu. To choose another color, pick Chooser from the menu and Imagine will bring up the Color Chooser dialog box to pick any color you wish. Each image may have four ROIs and each ROI may have its own color. The color you choose from the Color menu only affects the current ROI.
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Pad Image With Zeros
To perform convolutions you should pad the image edges with zeros. Using Fast Fourier Transforms also requires you to pad an image to the nearest power of 2; for example, a 216 by 216 pixel image must be padded to 256x256 pixels before performing the FFT. The pad routine does all of these for you. You fill out the dialog box to give the new number of rows and columns you want (greater than the original sizes) and click OK. Imagine will pad the image and adjust the Regions Of Interest (ROIs) and Line Of Interest (LOI) to match the change. When in the padding dialog box, clicking on one of the convolution or FFT buttons automatically fills in the correct new size of the padded image for you.
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Histogram Equalization
Histogram equalization is a standard image processing routine to adjust the values of image pixels for clearer viewing. A typical case is an underexposed photograph where most of the pixels appear very dark. Equalizing the photograph brightens the darker pixels to compensate for the underexposure. The theory is somewhat involved, but the routine changes the values of the pixels in an attempt to make the histogram of the image follow a particular model, usually based on human perception theory. The most popular is the uniform model, though other models work better in many cases. Note that the image values must all be positive for this command.
The histogram equalization routines present a dialog box from which you may choose your model and its parameters. When you pick a model, Imagine makes an intelligent guess for the parameters and plots the model in a windowpane in the right of the dialog box. You may change the parameters and redraw the plot, but the defaults are usually the best choice. To import your own histogram model, choose the Import.. radio button. The file must contain a list of 1024 numbers representing the target histogram. You may easily create the required file using a spreadsheet program and saving your work in TEXT format. You could also simply type in the data in any word processor or editor, placing each number on e separate line. Imagine will automatically scale the model as needed to work with the image.
The equalization depends not only on the model, but also on the histogram of the original image. Often the image may be improved by basing the histogram on only a Region Of Interest (ROI) which includes the objects of the image and excludes background pixels. To do this, draw a ROI on the image which excludes the background pixels and hold the Option key down (or turn on the ROI Option Lock in the Option menu) while choosing the Histogram Equalization from the Special menu. Notice the selected radio button in the lower left which says Apply To ROI Only. In this position, the modification is done only on the image within the ROI. Change the position to Entire Image to apply the modification to the complete image. Choose your model and click OK to enhance the image.
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Point Transformations
Point transformations change the value of a pixel based only on its original value, not the values of its neighbors. Histogram equalization is one common point transformation which Imagine supports directly. To allow any arbitrary transformation, you must create the transformation resource with the Transformation Editor under the Editors submenu. This editor allows you to create a two column table. The first column represents the incoming pixel value and the second column to outgoing pixel value, functioning as a look up table. Since this table could be quite small and the pixels may take on some 65,000 different values, Imagine uses cubic spline interpolation to estimate needed transformations between table entries. You may also import a transformation from an ASCII spreadsheet file using the Import... button while in the Editor. Once imported, you may edit, sort, and graph the transformation as you wish. When finished creating the transformation, click OK and the table will become a resource (a true Macintosh resource, in fact). After choosing Point XFormations from the Special menu, Imagine will offer a list of the available transformation resources. Choose a resource and click OK, or simply double click on the resource name, and Image will compile the look up table and perform the transformation.
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Image Convolution
Convolution of an image is the most fundamental filtering operation. Choose your filter from the list in the dialog box and click OK. Advanced users may use the Imagine utilities to create their own filters and add them to Imagine.
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Sobel Edge Enhancement
The Sobel operator extracts edges from an image. The image is convolved (filtered) with two different filters: one to find horizontal edges and another to find vertical edges. These two images are combined to give an image of all edges and the result, in turn, combined with the original image to enhance the edges. The percent enhancement in the dialog box determines how much to enhance the edges. 100 percent will produce an image of only edges while 0 percent does no enhancement at all. Try different values to get the effect you desire.
$134,7
Normalize Two Images
Before using the normalization, you must push the two images on the stack. The first image you push will be multiplied by a constant so that its average pixel value is the same as the average of the image on the top of stack. After the normalization the top of stack image is popped from the stack leaving the modified image on the top of stack.
You may also normalize images based on the average value of pixels only in a Region Of Interest (ROI) by holding the Option key down (or turning on the ROI Option Lock in the Option menu) while choosing Normalize Images from the Special menu.
$134,8
Two Dimensional Fast Fourier Transform
For advanced user, Imagine has an efficient implementation of the 2D Fast Fourier Transform (FFT.) Because the FFT generally involves the concept of complex image pairs, you should understand the theory of complex images. The 2D FFT will take the FFT of either a real image or a complex image pair. To take the FFT of a real image, simply place the image on the stack and choose 2D FFT from the Special menu. For the complex image pair, push the complex image on the stack and then push the real image so that the real image is on the top of stack before choosing the FFT routine.
