Image SXM History

History 1993-2000

Listed here are all the changes that have been made to Image SXM from its origins
in 1993 up to April 2000. For a list of more recent changes, see the History file. 162 | 161 | 160 | 159 | 158 | 157 | 155 | 154

162-7 (26 Apr 00)

Added features:

Two options have been added that affect the display of NanoScope III images: (i) the LUT can be set to the z range specified in the header rather than the full z range of the image, and (ii) the colour table specified in the header can be applied to the image rather than the default greyscale. The options are set by check boxes in the 'SPM Options' dialog box (with 'Digital Instruments' selected from the pop-up menu).
A 'Digital Instr' submenu has been added to the 'Color Tables' submenu, containing a number of the colour tables used in Digital Instruments software. If the option key is pressed then the submenu changes to 'Save Digital Instr' and the current colour table can be assigned to the menu item selected (with a change of name if desired). It is not advisable to change the resource ID of the colour table unless you know what you are doing.
Support has been added for SBIG CCD camera images.

Bug fixes:

When executing 'Browse', 'Batch Conversion' or 'Open All' operations, images will open only once. In most situations, opening an Omicron parameter or spectra file also opens the corresponding topographic image. This is a desirable feature when opening files one at a time, but it meant that when an image file and a parameter file were both opened, the image would be loaded twice. This behaviour is now suppressed when executing those operations that open all files in a folder. Not strictly a bug, but it was an annoyance to some users.

Other changes:

When editing a rectangle or line ROI, the Shift key and 'F' key now have the same effect as when creating the ROIs (ie, the Shift key constrains rectangular ROIs to be square and line ROIs to be horizontal or vertical; the 'F' key constrains the size of rectangular ROIs or the length of line ROIs to be equal to a power of two, ensuring that they are suitable for subsequent FFT operations).
The number of users who have returned the User Feedback form is disappointingly low. Reminders requesting the return of the form will appear with increasing frequency after the application has been launched 50 times. The reminders can be switched off by entering a number given in my email reply to the return of the form.

Changes to macros:

None.

162-6 (20 Feb 00)

Added features:

Two new items have been added to the SPM/Spectroscopy submenu, 'Make STS Map...' and 'Make STS Stack'. The first makes an image in which the pixel values are the STS currents at a user-specified voltage, and the second makes a stack of images in which each slice is an STS voltage. The z scale of the images is determined by the min and max scale values set in the 'SPM Options' dialog box.
A new 'Trim Image' item has been added to the SPM/Images submenu. If the option key is pressed then the blank space surrounding an image will be eliminated, otherwise it will be trimmed down to a 10-pixel border.

Bug fixes:

The default font size is now not changed by the 'Display Calib Bar' procedure.
Multiple browse windows can now be used when browsing selected images (images can be deselected from browse windows by option-clicking on them).

Other changes:

Selecting 'Better' in the '3d Plot' dialog box produces a higher-quality 3d plot, about twice the size as that produced by 'Faster', but it is significantly slower and requires more free memory (approx 50 times the image size, eg 12 Mb for a 512x512 image).
Options to set the foreground (pen/paintbrush) and background (eraser) colours of an image after loading have been added to the 'SXM Options' dialog box.
Header format variations have been seen in NanoScope III image files that have identical version numbers. These variations should be handled better now, but there may be more of them as yet undiscovered.
The 'Change File Types' command now sets to 'TEXT' those files whose suffix is '.par'. This deals with file types that may have been set incorrectly (eg, after text files have been FTP'd to the Mac as binary files).
The maximum number of images in an SPM stack has been increased to 256.
The maximum number of files that can be sorted into alphanumerical order has been increased to 1000.

Changes to macros:

Three new macro commands have been added to handle STS data: 'MakeSTSmap', 'MakeSTSstack' and 'SetSTSoptions'. The first two are described above and the third allows the min and max scale values to be set for the display of STS data as spectra or images.

162-5 (6 Dec 99)

Added features:

Support has been added for Molecular Imaging SPM images.
Support has been added for LEO SEM images.
Support has been added for Noran Vantage images.
Support has been added for FITS images.
Support has been added for Zeiss LSM (Laser Scan Microscope) images.
A new 'Preset Scale' submenu has been added to the Analyze menu. The spatial calibration of an image can be set to one of 8 preset values. Press the option key to save the spatial calibration of an image. Press the shift key to clear a preset value. This submenu can be used, for instance, to store the spatial calibration values corresponding to a selection of objectives of an optical microscope. The values are saved in the prefs file.

Bug fixes:

If 'Auto Get Info' was selected from the 'SXM Options' dialog box, the image info would be displayed before the z scale was updated, giving incorrect values for 'Depth'.
The 'Display Calib Bar' procedure would use the wrong colour to draw the bar if the display was set to 16-bit or 24-bit.

Other changes:

An option to automatically display a calibration bar whenever a preset scale (see above) is selected has been added to the 'Display Calib Bar' dialog box.
Holding the shift key down now suppresses the 'Save...?' dialog boxes for text as well as image windows.
On G3/G4 keyboards, the '§' key is to the left of the '1' key, and so for consistency cmd-§ now has the same effect as cmd-` (to the left of '1' on older keyboards), namely resizing the current window to 50%.
A few minor changes have been made to default window positions.
An option to open a new Session Log automatically has been added to the 'SXM Options' dialog box.

Changes to macros:

None.

162-4 (24 Oct 99)

Added features:

Support has been added for Wyko OPD images. Real (32-bit) and integer (16-bit) image data can be loaded, and the parameters of the most recently loaded image can be listed from the 'Dump All Parameters' menu item in the SPM/Parameters submenu.
A new '3 Point Compensation' item has been added to the SPM/Compensation submenu, complementing the existing compensation items. After selecting three points with mouse clicks, the image is reloaded such that the three points appear at the same apparent height. The option and shift keys enhance and reduce, respectively, the contrast in the rectangular region enclosing the three points selected.
A new 5x5 hybrid median filter has been added to the 'Rank Filters...' dialog box. It replaces each pixel with the median value of (a) the median value of pixels on horizontal and vertical axes, (b) the median value of pixels on diagonal axes, and (c) the pixel value itself.

Bug fixes:

A bug in the Histogram routine made it run at about half its usual speed. This also affected inverse FFTs as they use a histogram to determine if a mask has been drawn on the FFT.
For images loaded from files containing 32-bit image data, the compensation menu items are now dimmed (as the compensation algorithms are implemented only for files containing 16-bit image data).
Shapes found in the 'Size Distribution' routine were not displayed.

Other changes:

The 'Depth Of Focus' algorithm for compositing slices in a stack has been modified. A dialog box allows the user to optimise the calculation for their images by setting the distances over which the calculation of the degree of focus is carried out. The dialog box is suppressed if the option key is pressed.
Balloon Help has been added for the 'Rank Filters...' dialog box.
Updated 'About This Mac...' to recognise G4 Macs and CPUs.
All windows now adopt the style used by the System rather than the (old) style defined in NIH Image. When running under System 8, all windows will be a few pixels larger than under System 7. To arrange the LUT, Tools, Map and Info windows neatly: (i) Uncheck the 'Save Window Positions' checkbox in the 'Preferences' dialog box and save the prefs, (ii) Quit and relaunch Image SXM, (iii) Check the 'Save Window Positions' checkbox and save the prefs.

Changes to macros:

None.

162-3 (23 Jun 99)

Added features:

None.

Bug fixes:

Images stored as unsigned integers (such as SPM images from Burleigh, Omicron or TopoMetrix) would not load correctly using the line-by-line compensation routines.

Other changes:

The size of all line buffers, which determines the maximum width of images that can be handled, has been increased from 4096 to 8192 pixels. As a result, the amount of memory used by Image SXM to store code and data has increased by 300 K to 1600 K.

Changes to macros:

None.

162-2 (30 May 99)

Added features:

A new 'Overlay Grid' item has been added to the SPM/Images submenu. This procedure draws a grid of parallel lines on the current image. If a rectangle or polygon region of interest (ROI) exists when this is selected then that ROI will be used for the initial grid outline. The number of cells along each axis can be changed by pressing a numeric key when the cursor is placed over the top left or bottom right corners of the grid. The grid shape and size can be modified by dragging the corners of the grid. The sizes and angles of the two vectors defining the grid lattice are displayed in the Info window. Grids can be saved, restored and propagated from one image to another in the same way as for any other ROIs.
A new 'Show Unit Cell' item has been added to the SPM/Images submenu. This procedure displays the contents of the unit cell, defined by the grid overlay (see above), by superposing all pixels in the region of interest. To obtain the registry of an adsorbate relative to a substrate lattice displayed in a separate image, the grid can be created and edited on the substrate image and then copied to the adsorbate image using 'Propagate/ROI' or the 'Save ROI' and 'Restore ROI' submenus.

Bug fixes:

Changes to NIH Image v1.62, made after Image SXM 162-1 was compiled, have been incorporated.

Other changes:

STS data in the Omicron SCALA format are now supported as for those from the earlier Omicron format. The spectra can be displayed individually by clicking on a specific pixel (using the selection tool), or displayed continuously as the cursor is moved over the image (using the crosshair tool). They can also be averaged by pressing the option key or by measuring over a region of interest.
Options to display smoothed STS spectra and to shift the STS spectra such that I=0 at V=0 have been added to the 'STS Options' dialog box.
The plot values of force curves and other line scan data can now be exported.
The 'Export...' item in the File menu now changes to 'Export Options...' if the option key is pressed. This allows various options to be set, including writing header information to exported data files and some control over the data formatting.
The 'SXM Preferences...' dialog box has been extended to include easy access to options for batch conversion, export, and particle analysis.
When thresholding the Info window now displays the z value corresponding to the threshold level.
Screen Machine framegrabber images can now be browsed.
Inverting the LUT using cmd-option-I now flips the z calibration over to preserve the z values of features.
The default memory allocation has been increased from 8 to 12 Mb.

