Select TIFF to open 8 and 16-bit TIFF files imported from other systems, such as a Macintosh. Once a 16-bit TIFF file has been imported, you can use Rescale (a k a Revert to Saved) to find the optimum 16-bit to 8-bit mapping. Select DICOM to import 16-bit files in the DICOM-3 (Digital Imaging and Communications in Medicine) format used in radiology. Select Text to import a two-dimensional array of numbers stored in tab-delimited text format, for example, a spreadsheet saved as Text Only. Values do not have to be in the range 0-255, and may be in decimal or scientific format. By reading in the text file twice, Scion Image is able to determine the number of rows and columns, and to scale to 8-bits (1-254). Blank cells are assumed to have a value of zero. If Fixed Scale is checked then automatic scaling is disabled, values are scaled to 8-bits from the range Min-Max, values less than Min are set to Min, and values greater than Max are set to Max. 10
Select Look-Up Table to import a 768 byte binary LUT consisting of 256 consecutive red values, 256 consecutive green values, and 256 consecutive blue values. The values should be in the range 0-255. Select Custom to open other types of 8-bit and 16-bit binary images. Width is the width of the image in pixels and Height is the number of lines in the image. For 16-bit images, the maximum value that can be entered for Width is 4096. Offset specifies the number of bytes Scion Image will skip before it starts reading the pixel data. For example, use an offset of 512 to skip over a 512 byte file header. Set Slices to more than one to import 3D data sets such as multi-slice volumes from medical scanners Scion Image computes the minimum and maximum pixel values of 16-bit images and uses this information to linearly scale to 8-bits (1-254). Check Swap Bytes when importing 16-bit images from big-endian systems, such as the Macintosh. If Calibrate is checked Scion Image automatically sets up a linear density calibration function to provide an approximation of the original 16-bit pixel values. The approximated values should not vary from the original 16-bit values by more than (Max-Min)/254, where Min and Max are the minimum and maximum 16-bit values. If Fixed Scale is checked then automatic scaling is disabled and the 16-bit data is linearly scaled from Min-Max to 1254. You can redo the 16-bit to 8-bit scaling at any time using the Rescale command Use the Import command to scale 16-bit images from medical scanners to the 8bit format required by Scion Image. For example, to import raw MRI scans from a GE SIGNA scanner, set width and height to 256, select 16-bit Signed, and set Offset to 14336. The macro Import GE Signa Files (in the file Stacks) will automatically import a series of raw GE SIGNA files. Check Open All to import all of the images in a directory. The images must all have the same width, height, etc. Open All does not work with imported text files and look-up tables. Check Invert to invert imported 8-bit images.

Subtract Background

The commands in this sub-menu remove smooth continuous backgrounds from gels and other images. 1D Horizontal - Rolls an arc (rolling arc) horizontally under each row (shrunk 2 or 4 times) of the image in order to remove the background. 1D Vertical - Rolls an arc (rolling arc) vertically under each column (shrunk 2 or 4 times) of the image in order to remove the background. 2D Rolling Ball - Rolls a patch from the top of a sphere (rolling ball) under every point in the image (shrunk 4 or 8 times) in order to find the background. 31
2D Remove Streaks - Gets rid of horizontal and vertical streaks as it removes background by calling 1D Horizontal and 1D Vertical consecutively. Faster - When checked, the image is shrunk 8 times (instead of 4) for 2D rolling ball subtraction. When the ball radius is less than 15 the image is shrunk 4 times (instead of 2). Set Radius - Allows you to set the rolling ball or disk radius. Generally, the disk/ball radius should be at least as large as the width/diameter of the largest object in the image that is not part of the background.

Apply LUT

Applies the current look-up table function to each pixel in the current selection (or the entire image if there is no current selection) and restores the default look-up table (the identity function). This modifies the gray values so that when the image is viewed using the default grayscale look-up table it will look the same as it did before. This command provides a way of making brightness and contrast changes permanent. It can be used to posterize (reduce the number of gray values) an image by loading and applying, for example, a LUT consisting of four shades of gray. It can also be used to convert color images to grayscale, and to convert a thresholded image to binary. If density slicing is in effect, a dialog box is displayed, allowing you to process highlighted pixels in one way, and all other pixels another way.

Enhance Contrast

Enhances the contrast of the currently active image. A new look-up table function is generated by doing a linear histogram stretch of the current selection. Use the Apply LUT command to make the contrast change permanent. Enhance Contrast does not work with true color images.

Equalize

Performs histogram equalization based on the density histogram of the current selection. A new look-up table function is generated that more evenly distributes the gray values of the image. The newly created function is displayed in the Map window. Use Apply LUT to make the contrast change permanent. Equalization does not work with true color images.

Fix Colors

Attempts to correct color anomalies by mapping pixels with values of either 0 or 255 to the nearest matching color in the other 254 LUT entries. This usually corrects pseudocolor problems due to the way Scion Image hard wires entries 0 and 255 to white and black respectively.

Stacks Menu

Use the commands in this menu to create or process stacks. Stacks are three dimensional images consisting of two or more slices. The slices can be consecutive serial sections in a 3D data set, frames in a movie loop, RGB (red, green and blue) channels in a 24-bit color image, or any related set of images. Use the < and > keys to move through the slices in a stack. The current slice and total number of slices are displayed in parentheses in the title bar. Stacks are displayed in a single window and can be saved to a single disk file using the Save, Save As or Export commands. Most commands in Scion Image, with the exception of Save, Save As, Export and Open, operate only on the current slice. There are, however, macros available (in the file Stacks) that operate on all the slices in a stack

Windows to Stack

Converts the set of images currently being displayed in separate windows to a stack. The images must all be the same size. A macro, also called Window to Stack (in the file Stacks), is available that works with windows that are not the same size.

Stack to Windows

Converts the currently active stack to windows. A stack with 20 slices would be converted to 20 normal image windows.

Add Slice

Adds a new blank slice to the stack following the currently displayed slice. The maximum number of slices in a stack is 1000.

Delete Slice

Deletes the currently displayed slice. You can use Undo to restore it.

Next Slice

Displays the slice following the currently displayed slice. A shortcut to get the next slice is to press the > key.