The FFT dialog box presents the window choices usually used with the FFT for spectral estimation. If you are using the FFT to perform filtering, use the rectangular window option. You may also choose the inverse or forward FFT as well as three options, Centering, Magnitude, and dB. The Centering option tells imagine that you assume that the origin is at the center of the image, otherwise located at the upper left corner. The Magnitude option takes the magnitude of the complex FFT result as the final answer and the dB option takes the log of th magnitude and scales it to give an image in dB. Notice turning on the dB option implies the magnitude option.
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Adding Two Images
To add two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Add routine to compute A = A + B. Imagine removes image B from the stack, leaving image A, the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Adding a Constant to an Image
To add a constant to an image, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Add routine to compute A = A + B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine adds the constant only to the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Subtracting Two Images
To subtract two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Sub routine to compute A = A - B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Subtracting a Constant from an Image
To subtract a constant from an image, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Sub routine to compute A = A - B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine subtracts the constant only from the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Multiplying Two Images
To multiply two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Mul routine to compute A = A * B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Multiplying an Image by a Constant
To multiply an image by a constant , place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Mul routine to compute A = A * B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine multiplies by the constant only in the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Dividing Two Images
To divide two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Div routine to compute A = A / B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Dividing an Image by a Constant
To divide an image by a constant, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Div routine to compute A = A / B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine divides by the constant only in the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Maximum of Two Images
To take the maximum of two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Max routine to compute A = max(A, B) by comparing each pixel in image A with the corresponding pixel in image B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Taking the Maximum of an Image and a Constant
To take the maximum of an image and a constant, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Max routine to compute A = max(A, B) by comparing each pixel in image A with the number B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the max only for the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Inverse of an Image
To divide two images, place the first image, image A which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Div routine to compute A = A / B. Imagine removes image B from the stack, leaving image A, the result on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Minimum of Two Images
To take the minimum of two images (the images must be the same size), place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Min routine to compute A = min(A, B) by comparing each pixel in image A with the corresponding pixel in image B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Taking the Minimum of an Image and a Constant
To take the minimum of an image and a constant, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Min routine to compute A = min(A, B) by comparing each pixel in image A with the number B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the min only for the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Inverse of an Image
To take the inverse of an image, place the image, image A, on the stack and choose the Inv routine to compute A = 1/A by taking the inverse of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the inverse only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Square of an Image
To take the square of an image, place the image, image A, on the stack and choose the SQR routine to compute A = A*A by taking the square of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the square only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Square Root of an Image
To take the square root of an image, place the image, image A, on the stack and choose the SQRT routine to compute A = sqrt(A) by taking the square root of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the square root only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Absolute Value of an Image
To take the absolute value of an image, place the image, image A, on the stack and choose the ABS routine to compute A = |A| by taking the absolute value of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the absolute value only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Changing the Sign of an Image
To change the sign of an image, place the image, image A, on the stack and choose the ABS routine to compute A = -A by changing the sign of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine changed the sign only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Thesholding an Image
To threshold an image by a constant, place the first image, image A, which will receive the result, on the stack followed by a number B. Often the number B will be pushed by one of the Push items of the Edit menu (brightness for example.) The number B should now be on the top of stack with image A just below. Choose the Threshold routine to to bring up the thresholding options dialog box. When Imagine thresholds the image, it compares each pixel with the threshold (number B). If the pixel exceeds the threshold, Imagine replaces the pixel by the value you provided in the upper box or, if you checked the Pixel Value item of the upper box, it leaves the pixel unchanged. If the pixel is below the threshold, Imagine replaces the pixel by the value you provided in the lower box or, if you checked the Pixel Value item of the lower box, it leaves the pixel unchanged. By default, Imagine replaces the pixels above the threshold by 1 and those below by 0. As usual, if you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine thresholds only the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.) Also see help information on the Threhold Toggle button of the tool window.