Changes to macros:

Two new macro commands have been added, 'GetZscale' and 'GetXYscale'. 'GetZscale' provides access to the value and units of the z scale calibration, complementing the existing NIH Image macro command 'GetScale' for the xy scale calibration. 'GetXYscale' is functionally identical to 'GetScale' and is provided to reduce ambiguity. The 'GetScale' macro command is retained for backwards compatibility.
'KillROI' and 'RestoreROI' now save and restore the xy coordinates used to define a polygon or freehand ROI and so that after restoring a ROI a measurement of the perimeter/length does not give a zero value. Note that the coordinates of the ROI are also saved when the window is closed (using 'Close' or 'Dispose') or another window is selected (using 'NextWindow' or 'SelectPic') and that the coordinates of the ROI are also restored when the slices of a stack are selected (using 'AddSlice', 'DeleteSlice', 'ChooseSlice' or 'SelectSlice').
A new 'RequiresSXMversion' macro command has been added to complement the NIH Image macro command 'RequiresVersion'.
Macros can now access the rUser3, rUser4 and rUser5 data arrays.
A new 'PlotUserData' macro command has been added to plot the data in the rUser arrays.

162-1 (21 Apr 99)

Added features:

A new 'Auto Register' item has been added to the Stacks menu. This procedure brings all the slices of a stack into registry with the current slice using cross-correlation of the images. The shift applied to each slice is recorded in the Session Log. The corresponding macro procedure is 'AutoRegister'.
Two new submenus 'Save ROI' and 'Restore ROI' have been added to the Options menu. Up to eight ROIs can be saved and restored later to any image.
Image SXM can now read JEOL SPM image files.

Bug fixes:

NIH Image v1.62 fixes a number of bugs present in v1.61. See the NIH Image documentation for details.
The 'Tip Locus Effect' calculation did not account correctly for a parabolic-shaped SPM tip.
When switching between windows some images could update incorrectly.

Other changes:

Browsing now reads images in alphanumerical order (ie, numbers embedded in filenames are handled numerically rather than alphabetically).
The 'cmd-cursor arrow' shortcuts now work for any image file. Pressing 'cmd-right' or 'cmd-down' will load the next file in the same folder as the current file. Pressing 'cmd-left' or 'cmd-up' will load the previous file.
Balloon Help for the NIH Image menu items has been rewritten and extended to include SXM items that have been added to existing menus.
Improved support for Screen Machine framegrabber image format.
The on-line help pages can now be displayed if the monitor is set to any bit depth.

Changes to macros:

The 'Surface Roughness' item now has a corresponding macro function 'SurfaceRoughness'.
The 'ResizeWindow' macro now has an integer parameter (% = 20, 25, 33, 50, 100, 200, 400).

161-9 (14 Dec 98)

Added features:

A new 'DNA Strand Lengths...' item has been added to the Analyze menu. This procedure uses the 'Analyze Particles' routine to find strands of DNA molecules in SFM images and measure their lengths. If appropriate, the image is first processed using the 'Curvature' procedure (see below). The image is then thresholded at the 'background' level, smoothed and thresholded again at the 'analyse' level to rejoin fragments of strands that were fragmented by the first thresholding. After the particle analysis has been carried out, the aspect ratio of each particle is calculated and particles with low values are rejected. The lengths of the strands (calculated from their perimeters and areas, correcting for end effects) are displayed under the heading 'StrL' in the Results window. The user-defined measurement 'User2' is used to store the particle numbers corresponding the the labelling of particles carried out by the 'Analyze Particles' routine. The corresponding macro procedure is 'StrandLengths'.
A new 'Curvature' item has been added to the Process menu. It applies four convolution kernels in succession (equivalent to calculating the curvature in the horizontal, vertical and two diagonal directions) and then adds the resulting images together. The curvature values are truncated above zero to enhance regions with high negative curvature (ie, it enhances the tops of 'mountains' and suppresses the bottoms of 'valleys'). This procedure is used by the 'DNA Strand Lengths...' analysis procedure (see above).
A new 'Surface Roughness' item has been added to the SPM/Calculation submenu. The values of rms deviation from the mean (rms) and absolute deviation from the mean (Ra) are calculated for z values within a selected region (or the entire image if no ROI is selected). The values are displayed in the Info window (together with the max-min z values) and are also logged to the Session Log.

Bug fixes:

The image compensation procedures, when used with the shift key pressed, did not correctly ensure that all pixels in the image were within the range of the LUT (ie, some pixels could saturate).
SPM images from RHK Technology were displayed inverted top-to-bottom and the z values displayed in the Info window were in units of m, not nm!
The 'List Params for File(s)...' procedure in the SPM/Parameters submenu could leave some image windows open after extracting their parameters. The windows were offscreen, and hence not visible, but appeared in the Windows menu list.

Other changes:

Updated support for Digital Instruments NanoScope III v4.41.
Selecting 'Calibrate Distortion' with the option key pressed now leaves the aspect ratio of the shape unchanged rather than using the fixed aspect ratio specified by 'Change Aspect Ratio'.

161-8 (8 Aug 98)

Added features:

A new 'Tip Locus Effect' item has been added to the SPM/Images submenu. This compensates for the effect of a finite-radius SPM tip imaging a surface. The radius of the parabolic tip should be set to a value comparable to the apparent resolution of the image. Entering tip radii that are too large can produce unphysical results. The corresponding macro commands are 'TipLocusEffect' and 'SetTipRadius'.
A new 'Surface Area' item has been added to the SPM/Calculation submenu (see 'Other changes'). The value is displayed in the Info window, together with the selected area (xy projection) for comparison. The value of the surface area is also logged to the Session Log. The corresponding macro function is 'SurfaceArea'.
Image SXM can now read Oxford Instruments TOPSystem 3 SPM image files.

Bug fixes:

Histograms of rectangular selections would produce multiple entries in the Session Log.

Other changes:

A new 'Calculation' submenu has been added to the SPM menu. The 'Calc Step Height' menu item has moved from SPM/Images to SPM/Calculation.
The 'Image Correlation' menu item has moved from SPM/Images to the Analyze menu.
The 'Add Axes and LUT' menu item has been renamed 'Display Axes'. If the option key is pressed, this changes to 'Display Axes and LUT'. The corresponding macro command has been renamed 'DisplayAxes'.
A number of minor changes have been made to entries in the Session Log.
Pressing the Caps Lock key when the cursor is in a Profile Plot window will change the display in the Info window from values of X and Y to values of dX and dY relative to the original point.

161-7 (6 Jun 98)

Added features:

None.

Bug fixes:

Balloon Help did not display correctly for the SXM menus (a bug in the CodeWarrior compiler?).
Digital Instruments NanoScope III images earlier than v4.22 would load with spurious error messages.
Some menu item keyboard shortcuts were not set correctly for 'Image SEM'.
The date did not display correctly in the 'About...' box for some date formats.

Other changes:

None.

161-6 (16 May 98)

Added features:

Over 40 macro commands have been added to the existing complement of 250 to give access to most of the procedures in Image SXM. New items have been added to the Help menu -- 'Image SXM Macros' provides on-line help with the macro syntax (the macro names and parameters can be copied from any page using the usual copy command), and 'List Macros' produces a text window listing all the macro names and parameters. As for the Image SXM Help pages, an independent application 'SXM Macro Help' is provided from which all the pages can be printed.
The macro function 'GetStrFromWindow' has been added to extract strings from a text window. This function has no menu item equivalent. It allows, for instance, image file headers or parameter files to be loaded into a text window and the text read as strings by a macro. The associated command 'ResetGetStr' resets the function so that it reads from the beginning of the text window.
The macro command 'ReDrawPlot' has been added to enable a profile plot to be redrawn after the plot data has been modified by the user.
A new 'Session Log' item has been added to the Options menu. This creates a text window that records image loading, processing, and saving operations and the corresponding window name. If the limit of 32K characters is reached then either (i) the text is saved and a new window created, or (ii) the first entries are deleted. The default action is the first, but can be changed by pressing the option key when 'Session Log...' is selected.
A new 'Gradient Values...' item has been added to the Analyze menu (and 'Slope Histogram' has been renamed 'Gradient Histogram' for consistency). This produces a stack of two images: the first gives the magnitude of the local gradient and the second gives the uphill direction relative to one of the cardinal points. Moving the cursor over the first image produces a display in the Info window of both the gradient and direction.
The gamma of the LUT can be set interactively by clicking in the Map window with the control key pressed. As the mouse is dragged around the Map window, its x position determines the gamma value (from 0.4 to 2.5, or 0.05 to 20 with the shift key pressed) which is displayed in the Info window.
Image SXM can now read RHK Technology SPM images.

Bug fixes:

An 'unexpected quit' could occur if memory ran out during a 3d Plot.

Other changes:

Updated support for SPM images acquired using recent versions of commercial image acquisition software:
Omicron SCALA v2.2, TopoMetrix SPMLab v4, Digital Instruments NanoScope v4.31, Park Scientific HDF.
Image SXM can now read Digital Instruments NanoScope III scope data files.
The limit on images sizes in the 3d Plot routine (previously 1024 pixels image width) has been removed.
3d Plot windows larger than the screen size now have the plot centred in the window and a progress bar.
Browsing images is now more flexible -- multiple browse windows can be open and active simultaneously (so browsing through a folder does not deactivate any browse windows created previously).
Loading browse images and data created by a previous browse resets the image counter and so deactivates any open browse windows.
The maximum number of images that can be browsed has been increased to 1000.
Option-clicking an image in a browse window deselects it, indicated by the image being greyed-out. Selecting 'Browse Images...' with the option key pressed ('Browse Selected Images...') will create a browse window with only the selected images displayed.
In the dialog box for the 3d Plot the preview is not updated while a number is being edited.
Gradient Histograms (previously known as 'Slope Histograms') saved as PICT or TIFF files and loaded back in will now give the correct xyz values in the Info window.
After displaying the average of a set of profiles in the Profile Plot window pressing 'H' will calculate the step height of the averaged profile. (Pressing cmd-H will calculate the step height for the current profile as usual.)
When making a circle or square selection in an FFT window, the Info window now displays the frequency and period corresponding to the size of the selection. Pressing cmd-option-L or cmd-option-H will apply a low-pass or high-pass filter and then perform an inverse FFT. After making an annular selection, pressing cmd-option-B will apply a band-pass filter and then perform an inverse FFT.
The diamond symbols that appear in windows displaying images that are spatially or intensity calibrated can be suppressed using a checkbox in the Preferences dialog box.
The 'About This Mac...' information (for those who haven't yet found it, press the option key and look in the Options menu) has been updated to deal with the latest Mac models.
The function keys F1 to F4 (undo, cut, copy and paste) are now functional for images and text.