Previous Slice

Displays the slice before the currently displayed slice. As a shortcut, use the <.

Make Movie

Captures a series of video frames into a stack. Scion Image creates a stack the same width and height as the current selection and large enough to hold the number of frames specified. A dialog box allows you to specify the number of frames and the capture rate. The capture rate is specified by entering either the inter-frame interval (Seconds/frame) or the frame rate (Frames/second). Set the inter-frame interval to zero for the fastest capture rate. After Scion Image has completed recording the movie it will compute the actual frame rate and display it in the Info window. If the computed and desired rates are not the same then the frames were probably captured at uneven intervals. If even sampling is required, you should specify a slower rate, use a smaller selection, or try enabling Blind Capture.

The text file method uses relative coordinates of fiducial marks as recorded with some device such as a microscope digitizer. Let us call these coordinates stage coordinates. It also uses screen coordinates of fiducials in Scion Image. Before registration may take place, stage coordinates must be mapped to the Scion Image screen coordinate system. To do this, Scion Image reads the following, tab-delimited information from a text file. In every case, x-coordinates are followed by y-coordinates. line 1: the screen coordinates of a point which is fixed for every image captured. In the sample fiducial file, this is the point which corresponds to the cross hairs on the microscope at capture time. This is the image center point. line 2: the location, in screen coordinates, of two fixed points in an image. line 3: the location, in stage coordinates, of these same two fixed points. line 4: (and each subsequent line) the locations, in stage coordinates, of the image center and at least two, but nor more than 12, fiducial points for an image to be registered. Obviously, the stage coordinate system may not change in rotation, translation, or scale in the middle of a set of images being captured, so it is advisable to record stage coordinates at the time of image capture (without changing camera settings or the position of the object whose image is being captured). Lines 4-n must entered in the same order as the slices in the stack. It doesnt matter which one is the reference image. Where fiducial coordinates are unavailable or unreliable, use the number 10000 for both the x and y stage coordinate in the file. Each slice must be represented by the same number of fiducial coordinates in the data file. As you can see, using the text file method introduces many possible sources of errors, so results are not usually as good with this method as with the on-screen method.

Project

Generates an animation sequence by projecting through a rotating 3D data set onto a plane. Each frame in the animation sequence is the result of projecting from a different viewing angle. To visualize this, imagine a field of parallel rays passing through a volume containing one or more solid objects and striking a screen oriented normal to the directions of the rays. Each ray projects a value onto the screen, or projection plane, based on the values of points along its path. Three methods are available for calculating the projections onto this plane: nearest-point, brightest-point, and mean-value. The choice of projection method and the settings of various visualization parameters determine how both surface and interior structures will appear.

Reslice

Reconstructs a 2D image from the image volume contained in the current stack. Use the straight line selection tool to select were the reconstruction will be done. You will be prompted for the slice spacing (displacement between slices in the stack) in pixels if this information has not been previously entered. Macros are available (in the file Stacks) for repetitive reslicing of image volumes, for example, to generate a set of coronal slices from an MRI volume consisting of sagital slices.

Stack Info

Allows you to view and set the type, slice spacing, and frame interval of the current stack.
A Volume is a stack containing a 3D Image. A Movie is a sequence of frames captured using the Make Movie Command. An RGB Image is a 3-slice stack containing a 24-bit color image in RGB (Red, Green, Blue) format. An HSV Image is a 3 slice stack containing a 24-bit color image in HSV (Hue, Saturation, Value) format. Slice Spacing is the distance between the slices in a volume. Interval is the inter-frame interval in a movie.

RGB to 24-bit Color

Converts an RGB color image (in the form of a three slice stack) to a 24-bit color image. Filter operations such as smoothing and sharpening cannot be performed on the 24-bit image they must be performed on the RGB slices.

24-bit to RGB Color

Converts a 24-bit color image to an RGB three slice (red, green, blue) stack, a format that allows filter operations such as smoothing and sharpening to be performed. A macro can be created to automate the filtering process.

Windows Menu

Next Window
Deactivates the current image window and activates the next image in the image list, as shown at the bottom of the Windows Menu.

Cascade Windows

Expands all the image windows to their original size and redraws them slightly offset from each other. If you hold down the Shift key, all windows will be drawn in the same location, at the upper left corner of the screen, next to the tool palette.

Tile Windows

Shrinks all the images windows and repositions them so that they will fit on the screen without overlapping. Hold down the Shift key to draw tiled windows in Scal To Fit mode Scion Image supports synchronized scrolling of tiled windows. To try this out, open two or more windows (they must be the same size), tile them using Tile Windows, zoom in on one of them, then pan one of the images with the Scroll Lock key down. Notice how all the other images zoom and pan to the same relative location.

Show Paste Control

This will bring up the Paste Control dialog box. This dialog box is used for pasting operations. See Paste Control in the Windows section.

Show Full Path Names

If this item has a check next to it then the full path of files (text or images) will be shown on the title bar.

Line Selection Tools Use these tools to create straight, freehand or segmented line selections. A pop-up menu (note the little triangle) is used to select one of three line types. The pop-up menu is accessed by clicking on the line selection tools icon and holding the mouse button down for at least 1/2 second. Once you have created a line selection, you can measure its length using the Measure command, draw it using the Fill command, generate a density profile plot using the Plot Profile command, and outline the line (assuming line width is greater than one) using the Draw Boundary command. With straight lines only, you can dynamically vary the line width by clicking on the lines at the bottom of the tool palette. Freehand line selections are created in the same way as freehand region selections, except they are not required to be closed. Segmented line selections are created using a technique similar to the way polygon region selections are made, using a double-click to terminate the line. Line width is specified by clicking on the lines at the bottom of the tool palette. Straight lines can be constrained to be either vertical or horizontal by holding down the shift key. Line lengths recorded using the Measure command are given in pixels unless Set Scale has been used to perform spatial calibration. Type Control-F (Fill) and Control-1 (Measure) to quickly draw and measure the length of a line selection. Use Show Results to display the list of length measurements. Scroll Lock-Click with the text tool to label lines with the measured length. Double-click on the line selection tool to bring up the Set Scale dialog box. Line selections can be moved in the same way as region of interest selections by clicking inside the marching ants and dragging, although this has to be done carefully for one 58
pixel wide lines. Lines selections can also be nudged a pixel at a time using the arrow keys. Straight line selections have three handles drawn as small squares. The handles at either end swing and stretch the line and the one in the center is used to move the selection without changing its orientation.
Pencil Draws lines in the current foreground color. Click on the lines at the bottom of the tool palette to change the width of the line. Click in the LUT window, or Scroll Lock-Click in the image, to change the foreground color. Hold down the shift key to force pencil movements to be either horizontal or vertical.
Eraser Erases to the current background color. Click in the LUT window, or Scroll Lock-Click in the image, to change the background color. The color of the eraser indicates the current background color. The background color is used by the Cut, Clear and Photo Mode commands, and as the background color for text. Hold down the shift key to force eraser movements to be either horizontal or vertical. As a shortcut, you can double-click on the eraser to erase the entire active image.