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Taking the Logarithm (base e) of an Image
To take the logarithm of an image, place the image, image A, on the stack and choose the ln routine to compute A = log(A) by taking the exponential of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the logarithm only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
$140,2
Taking the Logarithm (base 10) of an Image
To take the logarithm of an image, place the image, image A, on the stack and choose the log routine to compute A = log(A) by taking the exponential of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the logarithm only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
$140,3
Taking the Exponential (base e) of an Image
To take the exponential of an image, place the image, image A, on the stack and choose the exp routine to compute A = exp(A) by taking the exponential of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the exponential only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Sine of an Image
To take the sine of an image, place the image, image A, on the stack and choose the sine routine to compute A = sin(A) by taking the sine (in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the sine only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Cosine of an Image
To take the cosine of an image, place the image, image A, on the stack and choose the cosine routine to compute A = cos(A) by taking the sine (in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the cosine only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the Tangent of an Image
To take the tangent of an image, place the image, image A, on the stack and choose the tan routine to compute A = tan(A) by taking the tangent (in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the tangent only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the ArcSine of an Image
To take the arcsine of an image, place the image, image A, on the stack and choose the ASine routine to compute A = arcsin(A) by taking the arcsine (result in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the arcsine only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the ArcCosine of an Image
To take the arccosine of an image, place the image, image A, on the stack and choose the ACosine routine to compute A = arccos(A) by taking the arccosine (result in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the arccosine only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Taking the ArcTangent of an Image
To take the arctangent of an image, place the image, image A, on the stack and choose the Sine routine to compute A = arctan(A) by taking the arctangent (result in radians) of each pixel in image A. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine computes the arctangent only for the area of the image contained in the Region Of Interest (ROI.) The stack is not changed.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Adding Two Complex Images
To add two images, place the first image, image A, which will receive the result, on the stack followed by image B. Image B should now be on the top of stack with image A just below. Choose the Add routine to compute A = A + B. Imagine removes image B from the stack, leaving image A, the result ,on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
Adding a Constant to a Complex Image
To add a constant to an image, place the first image, image A, which will receive the result, on the stack followed by a number B. The number B should now be on the top of stack with image A just below. Choose the Add routine to compute A = A + B. If you hold down the Option key (or the ROI Option Lock item of the Option menu was enabled), Imagine adds the constant only to the area of the image contained in the Region Of Interest (ROI.) Imagine then removes the number from the stack, leaving image A ,the result, on the top of stack. Imagine also brings image A to the front of the desktop so you can see the result.
If you do not know about the Imagine stack, click on the Done button below and then click, with the question mark cursor, on the stack windowpane (the window pane with four lines at the lower left corner of your screen next to the Pop and Last X buttons.)
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Reprojection
Advanced Tomography Users:
To reproject an image, place it on the stack and choose Normal from the Reprojection menu. You may choose any number of angles and rays per angle. The centering vector, which you may optionally import, is an ascii file, tab or <cr> delimited, with the number of entries equal to the choosen number of angles. Each entry specifies the center ray for that angle number. The pixel height of the resulting image equals the angle increment in radians (as it should since it is in projection space) and the pixel width equals the ray spacing in units of the original image. The inverting processes, filtered backprojection, expects this dimensionality.
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Attenuated Reprojection
Advanced Tomography Users:
Attenuated reprojection reprojects an activity image in an attenuation image. The pixel values of the attenuation image give the attenuation coefficient per pixel such that the attenuation = exp(-pixel_value). Place the activity image on the stack followed by the attenuation image. After processing, the attenuation image is popped from the stack and the result placed in the activity image. You may choose any number of angles and rays per angle. The centering vector, which you may optionally import, is an ascii file, tab or <cr> delimited, with the number of entries equal to the choosen number of angles. Each entry specifies the center ray for that angle number. The pixel height of the resulting image equals the angle increment in radians (as it should since it is in projection space) and the pixel width equals the ray spacing in units of the original image. The inverting processes, filtered backprojection, expects this dimensionality.
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Reprojection - Maximum Value
Advanced Tomography Users:
The maximum pixel reprojection of this routine finds its greatest utility in 3D volume rendering in Single Photon Emission Tomography (SPECT) and Magnetic Resonance Imaging (MRI). To reproject an image, place it on the stack and choose Maximum from the Reprojection menu. You may choose any number of angles and rays per angle. The centering vector, which you may optionally import, is an ascii file, tab or <cr> delimited, with the number of entries equal to the choosen number of angles. Each entry specifies the center ray for that angle number. The pixel height of the resulting image equals the angle increment in radians (as it should since it is in projection space) and the pixel width equals the ray spacing in units of the original image.
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Chang Map Creation
Advanced Tomography Users:
This routine creates the Chang map neccessary for first order or iterative Chang inversion of the attenuated Radon transform. Place an attenuation image, whose pixel values give the attenuation coefficient per pixel such that the attenuation = exp(-pixel_value), on the top of stack. You may choose the number of angles, typically 32. When the Reduced Data Set box is checked, the routine profits from the smooth nature of the Chang map to reduce processing time by a factor of about 8. After processing the Chang map will replace the attenuation image.
