
Image SXM history        v1.55        ( Jun 94 - Jan 95 )
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v1.55    ·B    (30 Jan 95)

Added features:
	¥	Image SXM can now read image files produced by the Burleigh instructional air STM. The image scale, sample voltage and tunnelling current settings are read from the parameter block at the end of the file (the last 40 bytes). The same tilt compensation routines are employed as for Omicron STM files.

Bug fixes:
	¥	None.

Other changes:
	¥	None.
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v1.55    ·9    (15 Dec 94)

Added features:
	¥	The histogram can now be drawn using the same LUT (look-up table) as the image for which it is calculated. Uncheck the relevant item in the 'Preferences' dialog box to display the old black and white histogram. Using a greyscale histogram is particularly useful when density slicing (see items in 'Other changes'). 
 
Bug fixes:
	¥	None.

Other changes:
	¥	The 'Browse SEM' command can now be used to browse PICT and TIFF files as well as SEM image files.
	¥	Browsing SEM and STM images can now handle up to 100 images in a montage window.
	¥	SEM images can now be loaded and displayed in a window reduced to 20%, 25%, 33% or 50% of full size. This option is set in the 'SEM Options' dialog box. A new 'Resize Window' command has been added to the SEM menu to change the window size to preset values. This does not affect the option of auto size reduction on loading.
	¥  After selecting phase % (or black and white %) calculation when density slicing (or thresholding), the % is continuously recalculated if the user varies the slice limits (or threshold level). If a different image is selected, or a selection of the current image is made or moved, then the histogram is recalculated to ensure that subsequent % calculations are correct. Calculation of the histogram may take several seconds for large images.
	¥	When density slicing with a histogram visible, the slice limits can be set by dragging in the Histogram window. Previously, this could only be done in the LUT window.
	¥	The two variants of Image (SEM and STM) now assign some cmd-key shortcuts to menu items independently (i.e., cmd-B is a shortcut for 'Browse Images...' from the SEM menu when running Image SEM, and the same key is a shortcut for 'Browse Images...' from the STM submenu when running Image STM).
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v1.55    ·8    (20 Nov 94)

Added features:
	¥	Two new commands have been added to the 'Spectroscopy' submenu of the STM menu. 'Save As Reference' saves the current STS spectrum to act as a reference for future STS plots. 'Subtract Reference' displays the difference between the current spectrum and the reference spectrum. This option remains on (with the menu item checked/ticked) until the menu item is selected again. When the mouse is clicked in the STS plot window, a cursor is displayed in the image window indicating the position of the pixel for which the most recent STS spectrum was measured. If a reference spectrum has been saved, its position is indicated by the centre of the 'R' character drawn in the image window.
	¥	A new menu item has been added to the 'Parameters' submenu of the STM menu. 'Print Parameters' now prints the principal parameters relating to the image in the front window. 'Print Params for File(s)...' prints the principal parameters for a selected file or all files in a selected folder.
	¥	The aspect ratio of the Info window can now be toggled between two preset values by selecting the 'Info Window Horizontal Format' option in the Preferences dialog box. The preferred aspect ratio is saved with 'Record Preferences' in the 'File' menu. The normal format is unchanged and the horizontal format may be found to be more suitable for smaller video monitors (12"-14").

Bug fixes:
	¥	None.

Other changes:
	¥	In common with the Profile Plot window, the contents of the STS plot window can now be copied and pasted into an image window (e.g., for comparison between many STS curves). Also, the I-V data can be exported to a text file.
	¥	The procedures that display and print STM acquisition parameters now also handle STS parameters and the scan angle (the nominal angle between the X axis of the scan and the true horizontal).
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v1.55    ·7    (7 Nov 94)

Added features:
	¥	The STM menu has been rearranged so that commands relating to calibration of STM images are grouped together in a separate 'Calibration' submenu. A new 'ReCalibrate Z...' command has been added (and the old 'ReCalibrate...' command has been renamed 'ReCalibrate XY...' to avoid confusion). The command is designed to be called after step height measurements have been made. The mean value of up to 10 of the most recent step height measurements is calculated and the user types in the corresponding known value. The ratio of these two values is calculated and the Z scale of the image rescaled accordingly. This ratio can be used subsequently to calibrate other images using the 'Apply Z Calibration' command.
	¥	A new 'Spectroscopy' submenu has been added to the STM menu. STS spectra can be automatically loaded and displayed continuously as the crosshair cursor is moved over the image (the crosshair tool is to the right of the angle tool). An STS data set requires typically about 2-3 Mbytes of free memory. The maximum number of data points per spectrum is 100. Only one data set can exist at any one time. Using the 'Measure' command on a rectangular or freehand area selection will calculate the average STS spectrum for all the pixels selected. Various options can be set in the 'STS Options' dialog box. 

Bug fixes:
	¥	None.

Other changes:
	¥	The FFT buffers are now only created when items from the FFT menu are selected. Thus, if FFTs are not required then no memory is used. When the user has finished with the FFTs, the 'Free Memory' command will dispose of the buffers and release the memory that they used (about 1.5 Mbytes). This will probably be necessary to allow the STS routines to work after using FFTs.
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v1.55    ·6    (23 Oct 94)

Added features:
	¥	A new 'FFT' menu has been added to Image SXM. Direct and inverse FFTs can be calculated, and there are menu options for filtering the original image (with a cosine mask) and the FFT. The FFT algorithms are limited to square images whose size is an exact power of 2 up to 256x256. With the selection tool selected, option-clicking in an image will select the largest such square.
	¥	A new 'ShadowPlot' procedure has been added to the STM menu. This brings up a dialog box which allows the user to specify the direction from which the surface is viewed and the direction from which is illuminated. Rendering the image at full resolution (step size=1) can be slow on some Macs, and so it is recommended that the step size is large (>4) while experimenting with different view and lighting angles.