Paint Bucket Flood fills, using the current foreground color, the area with the same color as the point you click on. Note that the hot spot is at the end of the paint coming from the bucket.
Text Tool Use this tool to add text to images using a typeface and style chosen from the Choose Font sub-menu in the Options menu. Various attributes, such as typeface, size and color, can be changed after the text has been entered. Once you choose another tool, however, or type return, the text becomes part of the images bitmap. Hold down the Scroll Lock key to get the text tool to automatically type in the most recent length, angle, or area measurement. Clicking repeatedly with the Scroll Lock key down enters multiple readings, starting with the most recent one.
Eyedropper Sets the foreground color by picking up colors from the image or from the LUT window. Control-click to change the background color. If you are using pseudocolor, double-clicking on a color in the LUT window causes the Color Picker dialog box to be displayed, allowing you to modify that color. In density slicing mode, double-clicking in the LUT window allows you to change the density slice color. Note that, when using this tool, pixel values are displayed in the Info window as RGB components.
Angle Tool Measures the angle formed by two lines drawn through a point. The angle is displayed interactively in the Info window as the lines are drawn. Use Show Results to display the complete list of angle measurements. The angle tool creates a line selection that can be used to draw the angle using the Draw Boundary command. The value of the angle can be permanently displayed in the image by Scroll Lock-clicking with the test tool.
Cross Hair Tool Counts objects and records their X-Y coordinates, leaving markers so objects are not counted twice. The markers are drawn in the current foreground color and their size is related to the current line width. Holding down various modifier keys alters the behavior of the cross hair tool. Use the control key to display X-Y coordinates. Use the shift key to decrement the count and leave a marker in the background color. Use the Choose Font sub-menu in the Options menu to vary typeface, size, etc. Use Show Results to display the list of X-Y coordinates. The cross hair tool alters the image pixel data. To avoid this, duplicate the image and work on a copy.
Line Width Allows you to vary the line width used by the line selection tool, the line drawing tool, the profile plotting tool, or the Draw Boundary command. The lines are 1, 2, 3, 4, 6, or 8 pixels wide. Line widths greater than eight can be specified in the Profile Plot Options dialog box.

W INDOWS

Image Windows
Images are displayed in windows such as the one above. Image windows are created when you use the New, Open, Import or Duplicate commands. Click on the Close Button to close the window and free the memory used to store the image. An alternate way to close the window is to click with the mouse on the Control Button. A menu will drop down and you can then choose Close. The window can be resized by clicking and dragging the corners or sides of the window. In Scale to Fit mode, the image will be rescaled to fit any resized window. For magnified images, you can use the resize the window to make it larger than its original size. A asterisk (*) is displayed in the title bar of spatially calibrated images and caret (^) if the image is density calibrated.

Paste Control Window

The Paste Control window allows you to control how image selections are pasted, or to do image arithmetic on pasted images. It is only effective during paste operations. Use the Transfer Mode pop-up menu to specify the method (Copy, And, Or, Xor, Replace or Blend) used to copy the image during a paste operation. The Paste Control window is activated by selecting Paste Control from the Windows menu, or by typing Control-Y. In the default Copy mode, pasting occurs normally. When And, Or, or Replace are selected, the selection is copied to the screen using And, Or, or Replace with Transparency modes, respectively, allowing you to see both the object being pasted and the underlying image. When attempting to align two images, it is usually easier if one of the images is first converted to binary using Make Binary, Find Edges, or Dither. Macros are available in the file More for rapidly switching among the different transfer modes. The foreground color is initially set to black and the background color to white whenever And, Or, or Replace are selected, but you can vary the foreground and background colors during the paste operation by clicking (or Scroll Lock-clicking) in the LUT window. This will produce some interesting, and possibly useful, effects. Or mode can be used to color objects in binary images created by Scion Image. Simply select the object you want to color, Copy, switch to Or mode, then select a color by clicking in the LUT window. Replace mode replaces the destination pixel with the source pixel if the source pixel isnt equal to white. Replace mode is useful for overlaying colored objects with white backgrounds (e.g. text or plots) onto another image. In Blend mode, destination pixels are replaced with the arithmetic average of the source and destination pixels. It is similar to an Add operation with Scale Math checked. Blend mode, however, works with true color images, and does not terminate the paste operation. Color images to be blended must have the same color palette. Clicking on Add, Subtract, Multiply or Divide causes the specified image arithmetic operation to be performed and terminates the paste operation. For example, clicking on Subtract subtracts the selection being pasted from the current window. If Scale Math is checked, arithmetic operations are done in two passes. In the first pass, Scion Image determines the minimum and maximum gray levels that would result from performing the operation. In the second pass, the image arithmetic is actually performed and the resulting pixel values scaled to the range of 0 to 255. Results are clipped to 0 and 255 if Scale Math is not checked. Arithmetic operations are always done on raw pixel values, ignoring any density calibration that may be in effect. Add, Subtract, Multiply and Divide only work with rectangular selections.

