
Image SXM history        v1.61        ( Jan 97 - Dec 98 )
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v1.61-9    ( 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'.
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v1.61-8    ( 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.
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v1.61-7    ( 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.
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v1.61-6    ( 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.
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v1.61    ·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 ”m rather than  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.
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v1.61    ·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.
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v1.61    ·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.
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v1.61    ·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.
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v1.61    ·1    ( 9 Mar 97 )    General release

Functionally identical to v1.61  §5.
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v1.61    §5    ( 6 Mar 97 )    Beta release

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.
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v1.61    §3    ( 10 Feb 97 )    Beta release

Added features:
 „ Image SXM can now read DME RasterscopeȘ 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.
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v1.61    §1    ( 19 Jan 97 )    Beta release

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.
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