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Backprojection
Advanced Tomography Users:
The backprojection process expects an image in projection space, i.e. the pixel height equals the angular spacing in radians and the pixel width equals the ray spacing. To backproject an image, place it on the stack and choose Backprojection from the Computed Tomography menu. The centering vector, which you may optionally import, is an ascii file, tab or <cr> delimited, with the number of entries equal to the choosen number of angles (the number of image rows in projection space.) Each entry specifies the center ray for that angle number. To invert the Radon transform (reprojection) you must use filtered backprojection.
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Backprojection - Filtered
Advanced Tomography Users:
Filtered backprojection is the most fundamental operation in computed tomography, used in fields from astronomy to medical imaging. The process expects an image in projection space, i.e. the pixel height equals the angular spacing in radians and the pixel width equals the ray spacing. To backproject an image, place it on the stack and choose FIltered Backprojection from the Computed Tomography menu. The centering vector, which you may optionally import, is an ascii file, tab or <cr> delimited, with the number of entries equal to the number of angles (the number of image rows in projection space.) Each entry specifies the center ray for that angle number. Imagine has several built in filters, or you may import you own, also an ascii file, easily created in a spreadsheet. The filter length must be equal to the number of columns in the reconstructed image PLUS ONE. The first point is f=0 and the last point is f=folding frequency.
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Dilation
Morphological dilation compares each pixel with its neighboring pixels, finds the maximum, and assigns this maximum to this pixel. The net effect increases, dilates, the size of bright (high pixel value) objects. Morphological erosion complements dilation in that it finds the minimum of the neighborhood and decreases or erodes the size of bright (high pixel value) objects. See also the Nth order filter which is a generalization that includes dilation, erosion, and median filters.
The mask, often called a structuring element, determines the size and shape of the neighborhood. For advanced users, Imagine supports custom 2D and 3D structuring elements through the Morphological Editor utility of the Editor submenu. For 3D morphology, all the coefficients of the structuring element with a defined numerical value constitute the neighborhood; the coefficients of 'N' value excluded from the neighborhood. The values of the structuring element coefficients are added to the image pixels before searching for the min or max. This technique permits some interesting filter forms such as the 'Rolling Ball' filter. Notice that the same mask applied to two images, one a scaled version of the other, produce different results. Users who wish to explore morphology to this extent should consult one of the recommended references.
Like all the other morphological operators, dilation may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Erosion
Morphological erosion compares each pixel with its neighboring pixels, finds the minimum, and assigns this minimum to this pixel. The net effect decreases, erodes, the size of bright (high pixel value) objects. Morphological dilation complements erosion in that it finds the minimum of the neighborhood and increases or dilates the size of bright (high pixel value) objects. See also the Nth order filter which is a generalization that includes dilation, erosion, and median filters.
The mask, often called a structuring element, determines the size and shape of the neighborhood. For advanced users, Imagine supports custom 2D and 3D structuring elements through the Morphological Editor utility of the Editor submenu. For 3D morphology, all the coefficients of the structuring element with a defined numerical value constitute the neighborhood; the coefficients of 'N' value excluded from the neighborhood. The values of the structuring element coefficients are added to the image pixels before searching for the min or max. This technique permits some interesting filter forms such as the 'Rolling Ball' filter. Notice that the same mask applied to two images, one a scaled version of the other, produce different results. Users who wish to explore morphology to this extent should consult one of the recommended references.
Like all the other morphological operators, erosion may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Opening
Opening, one of the basic morphological filters, consists of an erosion followed by a dilation. The two operations tend to remove thin connections between bright objects and to remove 'peninsulas' from the perimeters of bright objects. Also see erosion and dilation.
Like all the other morphological operators, opening may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Closure
Closure, one of the basic morphological filters, consists of an dilation followed by a erosion. The two operations tend to join bright objects that are close together and to fill in concavities in the perimeters of bright objects. Also see erosion and dilation.
Like all the other morphological operators, closure may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Geodesic Dilation
The geodesic morphological operations, often referred to as reconstructions, involve two images, one of which is said to be processed (dilated, eroded, opened, closed) under the other. Imagine operates on the image in the second position on the stack under the image in the first position, or top of stack. Each iteration of geodesic dilation is a two step process beginning with dilation of the first image. In the second step, the image is replaced by the minimum (on a pixel by pixel basis) of the two images. In this way the pixels of the first image can never exceed those of the second image: the first image under the second image. The number of iterations depends on the purpose of the processing, but for reconstruction, 2 times the diagonal length of the image (in pixels) usually suffices.
A typical application would be removing small binary objects (i.e. the image consists of only two values: object value and a lesser background value) from the image. Initially a copy of the image is eroded until all traces of the small objects have disappeared. Then the original image is brought to the front (the eroded copy will now be second position in the stack with the original on top) and the geodesic dilation carried out for a sufficient number of iterations. The final image will look like the original, except the small objects has been removed. If the objects had been of lower value than the background (like black objects on a white background) a dilation should replace the initial erosion and geodesic erosion done in place of the geodesic dilation.