161-5 (4 Oct 97)

Added features:

A new 'Hough Transform' item has been added to the Process menu and a 'Size Distribution' item to the Analyze menu. The latter calculates the size distribution of circles within an image using Hough transforms for a range of circle radii. A demo image is in the 'Demo images' folder.
The FFT command can now be applied to Profile Plots. Selecting a line while pressing the 'F' key constrains the length of the selection to be an integer power of two, making it suitable for a subsequent FFT.
A new 'Depth Of Field' item has been added to the Process menu. This produces an image which is a weighted average of the images in a stack. The weighting factor varies for each pixel and is dependent upon the the contrast in surrounding pixels. Thus the weighting depends on how well that part of the image is focused, and so the composite image will compensate for the limited depth of field of images.
Support has been added for images saved as text files containing xyz data values. The x, y and z values on each line can be separated with spaces, tabs or commas. The filenames should be suffixed '.xyz' or '.XYZ'.
Support has been added for TGA image files. These images are loaded in the same way as 24-bit RGB TIFF images -- a stack of red/green/blue images plus a colour composite image are produced.
A new 'Batch Conversion' item has been added to the SPM/Files submenu. It can load all the SXM images in a selected folder and save them in PICT or TIFF format in either the same folder (with the file type appended to their filenames) or in a new folder.
Support has been added for Scion PCI framegrabbers.

Bug fixes:

After browsing a folder containing DI NanoScope III force curves, some windows were left open.
The z scale calibration of Burleigh v2 images was read incorrectly.
The z scale calibration of DI NanoScope II images was calculated incorrectly.
Unchecking 'Add RGB Colours to LUT' in the Profile Plot Options dialog box would cause Image SXM to quit.
Some Park Scientific Instruments SPM images would load with dimensions of µm rather than Å or nm.
Using cmd-arrow to load images numerically adjacent to the current image did not interpret the hexadecimal digits in Park Scientific Instruments HDF image filenames correctly.

Other changes:

Using cmd-arrow to load images numerically adjacent to the current image now skips missing image files.
Comments are now read from Park Scientific Instruments HDF image files.
In the Browse dialog boxes, selecting or changing folders now returns the user back to the dialog box again.
Items in the SPM/Files submenu that are specific to Omicron STM images are now dimmed if 'Omicron' is not selected in the SPM Options dialog box.

161-4 (30 Apr 97)

Added features:

Support for Park Scientific Instruments HFS-LIF images has been improved. Dual images, each taken at a different bias voltage, can be loaded and displayed either in separate windows or in a stack.

Bug fixes:

Browsing large 16-bit TIFF images, such as 4 Mb images produced by Gatan DigiScan, could cause problems if Image SXM was not allocated sufficient memory.

Other changes:

The warning message "The text file xxx is actually an image file..." that was posted if a text file was found to contain an image (indicating that the file has the wrong file type) has been suppressed by user request.
Resizing a window using the Windows/Resize Window submenu or the keyboard shortcuts cmd-1, cmd-2 or cmd-4 will now clip the window to stay onscreen and attempt to position the point under the cursor centrally in the window.
When saving a browse window ('Browse in xxx'), an additional data file ('Data xxx') is now saved which contains information such that, when the browse window is reloaded, double-clicking to load the images that were browsed still works. The two files must stay together, but need not be in the same folder as the images browsed. This means that an index of images on CDs can be created and saved for future use. This is very useful for PhotoCDs, where generating a browse window containing many large images can take many minutes.
STS spectra can now be averaged by option-clicking. The STS Plot window will display a running average until the user clicks in the image without the option key pressed.
The content of an STS Plot window can now be duplicated into an image window using the standard 'Duplicate' menu item or keyboard shortcut cmd-D. This is now consistent with the behaviour of Profile Plot windows.
The icons used by Image SXM now default to those defined by NIH Image. Select 'Use Image SXM Icons' in the Preferences dialog box if you want to use the greyscale icons for Image SXM and its associated files.

161-3 (20 Apr 97)

Added features:

None.

Bug fixes:

Creating an image caption would place the caption window offscreen on monitors less than 640 pixels wide.
In the 'SXM Preferences' dialog box, switching Balloon Help off would cause Image SXM to quit.

Other changes:

A 'User Feedback' item has been added to the Help menu. I am asking all users to feed back to me information about (i) who/where they are, (ii) the SEM, SPM or SAM system that they use, (iii) the Mac on which Image SXM runs, and (iv) how they obtained their copy of Image SXM. The specification of the Mac is generated automatically. Comments, as always, are welcome.
The 'Match LUTs' menu item now changes to 'Change LUTs' if the option key is pressed. A dialog box then allows the user to specify the min/max values of z used to display each open image, and the LUT of each image is changed accordingly.
Image SXM now handles images produced by version 2 of the Burleigh Instructional STM software.

161-2 (23 Mar 97)

Added features:

None.

Bug fixes:

Images that have been post-processed by WA Technology SPM software may not have the correct z scale calibration. This bug has not been fixed, but the user is warned of the problem.
The on-line Help pages are not displayed if the monitor is not set to 8-bit (256 colours or greys) or 'Desktop Friendly' is selected (in the Preferences dialog box). Displaying the pages if the monitor was set to 16-bit or 24-bit could cause a crash. Displaying the pages if 'Desktop Friendly' was selected gave an unreadable display. The application 'Image SXM Help' can be used if on-line help is not available for either of these reasons.

Other changes:

Closing a text window containing a dump of parameters relating to Digital Instruments or WA Technology SPM images no longer produces a 'Save?' dialog box.

161-1 (9 Mar 97)

Added features:

Captions can now be added below a printed image by selecting the 'Create Image Caption' item from the SPM/Parameters submenu. The caption can be updated automatically using the 'Auto Update Image Caption' checkbox in the SXM Options dialog box. The caption can have up to 255 characters and can be split into any number of lines. After editing, the first 64 characters of the caption can be copied to the comment (the menu item changes to 'Save Caption As Comment' when the frontmost window is a text window) so that they will be saved with the image.
Image SXM can now read hkl mesh (diffraction) data generated by SPEC data acquisition software.

Bug fixes:

None.

Other changes:

Grid lines can now be added to profile plots. The 'Profile Plot Options...' dialog box has an extra checkbox, and also the grid lines can be added to or removed from the plot in the frontmost window by pressing 'G'.
Image SXM has had a Spring clean. This has involved moving some code around to make the internal structure more logical and thus improve the ease with which future modifications can be introduced. This should have no effect on the applications created, but the probability of introducing a bug in the process is not insignificant.

161-beta-3 (10 Feb 97)

Added features:

Image SXM can now read DME Rasterscope™ SPM images. The z scale calibration has not yet been verified.

Bug fixes:

The z scale calibration of Park Scientific HDF images was read incorrectly.
The 'Open All' checkbox in the 'Open...' dialog box now works for Digital Instruments NanoScope III force curves and WA Technology IV curves.

Other changes:

None.

161-beta-1 (19 Jan 97)

Added features:

None.

Bug fixes:

NIH Image v1.61 fixes a number of bugs present in v1.60. See the NIH Image documentation for details.
Image SXM would quit if a 3d Plot was created with 'Use Image LUT Colours' and 'Better' both selected.
The display precision of the xyz values of an inverse FFT were often incorrect.

Other changes:

The 'Save changes to...?' dialog box has been enlarged so that long names do not get truncated or disappear.

160-8 (18 Dec 96)

Added features:

Five new items have been added to the SPM/Calibration submenu. 'Calibrate Distortion' calibrates the geometric distortion caused by viewing a surface at an angle to the normal (seen in low-magnification SEM images of tilted surfaces or images of a viewing screen of a TEM). This correction can be applied subsequently to other images using the 'Apply Correction' command. Calibration data can be saved to a specified file or, if the option key is pressed, the default file 'Image SXM Geom Dist Calib' in the Preferences folder (which will be read automatically when Image SXM initialises). Data can be loaded from either a text file or from a text window. Requested by an Image SXM user.
Four new text translation items have been added to the SPM/Parameters submenu. These enable parameter files (or any other text files) to be translated between Mac and Unix or PC formats.
A new 'Differentiate' item has been added to the Process menu. The local gradient (top-left to bottom-right) is calculated for each pixel and scaled such that zero gradient is in the middle of the LUT. If the option key is pressed then the scale is expanded by a factor of x3.
A new 'Set Z Scale...' item has been added to the SPM/Calibrate submenu which allows the Z scale of images to be set by direct manual input of the Z values of the black and white pixels. Requested by an Image SXM user.
A new 'Slope Histogram...' item has been added to the Analyze menu. This produces a 2d histogram of the x and y slopes of the pixels in a rectangular region of interest (ROI). Requested by an Image SXM user.
Image SXM can now read Digital Instruments NanoScope III EC (electrochemical) STM images.
Image SXM can now read old-format Park Scientific Instruments images.

Bug fixes:

Pressing cmd-Z (for 'Undo') produced the 'Z' cursor. A zoom window can be produced only if the command key is not pressed, and so the cursor should not have changed.
Fixed a bug that caused a crash if a 16-bit TIFF image could not be loaded due to lack of memory.
Omicron SPM image files use the identifying letters 'tb' for one of two distinct purposes: as a prefix it identifies a friction image (old Omicron format) and as a suffix it means 'topographic backward' (new Omicron format). As a result of this, Image SXM could confuse new-format images with old-format images.
After selecting the 'Calibrate...' item, the display of the calibration curve was incomplete.
'Revert to Saved' ignored the 'Å' or 'nm' or 'µm' setting in the 'SPM Options' dialog box.

