
Image SXM history        v1.68-1.71        ( Feb 2002 - Aug 2003 )
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v1.71-1    ( 18 Aug 03 )

Added features:
 ¥ Support has been added for Bio-Rad images.

Bug fixes:
 ¥ Selecting units from the popup menu in the 'Set Scale' dialog box did not set the appropriate text box correctly.
 ¥ Suppressed the 'File format not recognised' message when running macros.

Other changes:
 ¥ To be consistent with other routines, the options for 'Display Unit Cell' are now displayed by default. Press the option key to suppress the dialog box.
 ¥ The 'Stack to Windows' item in the Stacks menu now changes to 'Stack to SubStack' when the option key is pressed, allowing a subset of contiguous slices to be extracted from a stack to make a new stack. The xy and z calibration of each slice is preserved. Selecting the first and last slices (the default values) makes a duplicate of the entire stack.
 ¥ 'Straighten Curvilinear Object' now displays in the Session Log two values for the length of the straightened object: (i) the distance between the points specified by the user mouse clicks (or the start and end points of the original line), and (ii) the distance between the points at which the intensity of the object has fallen to 1/e of the values at the points specified in (i). Thus, if the user selects an object by clicking on points slightly inside the ends of the object, then length (i) will be slightly less than length (ii).
 ¥ The keyboard shortcut cmd-H has been removed from the 'SPM/Calculation/Step Height' menu item so that the OS X command 'Hide Image SXM' adopts that shortcut.
 ¥ Opening and importing multiple files in the OS X version now sorts the filenames alphanumerically so that the files load in order. (This is not necessary with OS 9 as the files are loaded in name order or date order according to the settings in the Navigation Services dialog box.)
 ¥ In the OS X version, the 'SXM Preferences' dialog box can now be accessed from the 'Preferences...' menu item in the 'Image SXM' application menu. OS X insists on placing a duplicate (disabled) menu item below this item.
 ¥ Dialog boxes in the OS X version now use the themed background (ie, adopt the Aqua appearance). 

Changes to macros:
 ¥ None. 
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v1.70-1    ( 24 Jun 03 )

Added features:
 ¥ Support has been added for Nanotec Electronica WSxM images.
 ¥ Support has been added for Zeiss LSM stacks.

Bug fixes:
 ¥ Stacking windows could get mixed up if windows of different sizes were open.
 ¥ When analysing particles, updates to the Results window are now suppressed until the analysis is complete to circumvent a bug which blacked out some of the results lines.
 ¥ An undo of particle analysis now works correctly.
 ¥ Updating partially hidden windows with different LUTs could give odd (temporary) results.
 ¥ Fixed a bug in the calculation of a Hough transform.

Other changes:
 ¥ Updated support for Zeiss LSM images with 2 samples per pixel (ie, 2 channels of data acquisition). A checkbox in the 'SXM Options' dialog box determines whether the two samples are displayed as consecutive slices in a stack or in separate windows. Stacks of 2-sample images are handled in the same way.
 ¥ The 'Display Unit Cell' item in the SPM/Images submenu now how has a dialog box to set display preferences, such as making a montage of multiple unit cells. This dialog box is accessed by pressing the option key.
 ¥ When converting a stack to separate windows, the windows are now staggered by 21 pixels (the height of window title bars in Mac OS 8/9) rather than 50 pixels. If the staggered position reaches the edge of the screen, then the position is reset to the home position.
 ¥ When animating stacks, key '9' now animates at 60 fps and key '0' animates at maximum speed. None of the other keys have changed: '1' = 1 fps, '2' = 2, '3' = 5, '4' = 7.5, '5' = 10, '6' = 15, '7' = 20, '8' = 30 fps.
 ¥ The default memory allocation for the Carbon application has been increased from 16 to 24 Mb.

Changes to macros:
 ¥ None. 
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v1.69-3    ( 19 May 03 )

Added features:
 ¥ Multiple levels of undo/redo have been added. Up to 999 levels of undo can be set in an 'Undo Options' dialog box (cmd-option-Z), providing that sufficient memory is allocated to Image SXM. For a given amount of available memory, the size of the undo buffer can be reduced to allow more levels of undo. If the available memory is not sufficient for what you want to do, use the Finder to allocate more memory to Image SXM. Press the shift key to change Undo to Redo. An additional 'Undo History' submenu lists the available undo/redo operations. Selecting the menu item indicated by the letter 'U' is equivalent to 'Undo'. Similarly, 'R' for 'Redo'. Selecting a menu item below 'U' or above 'R' will perform multiple undos or redos, respectively.
 ¥ Pressing the option key when selecting Analyze/Show Histogram will now, in addition to displaying the histogram window, transfer the histogram data to a plot window (which can be customised using the Profile Plot Options by double-clicking in the plot window).

Bug fixes:
 ¥ When using 'Save As...', overwriting files could produce a spurious 'not enough disk space' error message.
 ¥ When importing images, changing the image type from the default type would not import images correctly.
 ¥ See also 'Changes to macros'.