Like all the other morphological operators, the geodesic dilation may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Geodesic Erosion
The geodesic morphological operations, often referred to as reconstructions, involve two images, one of which is said to be processed (dilated, eroded, opened, closed) under the other. Imagine operates on the image in the second position on the stack under the image in the first position, or top of stack. Each iteration of geodesic erosion is a two step process beginning with erosion of the first image. In the second step, the image is replaced by the maximum (on a pixel by pixel basis) of the two images. In this way the pixels of the first image cannot be less than those of the second image. The number of iterations depends on the purpose of the processing, but for reconstruction, 2 times the diagonal length of the image (in pixels) usually suffices. Also see Geodesic Dilation.
Like all the other morphological operators, the geodesic erosion may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
$145,7
Geodesic Opening
The geodesic morphological operations, often referred to as reconstructions, involve two images, one of which is said to be processed (dilated, eroded, opened, closed) under the other. Imagine operates on the image in the second position on the stack under the image in the first position, or top of stack. Each iteration of geodesic opening is a two step process beginning with opening of the first image. In the second step, the image is replaced by the maximum (on a pixel by pixel basis) of the two images. In this way the pixels of the first image cannot be less than those of the second image. The number of iterations depends on the purpose of the processing, but for reconstruction, 2 times the diagonal length of the image (in pixels) usually suffices. Also see Geodesic Dilation.
Like all the other morphological operators, the geodesic opening may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
$145,8
Geodesic Closure
The geodesic morphological operations, often referred to as reconstructions, involve two images, one of which is said to be processed (dilated, eroded, opened, closed) under the other. Imagine operates on the image in the second position on the stack under the image in the first position, or top of stack. Each iteration of geodesic closure is a two step process beginning with closure of the first image. In the second step, the image is replaced by the minimum (on a pixel by pixel basis) of the two images. In this way the pixels of the first image exceed those of the second image. The number of iterations depends on the purpose of the processing, but for reconstruction, 2 times the diagonal length of the image (in pixels) usually suffices. Also see Geodesic Dilation.
Like all the other morphological operators, the geodesic closure may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
$145,9
Local Maximum
Imagine passes the morphological mask, or structuring element, over the image much like for dilation or erosion, comparing each pixel against its neighbors. Unlike the dilation where the maximum of the neighborhood replaces the pixel, the local maximum operation simply tags the pixels as being the maximum or not being the maximum. Imagine then modifies the pixel values according to the parameters you supply in the dialog box. You may set all pixels identified as maximal pixels to a specific value or leave them unchanged by checking the 'pixel value' option. You make the same choices for pixels classified as non-maximal. The local maximum differs from the regional maximum in that the pixel must be greater than all its neighbors; for the regional case the pixel must be greater than or equal to all its neighbors.
Like all the other morphological operators, the local maximum may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
$145,10
Local Minimum
Imagine passes the morphological mask, or structuring element, over the image much like for dilation or erosion, comparing each pixel against its neighbors. Unlike the erosion where the minimum of the neighborhood replaces the pixel, the local minimum operation simply tags the pixels as being the minimum or not being the minimum. Imagine then modifies the pixel values according to the parameters you supply in the dialog box. You may set all pixels identified as minimal pixels to a specific value or leave them unchanged by checking the 'pixel value' option. You make the same choices for pixels classified as non-minimal. The local minimum differs from the regional minimum in that the pixel must be less than all its neighbors; for the regional case the pixel must be less than or equal to all its neighbors.
Like all the other morphological operators, the local minimum may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Regional Maximum
Imagine passes the morphological mask ,or structuring element, over the image much like for dilation or erosion, comparing each pixel against its neighbors. Unlike the dilation where the maximum of the neighborhood replaces the pixel, the regional maximum operation simply tags the pixels as being the maximum or not being the maximum. Imagine then modifies the pixel values according to the parameters you supply in the dialog box. You may set all pixels identified as maximal pixels to a specific value or leave them unchanged by checking the 'pixel value' option. You make the same choices for pixels classified as non-maximal. The local maximum differs from the regional maximum in that the pixel must be greater than all its neighbors; for the regional case the pixel must be greater than or equal to all its neighbors.
Like all the other morphological operators, the regional maximum may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
$145,12
Regional Minimum
Imagine passes the morphological mask, or structuring element, over the image much like for dilation or erosion, comparing each pixel against its neighbors. Unlike the erosion where the minimum of the neighborhood replaces the pixel, the regional minimum operation simply tags the pixels as being the minimum or not being the minimum. Imagine then modifies the pixel values according to the parameters you supply in the dialog box. You may set all pixels identified as minimal pixels to a specific value or leave them unchanged by checking the 'pixel value' option. You make the same choices for pixels classified as non-minimal. The local minimum differs from the regional minimum in that the pixel must be less than all its neighbors; for the regional case the pixel must be less than or equal to all its neighbors.
