
Image SXM history        v1.62        ( Apr 99 - Apr 00 )
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v1.62-7    ( 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.
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v1.62-6    ( 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.
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v1.62-5    ( 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.
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v1.62-4    ( 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.
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v1.62-3    ( 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.
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v1.62-2    ( 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.
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v1.62-1    ( 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).
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