Other changes:

A 'View History' item has been added to the Help menu. It displays this file and so provides a convenient way for the user to check on the most recent modifications to Image SXM.
When memory is low, opening an image can be quite slow as it is loaded line by line. The user is now warned of this situation and a progress bar is displayed during loading.
Axes can now be added to a 3d Plot by checking a checkbox in the dialog box. Axes can be added or removed from an existing 3d Plot window by typing cmd-option-A. To get the perspective of the axes right with respect to the image the 3d Plot routine has been partly recoded. As a result it is about 10% slower.
A 'Faster/Better' pair of radio buttons has been added to the 3d Plot dialog box. The 'Faster' option produces a 3d plot as previously. The 'Better' option enlarges the image, makes a 3d plot, smooths the plot and then reduces the size of the plot window slightly. The result is a higher quality 3d plot, but it takes about 4 times longer to draw and requires more free memory. Unlike for the 'Faster' option, the view angles of 3d plots created using the 'Better' option cannot be altered using the cursor keys. I would suggest that the 'Better' option is only used when you are sure of the view/shadow/magnification settings.
New-format Omicron SPM images will now load even if their parameter files are left in their original Unix format.
Support for Gatan Digital Micrograph (DigiScan) images has been improved.

160-7 (27 Oct 96)

Added features:

Image SXM can now read images from the Gatan DigiScan system saved in PICT, TIFF or native Gatan format. The TIFF image loading routines have been modified to handle the 16-bit TIFF images.
Image SXM can now read images saved by the Screen Machine frame grabber made by Fast Electronics GmbH.

Bug fixes:

When browsing Omicron SPM images using 'Browse Omicron...' the window title was displayed in the wrong font and size.
The text of two Balloon Help items were interchanged in the 'ReCalibrate Z...' dialog box.
In the 'Set Scale...' dialog box, changing the units from the pop-up menu would leave the display of the 'Known Distance' entry unchanged even though the scale had been changed. This was a bug in NIH Image.

Other changes:

Cosmetic changes have been made to all dialog boxes. They now have a grey background and some sets of radio buttons or checkboxes have been grouped together in an attempt to clarify their function. In dialog boxes that have had Image SXM items added to the original set of NIH Image items, these have now been separated for clarity. If you prefer the original white background to all dialog boxes, uncheck the 'Use Greyscale Dialog Boxes' item in the 'Preferences' dialog box. The change will take effect immediately.
A number of modifications have been made to the browsing routines. When browsing, the dialog box that appears after the window fills with images now has 'Print' button. A 'Print All Images' checkbox, added to both the 'Browse Images' and 'Browse Omicron' dialog boxes, will print all images browsed without bringing up the usual 'Print' dialog box. In addition, 'Browse Images' can be set to skip a specified number of images (which defaults to the number browsed previously).
The 'Get Info' display can be brought up automatically whenever an SXM image is opened or selected. This option is controlled from a checkbox in the 'SXM Options' dialog box.
When Image SXM opens a text file bigger than 32 kbytes, it tests to see if it is actually an SXM image file with the file type set incorrectly. If so, then it loads the image. If not, then it treats it as a text file.
If a line profile is too short to be used for the calculation of step heights (< 20 pixels), the user is informed.
The action required to create a Zoom window has been changed from Tab-click to z-click. The Zoom window, introduced in Image SXM v1.57, is a small window showing a magnified view of the region of the image around the cursor (default 2x magnification, 4x if the shift key is also pressed). The zoomed image can be temporarily frozen by pressing the caps lock key.

160-6 (6 Jul 96)

Added features:

A new 'Image Correlation' item has been added to the SPM/Images submenu. It produces a plot of the correlation between the intensities of pixels in the first image in a stack and those in the second. The value of a pixel in the correlation plot indicates the number of image pixels that have a given value in the first image (X-axis) and the second image (Y-axis) at the same position in each image. It is functionally the same as the 'imagecorrelation' macro posted on zippy.nimh.nih.gov, but is 100 times faster.

Bug fixes:

The independent Z scales for each slice in a stack of SPM images were incorrect if a slice was added or deleted manually after the stack was created. A slice added to such a stack will by default have the Z scale calibration of the slice after the current slice.
The image data types of multiple images in Digital Instruments NanoScope III files are now displayed correctly by 'Get Info'.
Browsing NanoScope III files containing multiple images would leave 'phantom' windows listed in the Windows menu.
After applying the 'Match LUTs' command the Z scale calibrations are now displayed correctly by 'Get Info'.

Other changes:

The 'SXM Help...' menu item, previously the first item in the SEM and SPM menus, has been moved to the Help menu (the '?' in the menu bar). The Help window can be left open when selecting 'Windows to Stack' from the Stacks menu -- it will be closed automatically and re-opened at the same page after the stack has been made.
WA Technology SPM images that have pixel aspect ratios other than unity (ie, different X and Y scales due to image processing by the acquisition software) now have the image stretched along one axis to restore the same spatial scale on both axes. This ensures that profile plots are labelled correctly.
'MatchLUTs' now only affects images that have Z scales with the same units as that of the frontmost image.
The icons used for Image SXM and its associated files can now be reset to the standard NIH Image icons by deselecting a checkbox in the 'Preferences...' dialog box.

160-6T (24 Jun 96) Test Release

Added features:

Image SXM can now read Digital Instruments NanoScope force curves. The curves are plotted (by the same routines that are used to plot line profiles) and then copied into an image window. The size of the plot windows and the choice of displaying extending or retracting curves are set in the 'SPM Options' dialog box (select Digital Instruments from the pop-up menu). Other options are set from the 'Profile Plot Options' dialog box. This new feature was requested by an Image SXM user.
Data from WA Technology IV spectra and Digital Instruments NanoScope force curves can be exported by choosing the Plot Values button in the 'Export...' dialog box. This will work only for the IV spectrum or force curve loaded most recently.
Two new items have been added to the 'FFT' submenu to be used with diffraction images. Low-energy electron diffraction (LEED) images can be transformed into real space images using 'Inverse FFT of LEED'. The LEED image is converted into an FFT and then an inverse FFT operation is applied. The LUT of the LEED image will be inverted if necessary. Converting a LEED image into an FFT using 'Make LEED into FFT' will enable the display of frequency and period values in the Info window (as for any 'normal' FFT) but will not apply an inverse FFT.

Bug fixes:

None.

Other changes:

Image SXM will now attempt to load any Digital Instruments NanoScope II image file, providing that the data file type read from the header is greater than 1 and less than 10. Previously, it would only load image files of data file type 7.

160-5 (15 Jun 96)

Added features:

A new 'Match LUTs' item has been added to the SPM/Images submenu. It changes the look-up tables of the open image windows such that they all have the same Z scale calibration (nm per grey level). This new feature was requested by an Image SXM user.

Bug fixes:

Converting 'Windows to Stack' or 'Stack to Windows' would crash Image SXM if there were more than ten images. This was due to the maximum number of images in an SPM stack being set to ten. Any number of images can now be stacked, but only the first ten slices can have independent Z scales and units (see 159-1).

Other changes:

None.

160-4 (12 Jun 96)

Added features:

None.

Bug fixes:

As a result of modifying the Profile Plot routines for WA Technology IV spectra and profiles of FFTs, the spatial scale of an image was inadvertently altered by the profile calculation.

Other changes:

Changing file types in the System Folder or Applications folder is now not permitted.

160-3 (9 Jun 96)

Added features:

None.

Bug fixes:

If selected via the 'SXM Preferences' dialog box, making changes in the 'LUT Options' dialog box would make Image SXM quit.
The last image loaded from a file containing multiple images would be displayed with a greyscale LUT, regardless of the LUT of the original image.

Other changes:

A JEOL WinSem image will now load even if the associated parameter file is missing or corrupt. The spatial scale will be uncalibrated.

160-2 (2 Jun 96)

Added features:

None.

Bug fixes:

The 'Image Math...' routines did not handle operations between FFTs correctly. This was a result of a small difference between the FFT routines in Image SXM v1.55-1.58 and those introduced into NIH Image v1.59. Some of the FFT macros, such as autocorrelation, use these routines and thus are now working OK.
Constraining line selections in FFTs is now more robust. One 'bug' still remains: Dragging the end of an existing line selection through an X or Y axis such that the line length reduces to zero momentarily will result in a one-pixel displacement of subsequent profile plots. This is a result of the 'start' and 'end' of the line selection being swapped over, and is awkward to fix.

Other changes:

The latest release of the CodeWarrior compiler generates more efficient PowerPC code compared to earlier versions, resulting in slightly faster execution speeds. The speeds tabulated in the last two pages of the Help display have not yet been updated. As an indication of the improvement: On a Power Mac 8100/100, the integer benchmark has dropped from 0.8 to 0.6 s and the floating point benchmark has dropped from 0.9 to 0.8 s.
Profiles can now be averaged. Pressing 'S' when a profile is displayed will store the current profile data. The line selection can be moved and the new profile stored an unlimited number of times. Pressing 'D' will display an average of the stored profiles. The Info window displays a count of how many profiles have been stored.

160-1 (19 May 96)

Added features:

None.

Bug fixes:

The display of frequency and period values in the Info window for FFTs of images with no spatial calibration was incorrect.
The display precision of measurements in the Results window was incorrect.

Other changes:

Plots of WA Technology IV spectra are now labelled with the filename in the top right corner.

160-beta-4 (15 May 96)

Added features:

Image SXM can now read WA Technology IV spectra files v3.0-v4.04. The spectra are plotted (by the same routines that are used to plot line profiles) and then copied into an image window. Pressing the option key while the IV spectrum is loaded will smooth the data. The size of the plot windows is set in the 'SPM Options' dialog box (select WA Technology from the pop-up menu) and other options are set from the 'STS Options' dialog box (shortcut: double-click or option-click in an IV plot window). This new feature was requested by an Image SXM user.

Bug fixes:

The units displayed in the 'ReCalibrate Z...' dialog box were 'Å' rather than the actual units of the current image.

Other changes:

The 'Unsharp Mask' command in the Process menu now uses a custom 11x11 convolution kernel. The effect of applying this convolution is the same as for the previous implementation (which subtracted from the original image a copy of the image that had been smoothed by convolution with a Gaussian). Pressing the option key uses a 7x7 kernel (faster, but less detail of the original image is retained). Pressing the shift key uses a 15x15 kernel (slower, but more detail is retained).
The 'SXM Help...' display can now be activated using the 'help' key on Apple extended keyboards. Also, the user can move from page to page by clicking in the bottom left or bottom right corners of a page.
Opening Omicron SPM image files that contain two images (scan left -> right and right -> left) now loads both images and labels them '>>>' and '<<<', respectively.
The code that handles the various image file formats that Image SXM supports has had a Spring clean. The number of formats supported is now more than a dozen, and the code was in need of a tidy up. Chunks of code that were similar for more than one format were combined and redundant code removed. This should not have any effect on loading images, but the probability of introducing a bug in the process is not insignificant.