Like all the other morphological operators, the regional minimum may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Nth Order Filter
The Nth order filter begins like dilation or erosion by passing the morphological mask, or structuring element, over the image and comparing each pixel against its neighbors. Instead of searching for the minimum (erosion) or maximum (dilation) the Nth order filter chooses some other order, the most popular being the central order or median filter. For example, using a 3x3 square mask (9 coefficients), an erosion would be equivalent to order 1, a dilation equivalent to order 9, and the median filter would take order 5. Of course Imagine supports 3D structuring elements as with all other morphological filters (fuzzy or rolling sponge filters.)
Like all the other morphological operators, the Nth order filter may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Watershed
The watershed process forms the basis for morphological segmentation. To understand the watershed, think of the image as a surface where the bright pixels represent mountain tops and the dark pixels valleys. In some of the valleys you could puncture the surface and slowly submerge the surface into a water bath. The water pours in each puncture and begins to fill the valleys, the water rising higher and higher as the surface sinks. You must prevent water from different punctures from mixing by building dams just before they meet. When the surface is completely submerged, all that remains above water are the dams. These are the boundaries and their interiors are the watersheds or basins. Note that there is one and only one basin for each puncture. Watershed comes from the same term relating to rivers and drainage basins.
To start the watershed you must puncture the surface by first ensuring that all pixels are greater than and not equal to zero (use the image statistics function and add a constant if necessary.) Then puncture the surface by setting the puncture points equal to zero, typically by using the regional minimum function. The surface is now ready for the watershed processing.
Like all the other morphological operators, the watershed may be done on just a Region Of Interest (ROI) by holding down the Option Key or turn on the ROI Option Lock option under the Options menu.
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Distance Function
For the distance function a copy of the image is repeatedly eroded and summed with the original until the maximum number of iterations is exceeded or the copy has been completely eroded to all zeros, which ever comes first. The result appears to have the same shape as the original but each object becomes what appears like a mountain range. For binary images where the objects have value 1.0 and the background 0.0, the crests of these mountains represent the skeleton of the object and the height of the crest corresponds to the distance from the crest to the nearest edge of the object. Advanced users familiar with morphology typically use the distance function as an aid in separating overlapping objects.
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ROI Option Lock
You can tell Imagine to process only the area of an image within the current Region Of Interest (ROI) by choosing the ROI Option Lock item. When the option is enabled, a check mark will appear to the left of the item. To disable the item, choose it again from the menu and Imagine will remove the check mark. You mat also invoke ROI selective processing by holding down the Option key while choosing the processing task from the menu. Almost all Imagine routines have the capability to perform ROI selective process (refer to the help information on each particular routine.)
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ROI Centering Option
You may enable the Region Of Interest (ROI) centering mode by choosing the ROI Centering item. When the option is enabled, a check mark will appear to the left of the item. To disable the item, choose it again from the menu and Imagine will remove the check mark. When resizing a ROI or Line Of Interest (LOI) with the Centering option enabled, Imagine forces the center of the object to remain in its original location. For example if you wanted to enlarge a square ROI by dragging the lower right corner, normally the upper left corner remains fixed, as in a draw program. With the centering option enabled, Imagine moves the upper left corner to maintain the ROI center as you move the lower right corner. If you do not know how to resize a ROI or LOI, click Done below and then click on the Arrow tool in the tool palette at the left of your screen.
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Paint ROI Option
After drawing many intersecting Region Of Interest (ROI) shapes, you may be confused as to what areas of the image lie within the ROI. Enable the Paint ROI Option by choosing it from the Options menu (a check mark will appear) and Imagine will paint the interior of the ROI to help clarify the situation. Choose the item again and Imagine redraws only the ROI outline.
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Show All ROIs Option
By default, only the current Region Of Interest (ROI) appears on the image, even though each image may have four ROIs. To change the current ROI to another ROI, click on the ROI indicator, the small colored square containing the ROI number at the lower left of the image window. The current ROI is removed and replaced with the next ROI belonging to the image. To view all four ROIs at once, choose the Show All ROIs option and Imagine will draw all four ROIs on the image. There is still only one current ROI, shown by the color and number of the ROI indicator. To change the current ROI you may click on the indicator, as before, or use the Point tool and click on the desired ROI in the window: the color of the ROI indicator will change to reflect the change of current ROI. To turn off the Show All ROIs option, choose it again from the Options menu.
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Combine ROIs Function
The Combine ROIs command presents a dialog box that allows to choose the source ROIs, the operation to be performed on the source ROIs, such as the union operation, and the destination ROI which will receive the result.