Bug fixes:
	¥	None.

Other changes:
	¥	Because of the computational demands of the FFT and Shadow Plot routines, Image SXM is now available in two versions - one that uses a floating point co-processor (FPU) and one that doesn't. The FPU version will not run on any Mac without an FPU (including a PowerMac) and displays an 'F' in the bottom right corner of the 'About Image SXM...' window. Calculating an FFT for a 256x256 image on a Quadra 900 takes 8 s (with FPU) and 38 s (without FPU). Creating a Shadow Plot rendered at full resolution takes 170 s and 315 s, respectively.
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v1.55    ·5    (10 Oct 94)

Added features:
	¥	Two new commands have been added to the SEM menu: 'Phase %' and 'B&W %'. The former is used when density slicing to calculate the percentage area of the image that has a grey level lying within the user-selected range (i.e., the % of the image that is coloured red). The latter is used when thresholding to calculate the percentage area of the image that is black and white. In both cases the calculated values are displayed in the Info and Results windows.

Bug fixes:
	¥	Fixed a bug (introduced when shuffling bits of code around) that caused Image SXM to crash if the machine RAM was less than 8 Mbytes or the monitor resolution was less than 832x624 pixels.

Other changes:
	¥	The font and font size used in the Plot window are now those set by the user rather than being fixed to the default settings (Geneva 9pt).
	¥	Minor cosmetic changes to the display of LUT values in the Info window.
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v1.55    ·4    (4 Sep 94)

Added features:
	¥	None.

Bug fixes:
	¥	None.

Other changes:
	¥	The values of step height and error (see v1.55 ·3) are now stored and displayed in the Results window. The precision is set to 2 automatically when step heights are calculated.
	¥	If a Plot window does not overlap the active image window, its size is preserved each time it is updated (previously, it always reverted to its default size).
	¥	The following keyboard shortcuts have been added: Browse (cmd-B) ReCompensate (cmd-R).
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v1.55    ·3    (2 Sep 94)

Added features:
	¥	When displaying a plot profile (cmd-K) of terrace steps in an STM image it is useful to be able to calculate the height of a step edge. This can now be done by selecting 'Calc Step Height' (or cmd-H rather than cmd-K). The same plot profile is produced, with the addition of tick marks at the one-third and two-thirds positions indicating the regions over which the mean heights of the terraces have been calculated (i.e., the middle third is ignored). If the terraces are tilted or highly corrugated on either side of the step a warning is displayed in the Info window above the value of the calculated step height. The value may be meaningless if the terraces are not flat on both sides of the step.

Bug fixes:
	¥	None.

Other changes:
	¥	None.
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v1.55    ·2    (1 Sep 94)

Added features:
	¥	None.

Bug fixes:
	¥	Minor cosmetic bug fixes.

Other changes:
	¥	The 'ReCompensate' command has changed slightly. It will now leave the dynamic range of the Z values in the image unchanged, but will shift the greyscale such that the mean value of Z in the selected region is in the middle of the scale. If you prefer the original operation, in which the image greyscale is reset to give maximum contrast in the selected region, then press the option key before selecting the 'ReCompensate' command (the menu item will appear as 'ReComp+Rescale' rather than 'ReCompensate').
	¥	The 'User4' variable displayed in the Results window, originally intended to hold the title of the active window every time a measurement is made, can now hold a user comment if the option key is pressed before selecting the 'Measure' command (the menu item will appear as 'Measure (comm)'
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v1.55    ·1    (21 Jul 94)    General release

Functionally identical to v1.55  §4.
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v1.55    §4    (30 Jun 94)

Added features:
	¥	None.

Bug fixes:
	¥	An incorrect minus sign has been removed from the calibration routine.

Other changes:
	¥	The 'Change File Names...' command now recognizes 'TEXT' files as well as 'iSXM' files, so filenames can now be changed even if the types are not set correctly.
	¥	The 'Change File Types...' command now works by checking filenames rather than the file creator and file type of the original file(s), so it will now work for files other than text files.
	¥	Reshuffled bits of code around, hopefully without introducing any new bugs!
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v1.55    §3    (28 Jun 94)    Development version.  Tested by STM users in Liverpool.

Added features:
	¥	None.

Bug fixes:
	¥	ReCalibration caused an 'Out of Memory' error if the lattice vectors chosen were more than ¹/2 from the positive x-axis. The calculation of the window size required to display the rotated image now uses ¹ minus the rotation angle if the latter is > ¹/2.

Other changes:
	¥	None.
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v1.55    §2    (26 Jun 94)    Development version.  Tested by STM users in Liverpool.

Added features:
	¥	None.

Bug fixes:
	¥	None.

Other changes:
	¥	Added submenus to STM menu.
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v1.55    §1    (26 Jun 94)    Development version.

Added features:
	¥	The original NIH Image v1.55 has a number of modifications with respect to v1.54, but the most important are (i) surface plots can now use a gradient colour fill, and (ii) a faster 'Scale and Rotate' algorithm has been implemented. The latter means that recalibrating the XY spatial scales of STM images (see next item) is much faster than could be achieved with v1.54.
	¥	Two new commands have been added to the STM menu. 'ReCalibrate...' allows the user to specify two surface vectors (using the Angle Tool) and then specify the known dimensions of and angles between these vectors. The image is then manipulated using rotation, magnification and skew transformations to make the specified points appear in the correct relationship to each other. The parameters required to calibrate the image in this way should be independent of the image being analysed (providing that the calibration of the STM itself does not change) and so these parameters can be saved in a file in the Preferences Folder. The same transformations can be applied to any other images using the 'Apply Calibration' command.

Bug fixes:
	¥	None.

Other changes:
	¥	None.
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