160-beta-3 (1 May 96)

Added features:

None.

Bug fixes:

If a line selection is nudged more than once to update a Profile Plot, then the line selection is redrawn on the image between each update. This ensures that the line selection is seen to move in synchronisation with the changing Profile Plot.
The 'OpenAll' checkbox in the 'Open...' dialog box now works again on SXM images (the bug was fixed in 159-beta-2, but reappeared when the SXM routines were spliced into NIH Image v1.60).

Other changes:

When browsing SXM images, the user now has the choice of displaying the images either at a fixed size (small = 64 pixels, large = 128 pixels wide) or at a fixed reduction factor (chosen from four values, as before). Borders are now drawn around each image (in black or white, depending on the background colour selected).
The compensation routines can now alter the LUT of the resulting image to cover all pixels in the image, eliminating saturated pixels. Thus, there are now three modes of operation: (a) selecting compensation (or recompensation) with no modifier keys pressed will apply the compensation and leave the LUT unchanged; (b) pressing the option key will enhance the contrast so that the image within the region of interest uses all the greys in the LUT; (c) pressing the shift key will reduce the contrast so that the entire image lies within the range of the LUT.

160-beta-2 (13 Apr 96)

Added features:

None.

Bug fixes:

The Profile Plot axes were not redrawn properly if the following three conditions were met: (i) an image window overlapped with the Profile Plot window, (ii) the option key was pressed to produce a profile overlay, and (iii) the line selection was dragged with the mouse rather than nudged using the arrow keys. If these conditions occur, the axes are now redrawn (causing some flicker on slower Macs).
After applying selective recompensation to an image, the next image to be loaded would have the compensation applied selectively rather than to the entire image. This bug has been fixed.
A memory leak in the compensation routines that would slowly eat up free RAM has been fixed.

Other changes:

Image headers saved in all PICT and TIFF files now store the identity of the original SXM format. This allows users of more than one type of SEM, SPM or SAM system to identify the origin of a PICT or TIFF image.
The maximum number of Z values in an image has been increased to 128K. Although 16-bit images can contain no more than 64K different Z values, calculating tilt or curvature compensation over a small selected region can yield a wider range of values if the surface is highly corrugated.
The keyboard shortcut cmd-option-D has been added for the 'Display Parameters' item of the SPM/Parameters submenu.
A new method of expanding the contrast of an image has been added. Double-clicking the LUT tool (the one above the 'A' in the Tool window) with the option key pressed puts two markers in the LUT and Histogram windows. The user can drag these markers and then select Apply LUT (cmd-L) to expand the contrast such that black and white then correspond to these markers. This option was requested by an Image SXM user.
The 'Browse Omicron...' command now recognises AFM friction images.

160-beta-1 (9 Apr 96)

Added features:

None.

Bug fixes:

NIH Image v1.60 fixes a number of bugs present in v1.59. See the NIH Image documentation for details.

Other changes:

The first items in each of the SEM and SPM menus have been renamed 'SXM Help...' and now produce a window which displays a sequence of help pages. These contain general information about Image SXM and a description of all the commands available from the SEM and SPM menus. The user can move from page to page using the '<' and '>' keys (and also the home, end, page up and page down keys).
A checkbox in the 'SPM Options' dialog box now allows the user to suppress the display of the window title suffix that indicates the compensation mode(s) that have been applied to the image.
When making a rectangular selection in a (non-FFT) image, pressing the Shift and 'F' keys constrains the selection to be a square of size equal to a power of two. This is an alternative to the 'Select Largest Square' command in the FFT submenu.
When selecting a rectangular or elliptical region of interest within an FFT image, pressing the Shift key constrains the selection to be a square or circle centred on the origin of the FFT. This makes filtering the FFT easier before doing an inverse FFT.
When the frontmost image is an FFT, the keyboard shortcut cmd-I executes an 'Inverse FFT' rather than the usual 'Get Info' command.
The Z scale calibration of old-format WA Technology STM images is now calculated using a slightly different algorithm. This should give the correct calibration for all such images, but is still largely untested.

159-2 (27 Mar 96)

Added features:

The compensation routines (available from the SPM/Compensation submenu) that were written for loading images from 16-bit data files, have been modified to work on 8-bit images. If a compensation item is selected for an SPM image, then the original (raw) 16-bit data will be loaded from the image file and used to generate the new image. If the image is not an SPM image (ie, an image loaded from a PICT or TIFF file that may, or may not, have originated from an SPM image) then the 8-bit data used to display the image in the window will be used to generate the new image. Applying the compensation routines to the smaller range of Z values in an 8-bit image, compared to the raw 16-bit data, will result in lower image quality, but has the advantage of allowing various compensation modes to be applied sequentially if desired.
The content of a Profile Plot window can now be duplicated into an image window using the standard 'Duplicate' menu item or keyboard shortcut cmd-D. This allows, for instance, many different profiles to be displayed, stacked, montaged, etc.
Substantial changes have been made to the way that the Profile Plot command works, controlled by check boxes added to the 'Profile Plot Options' dialog box. If the 'Colour Profile Plots' box is checked, then the profile will be drawn in the current foreground colour as indicated by the colour of the brush in the Tool window. (Note: Up to 6 colours can be added to any LUT from the 'LUT Options...' dialog box.) If the 'Add RGB Colours to LUT' box is checked, then the three primary colours will be added to the current LUT and the foreground colour set to red by default. The profile will be updated dynamically as the line selection is moved around the image, either by dragging with the mouse or by nudging using the arrow keys. The profile can be frozen by pressing the CapsLock key. Pressing the Option key changes the 'Plot Profile' menu item to 'Overlay Profile' and a second profile will be drawn without erasing the existing profile. This also will be updated dynamically. If the foreground colour selected for the overlay profile is the same as that used for the original profile, then an alternative colour will be selected automatically. If the 'Add Grey Border' box is checked, then a light grey border and drop shadow are added to the display.
Image SXM can now read Omicron AFM friction images (the default filename identifier is 'tb'). This has been tested on only a limited number of images.
Image SXM can now read old-format WA Technology STM images (pre-TOPSystem™). This has been tested on only a limited number of images.

Bug fixes:

The precision with which Profile Plot values were exported was sometimes incorrect (see below for other changes).
The compensation displayed by the 'Get Info' command now reads 'none' for SXM images read from 8-bit data files, such as JEOL SEM and old-format WA Technology SPM images.

Other changes:

The maximum width of an image has been reset to the NIH Image default of 4096 pixels (after being reduced to 2048 pixels previously due to problems allocating memory to certain variables). The maximum width of image that can be used to produce a 3d Plot involving shadow calculations has been increased from 640 to 1024.
Exporting Profile Plot values now produces two columns of data for the position (X) and intensity (Z) values. The precision with which the data are exported is always one decimal place more than that used for displaying the values in the Info window. If this is not sufficient, then the number of decimal places can be specified in the 'Options...' dialog box in the Analyze menu.
Changing the Zoom window magnification from x2 to x4 (tab-click or tab-shift-click) or vice versa no longer requires the image window to be in front of the Zoom window.

159-1 (9 Feb 96)

Added features:

Image SXM will now recognise Nanoscope III v4.1 images that record Amplitude, Current, Deflection, Frequency, Friction, Height or Phase. The Z scale calibration has been checked against a set of standard images and is OK.

Bug fixes:

The crash that occurred after cancelling 'List Params from File(s)...' has been fixed.
The display of Z values when the cursor was in the LUT window had the wrong units.
The Balloon Help text was wrong in the Analyse/Options dialog box. Now OK.
The Balloon Help text is wrong in Preferences dialog box. This a bug in NIH Image which is a bit tricky for me to fix as the text is embedded inside code where I can't edit it. I have left it for NIH Image v1.60 to fix.
Setting a custom LUT, saving the Preferences and then launching Image SXM caused unpredictable behaviour on FPU Macs. This bug has been fixed.
Browsing would crash if an alias was found in the folder. Aliases are now ignored.
The display of XY values in the Info window when the cursor is in the Plot window now always shows the correct XY values and units, even if original image from which the plot was taken has been closed or other images have been opened subsequently.
Changing the foreground or background colour (from the default black and white, respectively) of an image and then saving the Preferences file would result in Image SXM crashing the next time it was launched. This has been fixed.

Other changes:

Stacks now have independent Z scales for each slice in the stack. This is of importance for Nanoscope III files which contain multiple images, where each image may have different Z scales and units.
Display precision for XY values is now based on units (Å, nm, µm) per pixel, rather than image size.
Similarly, Z precision is based on units (nm, nA, V, Hz,...) per Z value.
Extra parameters are displayed in the 'Get Info' window for Nanoscope III images.
The Star Trek sound bites have gone! It's a pity, but it does result in a slightly smaller application.
Line-by-line least-squares fit subtraction can now be done using a 0th, 1st or 2nd order fit.
Balloon Help has been added to the 'Display Calib Bar...', 'Browse Images...' and 'Browse Omicron...' dialog boxes.
All SXM-related dialog boxes now have a Help button (indicated by a '?') which toggles Balloon Help on and off. If Balloon Help has been activated using this button, it will be deactivated automatically when the dialog box is closed. If Balloon Help is activated from the menu bar, it remains active until cancelled.

159-beta-2 (24 Jan 96)

Added features:

A new SPM/Compensation submenu has been added. In addition to the XY Tilt Compensation present in earlier versions, compensation for large-scale curvature of SPM surfaces and a line-by-line least-squares fit subtraction are available. The latter can be applied over a specified region of the image (not necessarily rectangular). The ReCompensation command has been left in the SPM/Images submenu for compatibility with earlier versions.
A new SPM/Dimensions submenu has been added to allow the XYZ units displayed in the Info and Results windows to be changed from the values set by default on loading. The changes can apply to all open images or only the frontmost image according to a checkbox setting in the SPM Options dialog box.
Image SXM can now read JEOL SEM images that do not originate on a WinSem™ system.