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ROI Line Width
The ROI line width dialog display several icons showing the line width choices. Click on the desired icon and click OK and imagine will draw all of the ROIs for the current image with the new line width.
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Choosing Eraser Shapes
You may choose the best eraser shape for your work with the Eraser Shape command. Simply pick the desired shape in the dialog box and click OK. Imagine will activate the Eraser tool and change the shape of the cursor when you pass the pointer over an active image.
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Disabling the Image Undo Mechanism
Before beginning an image processing task, Imagine saves a copy of the image to disk in the event that you would like to undo the modifications made to the image. To save time, you may suspend the image undo mechanism by disabling the Enable Image Undos item under the Options menu. In this suspended state, you may only undo changes to ROIs and LOIs.
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Enabling Multiple Cursors
When the Multiple Cursors option is enabled, Imagine draws a phantom cursor in each open image on the screen. The position of each phantom cursor relative to the upper left corner of its image is the same as the relative position of the real cursor to the upper left corner of the front image. Use this option as an positioning aid for comparing two images (such as the displacement of one image compared to another) or to outline a ROI on one image based on the form of another image.
$2,0
The Image Window
Each image has an image window to display the contents of the image. Since Imagine will read 3 and 4 dimensional images and the screen is only 2 dimensions, the image in the window is a slice through the higher dimensional volume. Examples would be a medical CT scan which is usually 3 dimensional: each slice representing a different cross section through the body. A movie loop is also three dimensional, but the third dimension is in time with each slice corresponding to an image at a particular point in time. You may view all the slices, one at a time, by clicking on the small '+' and '-' buttons at the left of the image window to move one slice forward or backward. The next slice will appear in the window and its position in time and space given in the time-position windowpane in the tool palette at the left of your screen (coordinates z and t.) You may skip directly by typing in the slice number while clicking on one of the slice buttons. Releasing the button prompts Imagine to load the selected slice. To choose whether you would like to view the slices by time or by position, choose the Info command from the File menu. Choose one of the two radio buttons in the lower left of the dialog box to select the viewing order. Notice single volumes should by view by position, movie loops by frame, and that two dimensional images, such as photographs, have only one slice.
Each image has four Regions Of Interest (ROIs) which you may draw using the Square, Oval, and Free Hand tools from the tool palette at the left of your screen. These ROIs specify a region of the image you wish to process or analyze separate from the rest of the image. For example, you may wish to know the average pixel value for a small region of the image. Draw a ROI around this region, hold the Option key down (this signals ROI selective processing) and choose Image Statistics from the Analysis menu. Image reports the statistics only for the area of the image contained in the ROI. Most of the Imagine commands will perform ROI selective processing. By default, only the current ROI appears on the image, even though each image may have four ROIs. To change the current ROI to another ROI, click on the ROI indicator, the small button to the left of the image with the ROI number shown in the ROI color. The current ROI is removed and replaced with the next ROI belonging to the image.
An image also contains a Line Of Interest (LOI) which you draw using the Line tool from the tool palette. Imagine uses the LOI for operations which process or analyze the image along a line through the image, such as graphing a cross section of the image.
You may zoom up to a factor of 8 or down to 1/2 using the two zoom buttons at image left (multiply and divide). The top two tools, the arrow tool and the hand tool, at image left provide an quick alternative to choosing these two tools from the tool window. If active, the local image tools override the tool selection in the tool window.
$3,0
Graph Windows
Graphs represent one dimensional sets of data, such as cross sections and histograms of images. Once created you may export the graph data in a spreadsheet compatible format by choosing the Export command from the File menu. This is useful for preparing presentation quality graphs from image data. You may also copy a foremost graph with the Copy command under the Edit menu. Both the graph data, in spreadsheet compatible format, and the graph itself are copied for pasting into other applications. To help view graphs, Imagine draws cross guide lines when you hold the mouse button down while the pointer lies in a graph rectangle.
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Help System
To use the help system, click on any window, object in the tool palette (such as the Point tool), or choose an item from any menu. When you have finished with the help, exit the help dialog box by clicking on Done and strike any key on the keyboard to return the cursor to its normal shape. To view the available list of help topics click on the Topics button.
$4,0
Message Window
When you perform an image analysis which gives a numerical result, such as the Image Statistics command, Imagine sends a description of the analysis and the result to the Message window. You may print all the messages with the Print command, export the messages to a spreadsheet compatible file with the Export command, or copy all, or a selected subset, of the messages to the clipboard for pasting into a spreadsheet, word processor, or any other program accepting text from the clipboard. To select entries click on the entry line with the mouse (the Message window must be active) and Imagine will hilite the selection. To extend the selection use the Shift key and to create disjointed selections use the Command key, as you would in a spreadsheet. The selected entries may be copied to the clipboard using the Copy command from the Edit menu or deleted using the Clear command. The Message windows holds a maximum of 256 entries.