Averages or integrates video frames. Str is some combination of Average, Integrate, Video Rate Capture and On-chip and frames is the number of frames. Any option not specified is disabled. Set frames to zero to display the Average Frames dialog box. AverageSlices(n, slices) Averages slices in the current stack starting at slice n for slices slices. If no arguments are set, the whole stack will be averaged. Beep Makes a short sound. BEGIN Key word. Bit24ToRGBColor Converts a 24-bit color image to an RGB stack. BitAnd(n1,n2) Returns n1 AND n2. BitOr(n1,n2) Returns n1 OR n2. BlueLUT Array[0.255]. BOOLEAN Variable type. Button True if mouse button is down. Calibrate(fit, unit, m1, k1, m2, k2,.) Fit is one of straight, poly2, poly3, poly4, exp, power, log, rodbard, uncalibrated or uncalibrated od. Unit is the unit of measurement, m1, m2, etc. are the measured values and k1, k2, etc. are the known values. For example, Calibrate(Straight, Invert, 0, 255, 255, 0) sets up a simple inverting function. Use Calibrate(Uncalibrated OD) to enable uncalibrated OD and Calibrate(Uncalibrated) to disable calibration. Calibrated Returns true if current image is density calibrated. Capture Captures and displays a single video frame. CaptureColor Captures a 24-bit RGB color image. CascadeWindow Expands all the image windows to their original size and redraws them slightly offset from each other. ChangeValues(v1,v2,v3) Changes pixels with a value in the range v1-v2 to a value of v3. Chr(n) Converts a positive integer in the range 0.255 to a one character string(e.g. chr(65) = A). ChoosePic(n) Selects Nth image window without activating it. Faster than SelectPic but changes, if any, are not displayed. Also accepts PidNumbers (see description of PidNumber function). ChooseSlice(n) Selects Nth slice in a stack without displaying it. ChooseSlice is faster than SelectSlice but changes, if any, are not displayed. Use SelectSlice before exiting the macro to make sure the stack is correctly displayed. Clear Erases current ROI to background color. Close Closes the active image, text, profile plot, histogram or results window. ColumnAverage Gets the average value of each column in the specified selection and plots it in the Plot window. Concat(str1, str2,.) Concatenates a series of strings. Will also convert one or more numbers to a string. 86

Writes str to the built in serial port of the CG-7 specified by Port. Port can be PortA or PortB. Like the Write routine, it accepts multiple arguments(e.g. PutSerial(v=,v:1:2)). PutColumn(x,y,length) Copies length pixels from the built-in LineBuffer array to a column starting at x,y in the current image. PutMessage(message) Displays message in a dialog box. Like the Write routine, accepts multiple string and numeric arguments. PutPixel(x,y,value) Displays value at location (x,y). PutRow(x,y,length) Copies length pixels from the built-in LineBuffer array to a row in the current image starting at x,y. PutSerial(str) Writes str to the modem port. Like the Write routine, it accepts multiple arguments(e.g. PutSerial(v=,v:1:2)). Random Returns a random number between 0 and 1. rAngle Array[1.<Max Measurements>]. rArea Array[1.<Max Measurements>]. rCount Returns current measurement counter value. REAL Variable type. RealToString(num) Converts the real number num into a string. Redirect(b) Enables/disables redirected sampling. b=true or false. RedLUT Array[0.255]. ReduceNoise Each pixel value will be replaced with the median value in its 3x3 neighborhood. REPEAT Key word. RequiresVersion(n) Aborts macro if Scion Image version number is less than n , where n is a real number. ResetCounter Sets the measurement counter to zero. ResetGrayMap Equivalent to using the Options/Grayscale menu command or clicking on the reset icon in Map window. Reslice Reslice stack along current line section. RestoreRoi Same as the Restore Selection menu command. RestoreState Restore settings saved by SaveState. RevertToSaved Restores the previously saved version of the current image from disk. RGBToIndexed(string) Converts a 3-slice RGB stack to an 8-bit image with color LUT. Where string contains some combination of System LUT, Existing LUT, Custom LUT and Dither. Custom LUT and Dither are the defaults. RGBto24BitColor 94
Converts an RGB stack to a 24-bit color image. rLength Array[1.<Max Measurements>]. rMajor Array[1.<Max Measurements>]. rMax Array[1.<Max Measurements>]. rMean Array[1.<Max Measurements>]. rMin Array[1.<Max Measurements>]. rMinor Array[1.<Max Measurements>]. RotateLeft(b) Rotates the current image or rectangular ROI counter-clockwise 90 degrees. Creates a new window if b is true. RotateRight(b) Rotates the current image or rectangular ROI clockwise 90 degrees. Creates a new window if b is true. Round(n) Converts a real value to integer with rounding. rStdDev Array[1.<Max Measurements>]. rUser1 Array[1.<Max Measurements>]. rUser2 Array[1.<Max Measurements>]. rX Array[1.<Max Measurements>]. rY Array[1.<Max Measurements>]. Save Resaves the contents of the current image or text window. SaveAll Saves all open image windows. SaveAs(name) Saves current image using the specified name. Use SetSave to specify the format. Uses the window title as the filename when saving a text file or if SaveAs is used with no argument. When saving images, the dialog box should only be displayed the first time SaveAs is called within the macro. For both image and text windows, name can be full directory path (e.g. C:\Images\MyImage). In this case no dialog box is displayed. Accepts multiple arguments. SaveState Saves foreground and background color, new window width and height, status of Invert Y flag, text attributes, and various ScaleAndRotate and SetScaling parameters. Use RestoreState to restore the saved settings. ScaleAndRotate(xscale,yscale,angle) Scales and/or rotates the current rectangular ROI, where 0.05 <= xscale, yscale <= 25.0 and -180 <= angle <=180. ScaleConvolutions(b) Sets or resets Scale Convolutions flag in Preferences, where b=true or false. ScaleMath(b) Sets or resets Scale Math flag in the Paste Control dialog box. b=true or false. ScaleSelection(xscale,yscale) Sets the scale for the Scale and Rotate command where 0.05 <= xscale,yscale <= 25.0. Scion Array[1.4] DACA, DACB, ControlRegRO, DigitalOutput. SelectAll 95