Bug fixes:

NIH Image v1.59 fixes a number of bugs present in v1.58. See the NIH Image documentation for details.
For Digital Instruments Nanoscope III v3 and v4.1, the Z scale is now read from the file header correctly.
The display of step heights in 'Calc Step Height' gave the correct values but the wrong units. This has been fixed.
The display of Z values when the cursor is in a Histogram window gave the correct values but the wrong units. This has been fixed. Not related to the bug mentioned above, surprisingly.
PICT and TIFF images displayed Z scale values but not the units. This has been fixed.
Some TIFF images gave a spurious 'Invalid TIFF header' message. This has been fixed.
The 'OpenAll' checkbox in the 'Open...' dialog box now works on SXM images.

Other changes:

A new FFT submenu was introduced in NIH Image v1.59. The FFT menu in earlier versions of Image SXM has therefore been removed to maintain compatibility with NIH Image. See the NIH Image documentation for details.
When the cursor is in an FFT window, the Info window displays frequency, period and polar angle as well as the XY coordinates.
The FFT command selects the largest power-of-two-sized square if no other selection has been made.
Up to 10 images can be loaded from one Digital Instruments Nanoscope III file. This feature is untested.
The calculation of Phase% now displays percentage values below the lower slice limit and above the higher slice limit, and the continuous display no longer flickers as the slice limits are varied.
The reference number of the folder containing the file from which an image is loaded is now stored for each image. Thus, if Image SXM needs to read the raw data of an SPM image, it should know where to find it.
Cmd -> and cmd <- now load the next and previous images in numerical sequence for Digital Instruments Nanoscope and Park Scientific SPM images -- previously this worked only for old-format Omicron STM images.
The 'Duplicate' command now adjusts the SPM parameters relating to the image size.
'Print Parameters for File(s)...' is now 'List Parameters for File(s)...', producing a list of parameters in a text window which can then be printed if desired. It now works for any SPM image -- previously this worked only for old-format Omicron STM images
A number of cosmetic changes have been made: 'STM' is now 'SPM' where a feature is equally applicable to STM and SFM images; the SXM menu has been removed; SAM Options is in the SEM menu; SXM Options and 3d Plot are in the SPM menu; the Resize Window submenu is in the Windows menu.

158-6 (3 Dec 95)

Added features:

A number of changes have been made to the 3d Plot dialog box. New options: (i) a 2d Plot option, producing a conventional flat image, may be useful for mixing the image colours with shadows to obtain a better impression of the surface topography; (ii) a 4d Plot option produces a 3d plot of an image with the colours of each pixel in the image tinted according to whether or not the corresponding pixel of a second image (which is assumed to have been density sliced previously) lies between the slice limits set. Selecting '3d Plot' with the Option key pressed now produces a smaller (faster) preview on 68K Macs and a larger (more detailed) preview on PowerMacs.

Bug fixes:

Some items in the ReCalibrate XY dialog box were inadvertently disabled in 158-5, resulting in miscalibration of images. These items have been enabled again.

Other changes:

A number of changes have been made to the STM Options dialog box. A popup menu has been added to allow the user to select options specific to the SPM that they use. If an SPM manufacturer is selected, the dialog box expands downwards to show any additional options. The options for XY tilt compensation or quadratic background subtraction have been simplified. Balloon Help has been added for the items in this dialog box.
There are now separate XY calibration files for Omicron, Burleigh, WA Technology, Digital, TopoMetrix and Park Scientific SPMs. Thus, calibration of an SPM image from one manufacturer does not affect the calibration of images from other manufacturers.
The 'ReCalibrate XY' command now works for images that are initially uncalibrated, such as PICT or TIFF images produced by other applications.
The continuous display of XYZ data in the Info window for FFT images now displays XY position (in pixels) and the frequency and period corresponding to that position.
The 'Resize Window' submenu has been moved from the SXM menu into the Windows menu. The keyboard shortcut cmd-1 has been added for the 100% setting.
The keyboard shortcut for 'Measure' in the Analyze menu has changed to cmd-M (previously cmd-1).
The 'Browse Images...' menu item has been removed from the SXM menu. This was functionally identical to the same menu item in the SEM and STM menus.

158-5 (5 Nov 95)

Added features:

Image SXM can now read HDF (Hierarchical Data Format) image files produced by the Park Scientific Instruments SPM. This has been tested on only a limited number of images.
A new 'Unsharp Mask' item has been added to the Process menu. It executes a convolution with a 15 x 15 Gaussian kernel, subtracts the result from the original image and then enhances the contrast. This command can be used to remove large-scale variations in intensity from an image to reveal smaller-scale detail.
A new option has been added to the STM Options dialog box. As an alternative to X and Y tilt compensation, a bi-quadratic background can be subtracted from an image during loading. This option was requested by an Image SXM user.
A new option has been added to the 3d Plot dialog box. The original image LUT colours and the shadows calculated from the illumination of the surface can be mixed together. This option was requested by an Image SXM user.

Bug fixes:

Digital Instruments Nanoscope images did not display the correct Z scale. This has been fixed.

Other changes:

Image SXM has been recompiled using CodeWarrior release 7.
When changing file types and creators, the dialog box now shows all files in the folder selected regardless of their type. Files of type 'APPL' and text files with filenames ending in '.PAR' or '.par' will not be altered.
The 'Resize Window' submenu has been extended to 400%. Keyboard shortcuts cmd-2 and cmd-4 have been added for 200% and 400% enlargement, respectively.

158-4 (1 Oct 95)

Added features:

None.

Bug fixes:

The FPU and noFPU versions of Image SXM 158-3 crashed on startup due to a compilation error. The PowerMac version appears to be OK. All versions have been recompiled.

Other changes:

Minor changes to 3d Plot dialog box.

158-3 (26 Sep 95)

Added features:

Image SXM can now read image files produced by the Digital Instruments Nanoscope. If the z scale of an AFM image is labelled as 'phase' then the image is identified as an MFM image. The full set of image parameters, stored in the header of the image file, can be displayed using the 'Dump All Parameters' menu item in the Parameters submenu of the STM menu.
Image SXM can now read image files produced by the TopoMetrix range of STMs and AFMs.
A new SXM menu has been added alongside the SEM and STM menus. The SXM menu contains various items that have been moved from the other menus as they can be applied to SEM, STM, SAM, AFM and MFM images. A new 'SXM Options...' menu item allows the user to specify that images larger or smaller than specified limits will be reduced or magnified automatically after loading. This can include PICT and TIFF images.
Multiple images can now be loaded as a stack rather than separate windows, determined by the settings of check boxes in the STM, SAM and SFM Options dialog boxes. The check box in the STM Options dialog box affects only dual images from the Omicron STM. The check box in the SAM Options dialog box is only active if the 'Display PEAK, BGND and RESULT images' check box is selected. The check box in the SFM Options dialog box affects only AFM/MFM images from the Digital Instruments Nanoscope.
A new 'FFT Options...' menu item has been added to the FFT submenu of the Process menu (the FFT menu was moved from the menu bar as space was tight on small monitors). This handles the selection of the maximum image size that can be FFT'd -- either 256x256 or 512x512. Images can be masked automatically before an FFT is calculated and unmasked after an inverse FFT.
A new 'Region Of Interest' item has been added to the 'Propagate' sub-menu in the Options menu. This copies the region of interest (usually a rectangle or line selection) to all other open windows. This is particularly useful when a number of images cover exactly the same spatial region of a sample (eg, SAM images).

Bug fixes:

The 'Z' cursor (see 158-2) is now only displayed when either the selection tool or the magnifying glass are selected. The zoom feature is only available when one of these tools is selected and so displaying the 'Z' cursor when other tools are selected is confusing.
For WA Technology STM images tilt compensation did not display the correct z scale calibration. This was due to the way that the calibration information is stored in the file header. This has been fixed. Images that had been 'normalised' by the WA Technology software to use the full ± 32768 range of z values would not load with tilt compensation. These images will now load, but the z scale parameter held in the file header is not the correct value for the image and so the z values are displayed incorrectly.

Other changes:

In the PowerMac version of Image SXM the Tool window is now displayed in greyscale (or as close to greyscale as is possible for any particular LUT). If the tools become difficult to see when the brightness or contrast controls have been adjusted, click in the Tool window, in the title bar of an image window or option-click in the Info window to restore the original Tool palette.
The title bars of SAM image windows now display the filenames in the format 'folder/filename' as the filenames alone convey little useful information regarding their origin.
A colour palette named 'Mandelbrot' has been added to the 'Color Tables' submenu in the Options menu.

158-2 (14 Aug 95)

Added features:

Image SXM can now read image files in the new Omicron STM format. STS data will follow.

Bug fixes:

The option to display STM image dimensions in Å rather than nm now works (previously, all STM images used Å as the default unit and so conversion from Å to nm was implemented, but not nm to Å).

Other changes:

A warning dialog is produced if the user FFTs an image that is not an integer power of two in size.
An image that has been masked, FFT'd and ReFFT'd can now have the mask removed. If this is done, then pixel values close to the edge of the image are unreliable. Use with caution.
The use of the modifier keys (Option, Shift, Control) when the selection tool (the default crosshair cursor) is active has been changed to make them consistent with NIH Image: Shift is used to constrain a dragged rectangle to be square; Option is used to subtract a new selection from an existing selection; Control is used to add a new selection to an existing selection. Creating a zoom window is now achieved by selecting the Tab key (previously the Option key) and clicking in the image. The cursor changes to a 'Z' when the Tab key is pressed to remind the user of its action. If the Shift key is pressed as well, then the cursor becomes a larger 'Z' to indicate the higher zoom magnification. Selecting the largest square that is an integer power of two in size is now achieved from the first item in the FFT menu (previously the Control key).
Animating stacks now updates the window title bar if the frame rates is below 10 frames per second. At higher rates it remains frozen at its initial setting.
Text files are displayed in Monaco by default (previously Geneva). This makes some files easier to read, such as the new format Omicron STM parameter files.

