
Image SXM history        v1.72-1.77        ( Jan 2004 - Oct 2005 )
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v1.77-1    ( 16 Oct 05 )

Added features:
 ¥ Support has been added for Seiko Instruments (SII NT) SPM images.
 ¥ Support has been added for Unisoku STM images.

Bug fixes:
 ¥ The routine that sorts filenames into alphanumerical order (used when opening or importing files in OS X) does not handle embedded numbers with ten or more digits. If such a string of digits is embedded in a filename, it is now treated as a character string rather than as a number. 

Other changes:
 ¥ The keyboard shortcut cmd-space now changes the current tool to the magnifying glass.

Changes to macros:
 ¥ The 'SetScaling' macro command now has the option of bicubic interpolation. 

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v1.76-1    ( 27 Jul 05 )

Added features:
 ¥ Support has been added for firewire video grabbing. The code was adapted from the source code of 'HackTV Carbon 1.2' (c) 2004 Apple. A video stream can be saved directly to disk and then optionally displayed as a stack.
 ¥ If an analogue video frame grabber is detected, the Special menu remains as it was in NIH Image. If the only video input is from the firewire interface, then the menu title changes to 'Video' and the menu contains items appropriate for grabbing digital video.

Bug fixes:
 ¥ Bitmap images with 8-bit data could load as 16-bit.
 ¥ Quesant Instruments SPM images would display the wrong z calibration. Using the gain parameters stored in the hardware configuration record of the file would give inconsistent results (is the documentation wrong?) and so the image parameter record has been used instead to determine the z calibration.
 ¥ Opening compressed SBIG images would have an effect on all 16-bit images imported thereafter.
 ¥ When saving and reloading a Browse window the location of the folder containing the images would not be determined correctly.

Other changes:
 ¥ For Nikon NEF images the algorithm used to convert the Bayer grid (RGGB) into RGB colours has been improved to give less 'jaggies' in the green channel.
 ¥ Using the automatic outlining (wand) tool to select multiple outlines will now store (and Export) the coordinates of all of the outlines. Previously, the coordinates of only the most recently selected outline were available. Each outline is separated by a dummy coordinate (0,0). Deselecting an outline removes those coordinates from the set.
 ¥ When extracting a subset of slices from a stack using 'Stack to SubStack', a rectangular region of interest can now be selected to make a cropped stack.
 ¥ When averaging the slices of a stack (with or without limits on the pixel values that contribute to the average) the range of slices that contributes to the average can now be specified.
 ¥ The routine to convert 24-bit RGB images to an 8-bit lookup table (LUT) has been completely rewritten. There is now no option for a custom LUT - only the system LUT is supported.
 ¥ When density slicing with a histogram displayed, the slice limits are also visible in the histogram and can be set by dragging in the Histogram window (the LUT cursor changes to a 'horizontal LUT cursor'). This feature has been present since v1.55-9 (Dec 1994) but was only effective when the monitor was set to 8-bit. It is now more common for monitors to be set to 32-bit and so some extra code was needed to reinstate this feature. 
 ¥ The default LUT or colour table (usually 'Grayscale') used when Image SXM launches can now be set to any of the entries listed in the 'Color Tables' submenu (previously it was restricted to only the first 9 colour tables).  

Changes to macros:
 ¥ The macro command 'AverageWithLimits' has been added to mirror its menu counterpart (see above).
 ¥ The macro commands have been separated from the video commands - they are now in a separate Macro menu rather than being added to the bottom of the Special (or Video) menu.
 ¥ The 'Export' macro command now works correctly when used with no argument. 

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v1.75-2    ( 13 Mar 05 )

Added features:
 ¥ Support has been added for NEF images from Nikon digital SLR cameras - uncompressed raw images (Nikon D1) or compressed raw images (Nikon D70).

Bug fixes:
 ¥ When holding the mouse button down in a Profile Plot window the cross that is displayed at the corresponding location in the image window now works in OS X and flashes at a slightly slower speed to improve visibility.
 ¥ When loading JPK Instruments SPM image files the images are now oriented and scaled correctly.
 ¥ Fixed cosmetic bug in 'SPM Options' dialog box.