Creates a rectangular ROI consisting of the entire image. SelectPic(n) Activates Nth image window. Also accepts PidNumbers (see description of PidNumber function). SelectSlice(n) Display Nth slice of the current stack. SelecTool(tool) Selects a tool from the tool palette, where tool is one of magnifier, grabber, pencil, eraser, brush, drawline, paintbucket, profile, wand, angletool, rectangle, oval, polygon, freehand, straightline, freehand, straightline, segmentline, lut, text, spraycan, picker and crosshair. SelectWindow(name) Activates the window with the title name. SetBackgroundColor(c) Sets the background color, where 0 <= c <= 255 (note that 0=white and 255=black). SetBinaryCount(n) Allows you to specify the number of adjacent background or foreground pixels necessary before a pixel is removed from or added to the edge of objects during erosion or dilation operations. The default is four. SetChannel(channel) Sets the video input channel, where channel=1, 2, 3, or 4. SetCounter(n) Sets the measurement counter to n. SetCursor(shape) Changes cursor shape, where shape is watch, cross, arrow or finger. SetCustom(width,height,offset,slices) Specifies the width, height, offset, and number of slices for imported files. The slices argument is optional. SetDensitySlice(lower,upper) Sets the lower and upper threshold levels, where 1 <= lower,upper <= 254. SetDensitySlice(255,255) enables it density slicing without changing the levels. SetDensitySlice(0,0) disables density slicing. SetExport(mode) Sets various file Export options, where mode is one of: Raw, MCID, Text, LUT, Measurements, Plot Values, Histogram Values or XY Coordinates. SetFont(Font name) Specifies typeface used for drawing text, where Font name is any Windows font. SetFontSize(size) Set font size in points, where 6<=size<=720. SetForegroundColor(c) Sets the foreground color, where 0 <= c <= 255 (note that 0=white and 255=black). SetImport(string) Set various file Import options, where string contains some combination of: TIFF, DICOM, MCID, Palette, Text, Custom, 8-bits, 16-bits Unsigned, 16-bits Signed, Swap Bytes, Auto-Scale, Fixed Scale, Calibrate and Open All. SetImportMinMax(min,max) Disables auto-scaling and fixes the range of imported 16-bit images and images in text (ASCII) format. SetLineWidth(width) Specifies the line width (in pixels) used by LineTo, DrawBoundary and MakeLineRoi. SetMajorLabel(Label) Replaces label used for Major column in Results window. The maximum length of the label is 9 characters. SetMinorLabel(Label) Replaces label used for Minor column in Results window. The maximum length of the label is 9 characters. SetNewSize(width,height) 96

Specifies width and height of new image windows. SetOption Equivalent to holding down the Scroll Lock key while executing the immediately following macro command. SetOptions(string) Specifies measurement options as listed in the Options dialog box. Where string contains some combination of Area, Mean, Std. Dev., X-Y Center, Mode, Perimeter(or Length), Major, Minor, Angle, Int. Den., Min/Max, User1, or User2. Any variable not listed is disabled. SetPalette(string, ExtraColors) Loads a new look-up table, where string is one of: Grayscale, PseudoColor, System Palette, Rainbow or Spectrum. ExtraColors (optional) is the number (0-6) of LUT entries reserved for extra colors. SetParticleSize(min,max) Particles smaller than min (pixels) and larger than max (pixels) will be ignored by AnalyzeParticles. SetPicName(Name) Renames the active image window. Accepts multiple arguments. SetPlotLabels(b) Specifies whether or not profile plots are to be labeled, where, b=true or false. SetPlotScale(min,max) Set min and max to zero for auto-scaling. SetPlotSize(width,height) Set width and height to zero for auto-sizing of plots. SetPrecision(digits,fwidth) Specifies the format of displayed results, were digits is the number of digits to the right of the decimal point and fwidth (optional) is the field width. SetProjection(string,n) Specifies 3D projection variables, where n is integer and string is one of the following: Initial Angle, Total Rotation, Rotation Increment, Surface Opacity, Surface DepthCueing or Interior Depth-Cueing. Use SetDensitySlice to set the transparency bounds. SetProjection(string,b) Set projections flags, where b is boolean (true or false) and string is either Save Projections or Minimize Size. SetProjection(string) Set projection options, where string is one of: X-Axis, Y-Axis, Z-Axis, Nearest, Brightest, Mean Value. SetSaveAs(mode) Sets various file Save options, where mode is one of: TIFF, RGB TIFF, BMP, LUT or Outline. SetScale(scale,unit, AspectRatio) Scale is the number of pixels per unit of measurement. Set unit to nm, m(or um), mm, cm, me, km, in, ft, mi, or pixel or us an arbitrary unit up to 11 characters in length. AspectRatio (optional) is the x/y pixel aspect ratio. Use SetScale(0,pixel) to disable spatial calibration and SetScale(0,) to activate the Set Scale dialog box. SetScaling(string) Sets ScaleAndRotate options, where string contains some combination of: Nearest, Bilinear, New Window, Same Window or Interactive. SetSliceSpacing(n) Set slice spacing(in pixels) for use by Reslice and Project commands. SetText(string) Specifies text style, where string contains any combination of: Bold, Italic, Underline, Outline, Shadow, Left Justified, Right Justified, Centered, No Background, or With Background. SetThreshold(level) Sets the threshold, where 0 <= level <= 255. SetThreshold(-1) disables thresolding. SetUser1Label(Label) 97