The close box of the Message window hides the window from view. To show the window again, choose Message from the Windows menu. The zoom box allows you to zoom the window up to full screen size for easy viewing.
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Convolution Resource Editor
As with all the resource editors in Imagine, choosing the edit command first activates the generic resource picker. A list of available resources (such as convolution masks or color tables) appear in the list box at left and a column of buttons at right. By selecting a resource and clicking a button, you may add and remove resources at will. Clicking the Edit button, or double clicking on the resource name, starts a resource editor specific to the type of resource.
The Convolution resource editor displays the coefficients of the convolution mask in a spreadsheet format. The effective value of each coefficient is the value in the spreadsheet (which must be integer) multiplied by the scaling factor. Several aid buttons below the spreadsheet perform flips and rotates to speed the process of entering symmetric masks. The Separable button constructs an entire mask from the first row and the first column. The (i,j) coefficient equals the (i) coefficient of the first row times the (j) coefficient of the first column. The ambiguity of the upper left corner, which is the first coefficient of both the first row and first column, is resolved by placing the first coefficient of the first row directly below the second coefficient of the first row, rather than to the left. The Normalize button sets the scale factor low enough to avoid overflow (maximum gain of unity.) The graph at right displays the frequency response of the filter in the horizontal or vertical direction.
The convolution resources are true Macintosh resources and may be edited with the Resource Editor from Apple.
$147,2
Morphological Resource Editor
As with all the resource editors in Imagine, choosing the edit command first activates the generic resource picker. A list of available resources (such as convolution masks or color tables) appear in the list box at left and a column of buttons at right. By selecting a resource and clicking a button, you may add and remove resources at will. Clicking the Edit button, or double clicking on the resource name, starts a resource editor specific to the type of resource.
The Morphological resource editor displays the coefficients of the morphological structuring element in a spreadsheet format. The effective value of each coefficient is the value in the spreadsheet (which must be integer) multiplied by the scaling factor. Imagine supports 2 dimensional morphological structuring elements, such as the Rolling Ball, so the spreadsheet contains provisions for excluding neighbors from the structuring element. This is done by selecting the coefficient and choosing N from the entry bar. This process defines the extent of the neighborhood while the coefficient values define the surface height of the structuring element. Several aid buttons below the spreadsheet perform flips and rotates to speed the process of entering symmetric masks. The graph at right displays a cross section through the structuring element.
The morphological resources are true Macintosh resources and may be edited with the Resource Editor from Apple.
$147,3
Color Table Editor
As with all the resource editors in Imagine, choosing the edit command first activates the generic resource picker. A list of available resources (such as convolution masks or color tables) appear in the list box at left and a column of buttons at right. By selecting a resource and clicking a button, you may add and remove resources at will. Clicking the Edit button, or double clicking on the resource name, starts a resource editor specific to the type of resource.
The Color Table resource editor uses the concept of a knot. By creating a knot, you specify the color you want at some point, the knot location, in the color table. Imagine fills in the rest of the color table by smoothly grading the colors between knots. You are free to add and delete knots (except the first and last knots, which cannot be deleted) and change their color by using the scroll bars at right to adjust the amount of red, green, and blue or by using the Color Picker by clicking on the Color Picker button. You may view just a single color of the color table with the radio buttons near the color stripe.
The color table resources are true Macintosh resources and may be edited with the Resource Editor from Apple.
$147,4
Transformation Table Editor
As with all the resource editors in Imagine, choosing the edit command first activates the generic resource picker. A list of available resources (such as convolution masks or color tables) appear in the list box at left and a column of buttons at right. By selecting a resource and clicking a button, you may add and remove resources at will. Clicking the Edit button, or double clicking on the resource name, starts a resource editor specific to the type of resource.
Point transformations change the value of a pixel based only on its original value, not the values of its neighbors. Histogram equalization is one common point transformation which Imagine supports directly. To allow any arbitrary transformation, you must create the transformation resource with the Transformation Editor under the Editors submenu. This editor allows you to create a two column table. The first column represents the incoming pixel value and the second column to outgoing pixel value, functioning as a look up table. Since this table could be quite small and the pixels may take on some 65,000 different values, Imagine uses cubic spline interpolation to estimate needed transformations between table entries. You may also import a transformation from an ASCII spreadsheet file using the Import... button while in the Editor. Once imported, you may edit, sort, and graph the transformation as you wish. When finished creating the transformation, click OK and the table will become a resource (a true Macintosh resource, in fact). After choosing Point XFormations from the Special menu, Imagine will offer a list of the available transformation resources. Choose a resource and click OK, or simply double click on the resource name, and Image will compile the look up table and perform the transformation.