Other changes:
 ¥ 'Scale and Rotate' now has the option of bicubic interpolation, giving a better quality scaled image at the expense of execution time.
 ¥ When 'Batch Conversion' is set to load SXM images, files of all types (other than PICT and TIFF) are opened and converted if they are found to contain images. Parameter files with the suffix '.par' are not opened.
 ¥ When displaying information on Profile Plots, the coordinates in the Info window are labelled X and Z rather than X and Y to correspond with the labelling of images.
 ¥ When averaging stacks with pixel values within user-specified limits, a pixel will be set to zero if no stack slices have the corresponding pixel within the limits (previously the pixel was set to 1).

Changes to macros:
 ¥ None.

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v1.75-1    ( 9 Jan 05 )

Added features:
 ¥ The Carbon version of Image SXM now runs under Mac OS 9 and Mac OS X.

Bug fixes:
 ¥ Measurements applied to non-rectangular regions of interest (ROIs) would give zero or NAN (not a number) results for some calculations such as second moments for best-fit ellipses. This was a consequence of reorganising the Undo buffers (all NIH Image routines that originally used the Undo buffer as a temporary data store have now been rewritten to avoid this sort of problem).
 ¥ Popup menus in the 'Image Math' dialog box would not allow the last item to be selected.
 ¥ Certain key presses could result in the cursor icon changing to an inappropriate icon.

Other changes:
 ¥ Automatic compensation of z values of SXM images can now be either xy tilt or line-by-line (or neither), selected in 'SPM Options'. The order of the line-by-line compensation will be the order last used before saving the preferences file.
 ¥ Automatic QuickTime translation of file formats that are not native to Image SXM (such as gif, jpeg, png, etc) can be activated by a check box in 'SXM Options'. Note that images loaded from files that use compression algorithms contain artefacts that may invalidate the results of image analysis. Use with caution.

Changes to macros:
 ¥ None.

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v1.74-2    ( 14 Nov 04 )

Added features:
 ¥ None.

Bug fixes:
 ¥ The 'Differential' operation is now undoable.
 ¥ The size of a Browse window (with labels displayed below the images) could be set incorrectly.
 ¥ When closing the Clipboard window the user is now not prompted to save changes.

Other changes:
 ¥ The maximum image size than can be handled has been increased to 16000 x 16000 pixels (= 250 Mb). The maximum number of slices in a stack has been increased to 8000, giving an upper limit for the size of an image stack of 2 Tb (though OS 9 and OS X will both give up long before that limit is reached). To ensure that enough memory is available for the application, the default memory allocation for the Carbon version has been increased from 24 to 32 Mb and the minimum allocation from 12 to 16 Mb. The OS X version has a nominal memory allocation of 2 Gb which is set by OS X.
 ¥ The 3d Plot routines can now handle images up to 2 Mb in size when making high-quality plots (providing that sufficient memory is available). The resultant plots can be up to 20 Mb in size.
 ¥ When cmd-click-dragging to select slices in a stack (see 1.73-1 below) the full range of slices is accessed by moving the mouse across the stack window, regardless of the scale or offset of the images within the window.
 ¥ 'Measure' will now calculate the angle of a line selection relative to the x axis.

Changes to macros:
 ¥ The 'Open' macro command did not work correctly if the argument was a full path name. It will now work with (i) no name, (ii) a filename only, or (iii) a full colon-delimited path name. In the first case, the user is prompted to navigate to the desired file. In the second case, the file is loaded from the default folder (which is the one most recently accessed).

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v1.74-1    ( 25 Sep 04 )

Added features:
 ¥ Support has been added for JPK Instruments SPM images.
 ¥ Selecting 'Analyze Results' (from the Analyze menu with the option key pressed) now also displays a histogram of the particle size distribution.
 ¥ A new 'Window Options' dialog box (selected from the Windows menu) allows the user to specify the size of borders at the edge of the screen that are to be kept clear of windows. This avoids windows overlapping with applications like DragThing or the OS X dock. Other options from the 'SXM Options' dialog box have also been moved here.

Bug fixes:
 ¥ Results displayed in the Results window were duplicated when selecting 'Measure' when density slicing or thresholding an image.
 ¥ Loading multiple image files from a Navigation Services dialog box could give unpredictable results.
 ¥ The decimal precision was not set correctly after reading the value from the preferences file.
 ¥ Fixing the units of the z scales of images in the 'SPM Options' dialog box would display inappropriate values for images with non-spatial z scales.
 ¥ Nudging a region of interest (ROI) beyond the edges of an image would deselect the ROI.
 ¥ Filters applied to non-rectangular ROIs would not undo correctly.
 ¥ In the OS X version when cmd-click-dragging to select slices in a stack (see 1.73-1 below) the slice number in the window title bar now updates correctly.