Replaces label used for User 1 column in Results window. The maximum length of the label is 9 characters. SetUser2Label(Label) Replaces label used for User 2 column in Results window. The maximum length of the label is 9 characters. SetVideo(string,gain,offset) Where string is some combination of Invert, Highlight, Oscillating, Trigger, Blind, Math, Blank, Pass, Color, PAL, DMA , Odd or Separate. Any option not specified is disabled. Gain and Offset (optional) are integers in the range 0-255. If the command is used like this for the CG-7 in color then each RGB channel will be set to the specified Gain and Offset. SetVideo(string, RGain, ROffset, GGain, GOffset, BGain, BOffset) This only works with the CG-7 color frame grabber board. Where string is some combination of Invert, Highlight, Oscillating, Trigger, Blind, Math, Blank, Pass, Color, PAL, DMA , Odd or Separate. Any option not specified is disabled. RGain and ROffset are the gain and offset setting for the red channel. GGain and GOffset are the gain and offset for the green channel. BGain and BOffset are the gain and offset for the blue channel. All of these gain and offsets are integers in the range 0-255. Shadow(direction) Set direction (optional) to N, NE, E, SE, S, SW, W or NW. Sharpen Precede with SetOption for greater sharpening. ShowHistogram Generates a density histogram and displays it in the Histogram window. ShowMessage(message) Displays message in the Info window. Accepts multiple arguments in the same way the Write routine does. Use a back-slash(\) to start a new line. ShowPasteControl Activates the Paste Control window. ShowResults Displays the Results window. Sin(n) Returns sine of n (radians). Skeletonize Reduces objects to single pixel wide skeletons. SliceNumber Returns number of current slice in a stack. Smooth Precede with SetOption for unweighted smoothing. SortPalette Sorts the current LUT window. Sqr(n) Returns square of n. Sqrt(n) Returns square root of n. StartCapturing Starts live video capture. StopCapturing Stops live video capture. STRING Variable type. StringToNum(str) Converts a string to a real number. Returns zero if the string contains no digits. Subtract This command is equivalent to clicking the Subtract button in the Paste Control dialog box. This must be used immediately after the Paste command. Precede with SetOption to switch paste transfer modes, otherwise the operation is performed and the paste operation 98

I NSIDE SCION I MAGE FOR W INDOWS

General Information. 2

About this Document..2
Macro Examples, Techniques & Operations. 2
What is a macro and why write one?..2 Before you begin..3 For the programming beginner..3 Macro global vs. local vars.3 Putmessage, ShowMessage & Write..4 Switching and choosing windows..5 How to input a number or string..6 Looping...6 Regions of Interest (ROI)..7 Detecting the press of the mouse button..8 Detecting press of option, shift and control keys.8 Measurement and rUser Arrays.9 Placing macro data in the "Results" window.9 Operating on each image in a stack (SelectSlice).10 Accessing bytes of an image..11 Reading from disk (importing)..12 Batch Processing..12 Avoiding a macro dialog box..13 TickCount...14 Accessing an image Look Up Table (LUT).14 Placing time and date into your data.15 PlotData notes...15
General Information About this Document
This document is intended for beginners who never studied programming but need to use software and get the most out of it. You might have an image processing application that needs doing and don't want to figure out all the aspects of Windows. You can build your image processing application into the Scion Image program and save yourself from a lot of wasted effort. Hopefully, this manual may help you on your route to writing simple or complex macros.
Macro Examples, Techniques & Operations What is a macro and why write one?
A macro is text containing a sequence of calls or routines which Scion Image interprets and executes. To write a macro, you can choose "New" then "text window" to create a text window within Scion Image. You load the macro using "Load Macro". A rich set of example macro routines is distributed with the Scion Image program. You can try some of these out and borrow code from them in order to write your own macro. Simple macros, such as the one below, are useful utilities to save time and effort. This macro is an example of a macro which follows the same operations that could be performed by you from the Scion Image menus. It's operation is to clear anything outside of the Region of Interest (ROI) which you draw. Macros can, of course, be much larger and can include looping, calculations and basically an entire imaging application.
MACRO 'Clear Outside [C]'; {Erase region outside ROI.} BEGIN Copy; SelectAll; Clear; RestoreRoi; Paste; KillRoi; END;

Before you begin

It should not be hard for you to start writing a macro. You will want to do several things before you begin. Appendix A in the Scion Image users manual provides you with a complete list of all macro calls. The list is organized by the Scion Image menus and then is categorized in alphabetical order. After this locate the macros directory distributed with Scion Image. Open, load and examine some of the macros. Try using "Find" from the "Edit" menu on one of the open macros. "Find" is fairly useful in helping you debug a macro. It allows you to go to sources of error when you get error messages during the load or execution of a macro.
For the programming beginner
You probably don't need to study programming to write a macro. Depending on the complexity of your application, you might be able to pick up everything you need by examining some of the macros in the macros directory. To some a confusing aspect of writing macros is understanding what a function is and how it is used. A function returns a value or a boolean (true/false). In the example below, nPics is a function which will return an integer number of pictures open. KeyDown(control) returns a true or false depending on whether you hold the control key down.

Macro 'Function demo'; begin {Here is an example use of the nPics function returning a value} showmessage('Number of images open: ',nPics); {Here is an example use of keydown function returning a boolean} If KeyDown('control') then putmessage('Number of images open: ',nPics); end;
Macro global vs. local vars
Just as in pascal, C, or other programming languages, you can have a local or global variable. A global variable is declared at the top of the macro file and can be utilized by any procedure or macro in the file. A local variable is declared in the procedure or macro in which it is used. For the example macro set below, "A" and "B" are local to the 'Add numbers' macro. "Answer" is globally declared and used by both macros.
VAR Answer:real; Macro 'Add numbers'; Var A,B: real; begin A := Getnumber('Enter the first number',2.0); B := Getnumber('Enter the second number',3.14); Answer := A+B; end; Macro 'Show Answer'; begin ShowMessage(' The added result is: ', Answer:4:2); end;
Putmessage, ShowMessage & Write

PutMessage

PutMessage is perhaps one of the easiest ways to provide feedback to users. To use putmessage you simply call the routine with the message or string you wish to give to the user.
PutMessage('This macro requires a line selection');
You can pass multiple arguments with PutMessage if you needed to.
PutMessage('Have a ', 'Nice day');

ShowMessage

ShowMessage allows display of calculations, data, variables or whatever you caste as a string into the Info window.
Here is a simple example of output to the Info window:

ShowMessage('x1 = ',x1);

You can use the backslash ('\') character to do a carriage return for macros:
ShowMessage('Average Size=',AverageSize:1:2,'\TotalCount=',TotalCount);
You can also write data or info onto the image window with a macro call to Write or Writeln.
Diameter := Width / PixelsPerMM; {in MM.} MoveTo(300,10); Write('Diameter = ', Diameter:5:2,' mm.');
Switching and choosing windows
There are a number of ways to switch between windows in a macro. For the most part you will need to use the PidNumber function to identify a unique ID for that window. Pidnumber is a function which returns a value. For example you might have:
var MyPicID:integer; begin MyPicID := PidNumber; Duplicate('Duplicate image'); {some process} SelectPic(MyPicID); {To go back to the original}
Here the returned value from the PidNumber function was assigned to a variable called MyPicID. The variable MyPicID was then used later on in the macro to select the picture. As an alternative to SelectPic, you could have used ChoosePic(MyPicID). This would have selected the picture but would not have made it the active front window. This is useful when you flip between many windows, but do not need to activate the window. As a second alternative, you could can use SelectWindow('Window name') to select the window by its title.