158-1 (7 Aug 95)

Added features:

Image SXM can now read image files produced by the WA Technology STM. The small images that are a part of the image header are not used when browsing for the sake of compatibility with other formats.
Cmd-Option-I is a shortcut for executing the 'Invert LUT' and 'Apply LUT' operations in sequence.

Bug fixes:

WA Technology STM images are now flipped vertically to give the correct orientation.
The x and y calibrations of WA Tech STM images would appear negative for images greater than 32 nm due to a 16-bit integer overflow (32768 pm = 32 nm). This has been fixed using a 32-bit longint.
The 'Apply LUT' command would produce a dialog box and remove the density (z) calibration of STM images. This was a new feature in NIH Image v1.58 and has now been removed as it is not required -- Image SXM compensates for changes in the LUT when calculating z values.
The 'Plot Profile' command didn't display the plots correctly if the 'Fixed Y-Axis Scale' preference was checked. The axes and tick marks are now calculated correctly for fixed scale plots.
As in earlier versions of Image SXM, the Cmd-R keyboard shortcut is assigned to the 'ReCompensate' menu item, but in v1.58 this key had not been removed from the menu item assigned by NIH Image -- 'Rescale/Revert To Saved' in the File menu. This has been fixed.
The maximum image width of 4096 pixels on Power Macs gave problems when the total RAM was 16 Mb or less. The maximum width has been reduced to 3072 (as for non-Power Macs) until the bug is traced.
As in earlier versions of Image SXM, the Cmd-B and Cmd-F keyboard shortcuts are assigned to the 'Browse Images...' and 'Do FFT' menu items, but in v1.58 these keys had not been removed from the menu items assigned by NIH Image -- 'Draw Boundary' and 'Find...' or 'Fill' in the Edit menu. This has been fixed.
Fixed a bug that caused Image SXM to quit if a zoom window was created, the original image window closed and then the zoom window selected again by clicking in the window rather than on the title bar.
If the image window was small, a zoom window could be positioned partially offscreen. This has been fixed.

Other changes:

Cmd-Option-O is a shortcut for selecting the 'SXM Preferences...' menu item.
One of the menu items in the Files submenu of the STM menu has become two: 'Browse Images...' has been renamed 'Browse Omicron...' to make it clear that this browsing option expects to find files named according to the Omicron convention, and a new 'Browse Images...' item allows browsing of any other SXM, PICT or TIFF file.
The maximum image width has been increased to 3072 (non-Power Macs) or 4096 pixels (Power Macs).
The need for separate copies of the three SXM variants -- SEM, STM and SAM -- has been removed now that the application name determines not only the appearance of the splash screen and the assignment of keyboard shortcuts, but also the application icon. If the icon is not appropriate for the variant running, then when the application quits the user is given the option of changing the icon. The desktop will need to be rebuilt to see the new icon.
Printer halftoning options are now accessible from the 'SXM Preferences...' menu item.

158-Alpha (2 Jul 95) Development Version

Added features:

None.

Bug fixes:

NIH Image v1.58 fixes a number of bugs present in v1.57. See the NIH Image documentation for details.

Other changes:

Combining the source code for NIH Image v1.58 with that written for Image SXM v1.57 involves a large amount of editing -- Image SXM is now a total of 60 000 lines of code. Some coding errors are inevitable. This version is labelled a 'beta' version until it has been checked more thoroughly on other Macs.
There is an incompatibility between the image file headers used by NIH Image v1.58 and the file headers used by Image SXM v1.57. The problem only exists for stacks (ie, collections of images or slices saved as a single file). Stacks that are saved using NIH Image v1.58 can be opened by Image SXM but will have one of the file parameters read incorrectly. If this is a particular problem for some users, then let me know -- otherwise I will not attempt to recode Image SXM to get around the problem.

157-9 (1 Jul 95)

Added features:

A zoom feature has been added. By option-clicking in an image window, a small window is opened showing a magnified view of the region of the image around the cursor (default 2x magnification, 4x if the shift key is also pressed). If the click occurs close to a corner, the zoom window is placed in that corner, otherwise it is placed overlapping the right-hand edge of the image. The zoom window can be moved but not resized. The zoom image can be temporarily frozen by pressing the caps lock key. (Note that previously an option-click would select the largest square suitable for FFT operations. This selection is now made using control-click.)

Bug fixes:

When an SEM image was loaded and auto resized, clicking in the window's zoom box would send the window offscreen. This bug has been fixed.

Other changes:

The brightness and contrast of an image can now be changed by selecting the LUT tool and then pressing the caps lock key. Horizontal movement of the mouse changes the brightness and vertical movement changes the contrast. This method has an advantage over the conventional method (using the Map window) in that both the brightness and contrast can be changed continuously without any mouse clicks -- some may find this convenient.

157-8 (20 Jun 95)

Added features:

The 3d Plot dialog box now has the option of displaying a small preview of the plot. This makes setting the optimum values for the viewing angles easier. If the plot takes a long time to redraw every time the viewing angles are changed, try selecting the menu item with the Option key pressed -- this will produce a smaller preview image which should be redrawn more quickly.

Bug fixes:

None.

Other changes:

All Image SXM dialog boxes now respond to the escape key (Cancel) in addition to the return key (OK).

157-7 (1 Jun 95)

Added features:

None.

Bug fixes:

Fixed a bug that caused the 3d Plot routine to execute even if the dialog box Cancel button was pressed.
Discovered an obscure bug that manifests itself when running under System 7.5 on Power Macs (and System 7.5.1 on a Performa 5200/6200). The symptom is that when there are no image or text windows open, the user cannot return to the Finder by clicking on the desktop. It seems to occur when the small memory display window is selected, and so can be cured simply by deselecting that window by clicking on the Info window. Circumvented the problem by selecting the Info window when Image SXM initialises and whenever the last window is closed. Note that running System 7.5.1 on a Power Mac doesn't produce this problem (the upgrade 7.5 -> 7.5.1 is free from Apple).

Other changes:

The LUT saved in the 'Image SXM Prefs' file was not used as the default if it was one of the new palettes added in 157-1. Now any of the palettes available from the 'Color Table' menu item can be used as the default by selecting the desired palette and then either selecting 'Record Preferences' or saving the preferences using the 'SXM Preferences...' dialog box (see 157-6).
The position of the small memory display window (which defaults to the bottom right of the screen) is now saved in the 'Image SXM Prefs' file if 'Save Window Positions' is checked. The window can be moved by holding down the option key and dragging the window.

157-6 (8 May 95)

Added features:

A new 'SXM Preferences...' item has been added to the Options menu. This dialog box allows quick access to all of the other options/preferences dialog boxes that are usually accessed from other menus. It also allows the user to reload the Preferences file to reset all the parameters without restarting Image SXM.

Bug fixes:

In NIH Image v1.57 the profile plot scale of spatially uncalibrated images was set to zero. This caused problems with the latest version of the profile plot procedure as it uses this variable to plot the tick marks on the horizontal axis. Uncalibrated images now have the profile plot scale set to unity.
The 3d Plot procedure calculated the wrong dimensions for the plot window if the azimuthal view angle was negative (i.e., viewed from the left). The bug has been fixed by taking the absolute value of the view angle.

Other changes:

The preferences set in the SEM, STM, STS, SAM and 3d Plot dialog boxes are now saved in the preferences file when the 'Record Preferences' item is selected from the File menu.

157-5 (1 May 95)

Added features:

Balloon Help has been added to the SEM, STM and FFT menu items to aid new users of Image SXM.

Bug fixes:

The routine that calculates the z scaling for STM images had an unnecessary rounding error. STM images are now scaled correctly, but PICT or TIFF files saved using earlier versions of Image SXM will have this z scaling error. It will only be apparent for very flat images that have a small variation in z over the entire image. Reloading the original STM images and resaving them will correct the scaling. As accurate measurements can only be made on images that have been recalibrated (using 'ReCalibrate Z', which was not affected by this bug), this should not have caused any problems.
Burleigh STM images with an x or y range > 32767 Å would display negative dimensions. Changing a signed integer to an unsigned integer fixed this bug.

Other changes:

The routines that read the parameters from VG SAM image file headers have been changed so that they should work for all VG SAM files, not just the limited selection used to test version 157-3.
Zero-valued pixels are now ignored when calculating the minimum intensity of pixels in VG SAM images. Such pixels, which seem to occur occasionally due to glitches, caused problems in earlier versions.
The STM Options dialog box now has an option for the dimensional units used in all displays -- nm or Å. There is also a new checkbox for using µm for images larger than 1 µm in size.
Ticks have been added to both axes of profile plots to help with rough estimates of the size of features (accurate measurements are still displayed in the Info window as before).

157-4 (6 Apr 95)

Added features:

None.

Bug fixes:

In the non-FPU version of Image SXM the routine that reads floating point numbers from parameter files or image file headers sometimes gave the wrong results. The problem didn't arise in the FPU or PowerMac versions. It was traced to an incorrect evaluation of a transcendental function -- a bug in CodeWarrior or SANE? The problem was circumvented by rewriting the routine.

Other changes:

The spatial calibration of the 3d Plot window is now calculated from the calibration of the original image, so that a calibration bar can be added to the 3d Plot window if desired (see file 'Demo of 3d Plot'). As the effect of perspective in the 3d plot makes 'distant' features smaller than 'closer' features, don't rely on the spatial calibration for accurate measurements.

157-3 (31 Mar 95)

Added features:

Image SXM can now read image files produced by the VG Scanning Auger Microscope (SAM) system. The image magnification, beam voltage and beam current settings are read from the parameter block at the start of the file (the first 369 bytes!). The peak (PEAK.DTI) and background (BGND.DTI) images can be loaded and displayed individually, or both can be loaded and the resultant Auger image (= (peak-bgnd)/bgnd) calculated automatically. The options are set in the 'SAM Options' dialog box accessed from the SEM menu. The images can be browsed using the 'Browse Images...' command in the SEM menu. As SAM images are usually much smaller than SEM images, the reduction factor should be kept small.

Bug fixes:

None.