Other changes:
 ¥ Updated support for Gatan DigitalMicrograph v3 images.
 ¥ The Browse routine now allows the user to specify the size of the Browse window and images can be labelled with either filenames or comments. The comments can be taken from the Finder comments of the image files (check the option in the 'SXM Options' dialog box) or constructed from a set of acquisition parameters (select the 'Comm' button from the 'SXM Preferences' dialog box to specify the sequence of parameters). 
 ¥ Histogram windows can now be duplicated and saved (to conform with the behaviour of plot windows).
 ¥ When switching back to Image SXM from another application, the LUT, Tool, Map and Info windows are brought to the front of any other windows.
 ¥ OS X 10.3 does not have the Chicago or Charcoal fonts and so the Help pages have been reformatted in Geneva.

Changes to macros:
 ¥ The macro interpreter could produce an unexpected quit when handling a macro command that attempts to get xy or z calibration data from an uncalibrated image.

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v1.73-1    ( 18 Apr 04 )

Added features:
 ¥ Support has been added for NT-MDT SPM images.
 ¥ Support has been added for Digital Instruments NanoScope scanning capacitance spectroscopy (SCS) files.
 ¥ Stack slices can now be selected by holding down the cmd key (the cursor changes to a 'multiple slice' icon) and clicking the mouse. The horizontal position of the mouse within the stack window determines the slice selected, allowing selection of individual slices (by clicking) or stack animation (by click-dragging).

Bug fixes:
 ¥ In the OS X version a region of interest (ROI) is now visible when it is being created.
 ¥ In the OS X version the spinning disk ('idle' cursor) is now suppressed when creating ROIs and when the mouse is down in the LUT or Map windows.
 ¥ In the OS X version copying and pasting text now works.
 ¥ Bypassing the dialog box for 'Analyze Particles' by pressing the option key now works correctly.

Other changes:
 ¥ Updated support for Nanotec WSxM 64-bit images.
 ¥ Updated support for DME Dualscope SPM images.
 ¥ The chord that sounds on launching can now be muted using a checkbox in the 'SXM Options' dialog box.
 ¥ The maximum number of line scans that can be loaded from a file has been increased from 20 to 128.
 ¥ To be consistent with other routines, the options for 'Make Mosaic' are now displayed by default. Press the option key to suppress the dialog box.
 ¥ To maintain consistency between displays of force curves and scope plots, 'approaching' is indicated by a right arrow and 'retracting' is indicated by a left arrow.
 ¥ Help Tags have been added to some of the dialog box items in the Carbon version, activated using the '?' help button.
 ¥ The minimum memory allocation for the Carbon application has been increased from 8 to 12 Mb.
 ¥ The 'Image SXM Prefs' file is no longer copied to the Preferences folder by the installer, but is created when the application first runs if no existing preferences file is found. In the future, this approach will allow a single distribution of the installer of the Carbon application to work with both Mac OS 9 and OS X. 

Changes to macros:
 ¥  None.
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v1.72-1    ( 26 Jan 04 )

Added features:
 ¥ Support has been added for DME sdf (surface data file) format SPM images.

Bug fixes:
 ¥ The folder path names displayed in the 'Browse' and 'Batch Conversion' dialog boxes were truncated.
 ¥ Browsing some SPM images did not work correctly in the OS X version.

Other changes:
 ¥ Updated support for Quesant Instruments v4.0 AFM image files.
 ¥ Updated support for Molecular Imaging PicoScan v5.2 AFM image files.
 ¥ Improved the algorithm for averaging Omicron SCALA STS data for pixels within a specified region of interest.
 ¥ Help Tags have been added to menu and dialog box items in the OS X version.
 ¥ A checkbox has been added to the 'SXM Options' dialog box that allows suppression of warning dialog boxes when running macros. The suppression applies also to browsing images and batch conversion of image files.

Changes to macros:
 ¥  Macro commands 'MakeMontage' and 'AddCaptionToImage' have been added to mirror their menu counterparts.
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