How to input a number or string
Making a call to getnumber will allow you to enter a number into your macro. The GetNumber macro will return a real number, or if assigned to an integer variable, such as in this example, it will not pass the decimal digits.
var MyGlobalNumber:integer; macro 'Number input'; begin myGlobalNumber:=GetNumber('Enter number of iterations:',0); end;
The idea is the same for entering a string
var MyString:string; macro 'String input'; begin MyString:=GetString('What name?','Data'); end;

Looping

The Scion Image macro language has the standard set of pascal loops. This includes "for" loops and "while" loops. The Scion Image macro language is (almost) a subset of Pascal and the Pascal FOR statement does not have a BY option. Instead, use a WHILE loop. For example:
i:=1; while i<=fred do begin {process} i:=i+10;
Regions of Interest (ROI)
Before you start looking at macro ROI's an introduction to coordinates is worthwhile. See the picture below for a general guideline. Regions of interest are characterized by 'marching ants' which surround a selection.

Getting ROI information

GetRoi(left,top,width,height)
You will want to call this macro routine if you need any information about the current ROI. The routine returns a width of zero if no ROI exists.

ROI creation

SelectAll
The Selectall macro command is equivalent to the selects all of the image and shows the ROI's 'marching ants'.
MakeRoi(left,top,width,height)
This is as straight forward as the name implies.
MakeOvalRoi(left,top,width,height)
Not terribly differing to implement from MakeROI. If you want a circular ROI set width and height to the same value. See the example below.

Altering an existing ROI

MoveRoi(dx,dy)
Use to move right dx and down dy.

InsetRoi(delta)

Expands the ROI if delta is negative, Shrinks the ROI if delta is positive.
Other routines involving ROI's

RestoreROI,KillRoi

These are opposities. Copy,Paste,Clear,Fill,Invert,DrawBoundary
Detecting the press of the mouse button
The example below shows a macro which operates until the mouse button is pressed. Button is your basic true or false boolean and becomes true when the button is pressed.
macro 'Show RGB Values [S]'; var x,y,v,savex,savey:integer; begin repeat savex:=x; savey:=y; GetMouse(x,y); if (x<>savex) or (y<>savey) then begin v:=GetPixel(x,y); ShowMessage('loc=',x:1,', ',y:1, '\value=',v:1, '\RGB=',RedLUT[v]:1,', ',GreenLUT[v]:1,', ',BlueLUT[v]:1); wait(.5); end; until button ; end;

Detecting press of shift and control keys
The macro "KeyDown(key)" (Key = 'shift', or 'control') returns a boolean true or false. It returns TRUE if the specified key is down. The example macro below can be run on any stack, using shift to delay more or control to delay less.
macro 'Animate Stack'; var i,delay:integer; begin RequiresVersion(1.56); i:=0; delay:=0.1; repeat i:=i+1; if i>nSlices then i:=1; Wait(delay); SelectSlice(i); if KeyDown('shift') then delay:=1.5*delay; if delay>1 then delay:=1; if KeyDown('control') then delay:=0.66*delay; ShowMessage('delay=',delay:4:2); until button; end;
Measurement and rUser Arrays
There are a number of arrays in macros, but there are two varieties the measurement arrays and the rUser arrays. You can store macro data and results in the rUser arrays. These arrays are not affected by the Measurement counter (rCount) which works with measurements arrays such as rMean[rCount], rArea, etc. The current rCount for these is changed by doing a measurement or calling SetCounter. Example of storing data to the rUser arrays:
rUser1[1]:=SomeNumber; rUser2[1]:=SomeOtherNumber;
If you have more than two sets of data which you'd like to keep, and because there are only two rUser arrays, then you can access other macro arrays. This includes rArea, rMean, rStdDev, rX, rY, rMin, rMax, rLength, rMajor, rMinor, and rAngle. However you will need to be careful because these arrays are affected by the rCount value and you could write over your data. An example use of measurement arrays outside the intended use is a snipet of code from the Export look up table macro:
for i:=0 to 255 do begin rArea[i+1]:=RedLut[i]; rMean[i+1]:=GreenLut[i]; rLength[i+1]:=BlueLut[i]; end;
Here rArea, rMean and rLength are used for Red, Green and Blue instead of area, mean and length.
Placing macro data in the "Results" window
If you have particular information, data, calculated results, or any type of numeric data which you want to keep, you can redirect it into the Results window. Use the SetUser label commands to title your field name. The rCount function keeps the current index of the measurement counter. Since rUser1 and rUser2 are arrays, you specify the index of the array with the rCount value. See below.
macro 'Count Black and White Pixels [B]'; { Counts the number of black and white pixels in the current selection and stores the counts in the User1 and User2 columns. } begin RequiresVersion(1.44); SetUser1Label('Black'); SetUser2Label('White'); Measure; rUser1[rCount]:=histogram[255]; rUser2[rCount]:=histogram[0]; UpdateResults; end;