Other changes:

The Image SXM variant can now be changed without modifying the code of Image SXM itself. If the filename of the application is changed to 'Image SXM', 'Image SEM', 'Image STM' or 'Image SAM' then the splash box will display the corresponding name and various menu shortcuts will be set as appropriate.
Image SXM was given a Spring clean, removing redundant code and generally tidying things up a bit. The probability of introducing a bug in the process is not insignificant.

157-2 (24 Mar 95)

Added features:

None.

Bug fixes:

Fixed a bug that caused the dialog box for 'Change File Types...' to hang.

Other changes:

None.

157-1 (20 Mar 95)

Added features:

A number of extra palettes have been added to the 'Color Tables' submenu in the Options menu. These were available previously as separate files that could be loaded in when needed. They have been placed in this menu for convenience.

Bug fixes:

ReCompensation for x and y tilt now works correctly on Burleigh STM images.
Changing the contrast/brightness settings on a Burleigh STM image no longer removes the z calibration.

Other changes:

The 'Shadow Plot...' menu item in the STM menu has been replaced with '3d Plot...'. The routine has been rewritten from scratch for maximum computational speed -- an improvement of about x6 has been achieved, so that plots of a 256x256 image can be produced in 15 s on a Quadra, or 3 s on a PowerMac. The new routine produces a 3d plot of the surface, allowing the user to specify the direction from which the surface is viewed. The colours used for each pixel in the 3d plot can be taken from the original image LUT or from a calculation of the illumination of the surface from a light source in a specified direction. A third option calculates the effect of the specified illumination but doesn't produce the 3d plot. Once the 3d plot has been drawn, the view angles can be altered in increments of 10° using the four cursor keys. Holding down the Option key moves the viewpoint by 30°. Holding down the Shift key when pressing the up/down cursor keys increases/decreases the z magnification factor.
FFTs can now be calculated for images up to 512x512 providing that 6 Mbytes of free memory are available. The default maximum FFT size is 256x256, but this can be changed from the FFT menu if required.

157-beta-2 (12 Feb 95)

Added features:

A new 'Add Axes and LUT' procedure has been added to the 'Images' submenu of the STM menu. This adds a border to the image window, adds x and y axes, and displays the look-up table (LUT) of the image. The font, size and style of the text used can be set in the 'Options' menu.

Bug fixes:

NIH Image v1.57 fixes a number of bugs present in v1.55. See the NIH Image documentation for details.

Other changes:

As Image SXM now has the ability to read STM files of different formats (i.e., Omicron or Burleigh), the manufacturer's name is now stored in the image header. Images saved by previous versions of Image SXM will be read as 'NotSpec', meaning that the manufacturer is not specified. This should not have any serious effect on subsequent analysis of the image.
Separate calibration files are now used for Omicron and Burleigh STM images. The original calibration file is still supported for handling images saved with previous versions of Image SXM. All the data from the calibration files are loaded when Image SXM starts up. When recalibrating or applying a previous calibration, the data appropriate to the image being analysed are used.
In combining the source code for NIH Image v1.57 with that written for Image SXM, a large number of changes have been made. Apart from the added features noted above, most of these changes are cosmetic and should not result in any differences in the execution of the application compared to Image SXM v1.55. However, in 56 000 lines of code some errors are inevitable. This version is labelled a 'beta' version until it has been checked more thoroughly on other Macs.

155-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.

155-9 (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).

155-8 (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).

155-7 (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.

155-6 (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.

155-5 (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.

155-4 (4 Sep 94)

Added features:

None.

Bug fixes:

None.

Other changes:

The values of step height and error (see 155-3) 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).

155-3 (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.

155-2 (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)'.

155-1 (21 Jul 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!

155-beta-1 (26 Jun 94)

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.

154-8 (19 Jun 94)

Added features:

To make Image SXM more flexible in handling STM files, the file identifier labels are now user-selectable. In earlier versions, they were preset to the Omicron settings of 'ta' and 'tp' for the image and parameter files, respectively. Image SXM still defaults to the Omicron settings, but these can now be changed in the STM Options dialog box. Filenames can have any characters prefixing these identifiers and any characters suffixing the file number providing that the additional strings of characters do not contain an embedded identifier -- the longer they are, the more chance there is of accidentally including an additional identifier in the filename.
A new 'Change File Names...' command has been added to the STM menu. This allows filenames to be changed to names that are more meaningful to the user. If an SXM file or folder has not been selected previously then a folder must be selected -- this folder becomes the default folder for subsequent operations. The identifier labels to be found and replaced do not have to be the same length. The image and parameter file identifier labels must be different.
A new 'Add Border...' command has been added to the STM menu. This places the image in the front window into the centre of a larger window, preserving all the calibration data of the original image. By selecting the default option for the size of the border, image rotation operations can be carried out without clipping the corners of the image. Larger or smaller borders (user-selectable size) can be added if desired.

Bug fixes:

None.

Other changes:

Pressing the cmd-key together with any of the arrow keys when an STM image is in the front window will attempt to load the image with the next highest (->) or lowest (<-) file number. A file error is generated if another folder has been accessed since the original image was opened.

154-7 (12 Jun 94)

Added features:

None.

Bug fixes:

Fixed a bug in the 'ReCompensate' procedure that caused a crash if the rectangle used to define the region over which the tilt compensation was to be carried out was selected using 'Select All' rather than by dragging a rectangle.

Other changes:

Minor changes to the positions of items in various dialog boxes to make them consistent with Apple guidelines.

154-6 (9 Jun 94)

Added features:

None.

Bug fixes:

The 'Browse Images...' procedures are now a little more robust when browsing through folders that contain either no images or images of the wrong type (i.e., STM images when the procedure is expecting SEM images).

Other changes:

The Results window now has an extra option, referred to as 'User4' in the code and labelled 'Title' in the Results window. This records the active window title every time a measurement is made. This is useful if you want to jump from one image to another, recording measurements from more than one.

154-5 (8 Jun 94)

Added features:

None.

Bug fixes:

A bug was found in the original code for Image that gave incorrect tabbing in the Results window. This has been fixed.

Other changes:

The addition of an option to display the units used for each of the measurements in the Results window has been rewritten so that it does not use the 'User2' data structure. This means that it no longer interferes with any macros which use this structure. A new data structure has been created (referred to as 'User3' in the code and labelled 'Units' in the Results window) to hold the units for each measurement. If all this means nothing to you, then you don't have to worry about it.

154-4 (5 Jun 94)

Added features:

A new 'Browse Images...' command has been added to the SEM menu. The user can specify a folder to browse through and select the reduction factor to be used to display the images as a montage. If an SXM file or folder has not been selected previously then a folder must be selected -- this folder becomes the default folder for subsequent operations. The file name is displayed in the corner of each image. Browsing can be aborted when an image is being displayed (with cmd-period). Double-clicking on an image will load that image into a separate window, providing that it is one of the first 36 images that are displayed in the most recent 'Browse SEM Images' window.
A new 'Browse Images...' command has been added to the STM menu. The user can specify a folder to browse through, select a range of file numbers and the size of a window in which the images will be displayed as a montage. If an SXM file or folder has not been selected previously then a folder must be selected -- this folder becomes the default folder for subsequent operations. The file number, image size, tip voltage and tunnelling current are displayed in the corners of each image. If the largest display window size is selected, then the window is scaled to fit the monitor and the file numbers are displayed in the centre of each image using a larger font size. Browsing can be aborted when an image is being displayed (with cmd-period). Double-clicking on an image will load that image into a separate window, providing that it is one of the first 36 images that are displayed in the most recent 'Browse STM Images' window.
A new 'ReCompensate' command has been added to the STM menu. After an image has been opened and displayed, then the image can be reopened (into a separate window) with the XY tilt or Z drift compensation calculated over a user-selected rectangle drawn onto the original image. If a rectangle has not been drawn in an STM image window, then this menu item is dimmed.

Bug fixes:

It was found that sometimes the STM parameter file contains values for the size of the image (number of lines and number of pixels per line) that do not correspond to the actual image dimensions. To deal with such a situation, Image now calculates these numbers using the X and Y image dimensions (in Å) and the X and Y step size (in Å).

Other changes:

Holding down the shift key when closing a window bypasses the usual 'Save changes...?' dialog box if the window has been changed since it was opened or last saved. Use this with caution.
The tilt compensation algorithms now look at Z values at XY positions that are inset from the edges of the images by 0, 20 or 50 pixels, depending on the image size. These inset values are overridden if the 'ReCompensate' command is used (see above).
There are now three variants of the original Image application -- Image SEM, STM and SXM. There are no functional differences between them. The differences between them are purely cosmetic -- the appearance of the splash screen when the application is launched, etc. This has been done so that users see an acronym with which they are familiar.

154-3 (1 Jun 94) Development Version

154-2 (25 May 94) Development Version

154-1 (22 May 94)

Added features:

Image can now handle dual STM images (i.e., two images of the same area taken with two different sample voltages or tunnelling currents). The two images are renamed to make them distinct and can be saved individually. Because they have been renamed, the 'Rescale' command does not work for dual images. This may be rectified in a later version.
Option-clicking in the Plot window of an STM image will attempt to resize the plot such that the vertical and horizontal scales are the same, thus giving an undistorted height profile. Option-clicking a second time redraws the original profile plot. If the Z variation is small, requiring a Plot window wider than the display monitor, then the plot is not drawn.

Bug fixes:

The 'Rescale' command now correctly recalculates the Z values after the greyscale has been changed (in previous versions the scale did not get inverted, so that white pixels had a lower Z value than black pixels). If the command is called more than once, then the original Z values are forgotten. Note that the Z scale is correct, but the actual values assigned to each pixel may have an arbitrary offset relative to their original values.

Other changes:

Due to spurious Z values along the edges of dual images, the tilt compensation algorithms now look at Z values at XY positions that are inset from the edges of the images by 10 or 20 pixels, depending on the image size.
When the cursor is in a Plot window of an STM image, the X and 'Y' (i.e., Z height) values are both displayed in Å.
Minor changes to SEM menu layout.
Some SEM and STM menu items are now dimmed if the front window is not an SXM image.
Maximum image size is now limited to 2048 x 2048.

144-1 (31 May 93)

Added features:

Support has been added for JEOL SEM images.

Bug fixes:

None.

Other changes:

None.

Steve Barrett April 2000

S.D.Barrett@liv.ac.uk