Saving results data to a tab delimeted file
You can also save data from the macro, to a tab delimeted text file by adding several commands in your macro:
SetExport('Measurements'); Export('YourFileName');
Operating on each image in a stack (SelectSlice)
By using a loop (for i:= 1 to nSlices) you can operate on a series of 2D images. The nSlices function returns the number of slices in the stack.
macro 'Reduce Noise'; var i:integer; begin if nSlices=0 then begin PutMessage('This window is not a stack'); exit; end; for i:= 1 to nSlices do begin SelectSlice(i); ReduceNoise; {Call any routine you want} end; end;
See the series of stack macros distributed with the Scion Image program for more examples.
Extracting a substring from a string
Below is an example macro that will allow you to pull a substring out of a string.
{ An example routine to return a substring from a string in Scion Image macro. } var ReturnString:string; procedure copystring(SourceString:string,index:integer,count:integer); begin;
ReturnString:=SourceString; if index > 0 then Delete(ReturnString,0,index); Delete(ReturnString,count+1,length(ReturnString)-count); end; macro 'test copystring' var TestString:string; begin TestString:='This is a test'; copystring(TestString,11,4); PutMessage('The Returned String is : ' ReturnString); end;
Accessing bytes of an image
The macro commands GetRow, GetColumn, PutRow and PutColumn can be used for accessing the image on a line by line basis. These macro routines use what is know as the LineBuffer array. The example below is a macro which uses the linebuffer array. If you are interested in using a macro to get at image data, this example should be fairly clear.
Macro 'Invert lines of image' var i,j,width,height:integer; begin GetPicSize(width,height); for i:=1 to height do begin GetRow(0,i,width); for j:=1 to width do begin LineBuffer[j] := 255-LineBuffer[j]; end; PutRow(0,i,width); end;
Reading from disk (importing)
One simple way to load data from disk is to create a window and dump information to it. An example of this is a macro which imports files created by the IPLab program. The macro reads the first 100 bytes from the file into a temporary window. It erases the window when it is through finding useful header information.
macro 'Import IPLab File'; var width,height,offset:integer; begin width:=100; height:=1; offset:=0; SetImport('8-bit'); SetCustom(width,height,offset); Import(''); {Read in header as an image, prompting for file name.} width := (GetPixel(8,0)*256) + GetPixel(9,0);
height := (GetPixel(12,0)*256) + GetPixel(13,0); Dispose; offset:=2120; {The IPLab offset} SetImport('16-bit Signed; Calibrate; Autoscale'); SetCustom(width,height,offset); Import(''); {No prompt this time; Import remembers the name.} end;

Batch Processing

It's easy to write a macro to process a series of images in a directory as long as the file names contain a numerical sequence such as 'file01.pic', 'file02.pic', 'file03.pic', etc. Below is an example macro that does this.
macro 'Batch Processing Example'; { Reads from disk and processes a set of images too large to simultaneously fit in memory. The image names names must be in the form 'image001', 'image002',., but this can be changed. } var i:integer; begin for i:=1 to 1000 do begin open('image',i:3); {process;} save; close; end; end;
Avoiding a macro dialog box
You should be able to process many files and only have to see one dialog box. For example, only one dialog box appears when you run the following macro as long as 'A', 'B' and 'C' are in the same directory.
macro 'test'; begin Open('A'); Invert; Save; Close; Open('B'); end;
Another way to avoid the dialog box is to use full directory paths as in the following example.
macro 'test'; begin Open('c:\images\A');
Invert; Save; Close; Open('c:\images\B'); Invert; Save; Close; Open('c:\images\C'); Invert; Save; Close; end;

TickCount

Ticks are counted at the rate of 60 per second. You can varify this by running the enclosed macro and timing the interval between beeps.
macro 'TickCount Test'; {"Beeps" every 10 seconds} var interval,ticks:integer; begin interval:=600; ticks:=TickCount+interval; repeat if TickCount>=ticks then begin beep; ticks:=ticks+interval; end; until button; end;
Accessing an image Look Up Table (LUT)
You can modify the way an image appears by altering the RedLUT, GreenLUT and BlueLUT. This is simple and straightforward enough. You can access the RedLUT, GreenLUT and BlueLUT arrays from both macros and from Pascal. Here is an example macro which finds any gray or black components in a color image and sets them to white. It's useful for seperating certain kinds of medical data.
macro 'Remove Equal RGB [V]'; {Changes only the LUT, removes gray component from an image} var i,Value:integer; begin for i:=1 to 254 do begin If ((RedLUT[i] = BlueLUT[i]) and (RedLUT[i] = GreenLUT[i])) then begin RedLut[i] :=255; BlueLut[i] := 255; GreenLut[i] :=255; end;
end; ChangeValues(255,255,0); {remove black} UpdateLUT; end;
Placing time and date into your data
Here is a macro that writes the current date and time to a text window. It also stores results into the text window. Here is what the output from this macro looks like: Date=94:5:31 Time=14:45:24 Area=10000.000 Mean=80.198

macro 'Write Results to Text Window'; var year,month,day,hour,minute,second,dow:integer; begin GetTime(year,month,day,hour,minute,second,dow); Measure; NewTextWindow('My Results'); writeln('Date=',year-1900:1,':',month:1,':',day:1); writeln('Time=',hour:1,':'minute:1,':',second:1); writeln('Area=',rArea[rCount]:1:3); writeln('Mean=',rMean[rCount]:1:3); end;

PlotData notes

A command exists in the macro language for making profile plot data available to macro routines. It has the form "GetPlotData(count,ppv,min,max)", where count is the number of values, ppv is the number of pixels averaged for each value, and min and max are the minimum and maximum values. The plot data values are returned in a built-in real array named PlotData, which uses indexes in the range 0-4095. The macro "Plot Profile" in the "Plotting" file illustrates how to use GetPlotData and PlotData. To help explain further. 1. For a count value of n the PlotData array will have meaningful values from 0 to n-1 (higher array values are accessible but will contain old/meaningless results). 2. Count is equal to the line length, in pixels, rounded to the nearest integer value. 3. Substantially more pixels are usually highlighted by a line selection, and this seems to have only an approximate corelation with the pixels used by PlotData.
4 The PlotData array contains real-numbers (not integers) which presumably are derived from a weighted average of pixels rather than being the values of single pixels - even when ppv is 1. Because of this it is not possible to relate PlotData values to single locations. 5. My conclusion after some experimentation is that; after and GetLine(x1,y1,x2,y2,lw); GetPlotData(count,ppv,min,max);
The following function will probably return the centre of the location used to derive PlotData[c]: ypos:=y1+(c+0.5)/(count)*(y2-y1); xpos:=x1+(c+0.5)/(count)*(x2-x1);