Other changes:
 ¥ The 'SPM Options' dialog box and the SPM/Dimensions submenu have been modified to provide more flexible control over the units used to display xy and z dimensions. The preferred units for the xy scale and the z scale can now be specified independently. The scales can use fixed units or can be allowed to change to units that are appropriate for the size of the image.
 ¥ The 'Windows to Stack' item in the Stacks menu creates a stack comprising all windows of the same size as the front window (all windows of different sizes are left untouched). Windows are stacked in the order in which they were created. If the option key is pressed, then the menu item changes to 'Windows to This Stack' and the front window becomes the first image in the stack.
 ¥ When averaging the slices of a stack, pressing the option key now allows the user to set the limits of the pixel values between which the average should be calculated Ð pixel values outside these limits will not contribute to the average.
 ¥ The maximum width of stacked images that can be averaged has been increased from 2048 to 4096 pixels.
 ¥ Recoded the routine to check keys pressed so that additional features do not override keys assigned to macros.
 ¥ Updated support for Quesant Instruments SPM v4.0.
 ¥ Improved the speed of browsing images by up to 50%, depending on the type of images.
 ¥ When browsing images the filenames can now be displayed either in the top left corners of the images or below the images. The latter requires larger browse windows but may improve readability.
 ¥ A checkbox in the 'SXM Options' dialog box allows the F1 to F4 function keys to be either reserved for calling macros or used for the default commands of undo, cut, copy and paste, respectively.
 ¥ Minor changes have been made to the code of low-level routines to improve compatibility with Mac OS X.

Changes to macros:
 ¥ The macro command 'Import' now displays a dialog box only when necessary (usually the first time it is called).
 ¥ The macro command 'SaveAs' would not save correctly if the argument was a full path name. 
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v1.69-2    ( 18 Dec 02 )

Added features:
 ¥ None.

Bug fixes:
 ¥ Recoding some of the calls to the Mac OS that involve colour indexing has circumvented the problems found when running under Mac OS 9.2.2. Thanks to Norbert Vischer, author of Object-Image, for saving me many days of detective work on this one.
 ¥ Copying images to and from other applications is now working correctly in the Carbon version.
 ¥ See also 'Changes to macros'.

Other changes:
 ¥ In a 3d Plot the view and light angles can now be changed by dragging the small circles of the geometry icon (in the top right of the plot window). Clicking in the square resets all the view, light and z scale parameters to their initial values. Option-clicking in the square resets the parameters to their default values. Using the geometry icon in these ways is an alternative to using the cursor keys (see the Help pages) or holding down the space bar and dragging the mouse around in the plot window.

Changes to macros:
 ¥ The 'Straighten Curvilinear Object' item now has a corresponding macro command 'StraightenCurv'. The xy coordinates of the end points of the object to be straightened are passed as four integers x1, y1, x2, y2.
 ¥ Due to changes made when Carbonising the source code, the 'GetStrFromWindow' macro command would not recognise a carriage return character correctly.
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v1.69-1    ( 15 Sep 02 )

Added features:
 ¥ A new 'Analyse Results' item has been added to the Analyze menu. It calculates the nearest neighbour (nn) distances between the particles found using the 'Analyze Particles' routine. The mean nn distance, its standard deviation, the mean azimuthal direction of the nn (x axis = 0¡, y axis = 90¡) and the anisotropy of the particle distribution (random = 0, fully aligned = 1) are displayed in the Info window and in the Session Log. This menu item is accessed by pressing the option key.
 ¥ Support has been added for window proxy icons. A small icon appears in the title bar of each image and text window that corresponds to the file from which the image/text has been loaded or to which it has been saved Ñ 
a blank square for new image windows; an SXM icon for SXM images; a square with the letter P for PICT images or T for TIFF images; a generic document icon for new text windows; an SXM text document icon for saved text files. (If the icons do not appear as described, try rebuilding the desktop file.) When changes are made to an image or text window, the icon is dimmed. An (undimmed) icon can be dragged from a window title bar to the desktop or a Finder window to move or copy the corresponding file (hence the name 'proxy icon'). Cmd-click the window title to get a drop-down menu showing the folder path locating the file. Selecting a folder in the file path opens the corresponding Finder window in the background (but does not bring the Finder to the front). A checkbox in the (General) Preferences dialog box switches window proxy icons on or off.  You may wish to use Image SXM icons rather than the original NIH Image icons, but this is not a prerequisite for using window proxy icons.
 ¥ TIFF images can now be saved with the x and y resolution tags set to either the value corresponding to the spatial calibration of the image (pixels per cm) or to one of five preset values (72, 150, 300, 600 or 1200 dpi). The choice is made in a popup menu in the SXM Options dialog box. Note that other applications such as Photoshop will read the resolution tags correctly, but may assume that very large values are incorrect and hence display a default value of 72 dpi. 
 ¥ When loading Omicron SCALA images, the lowest z value in an image can be set either to the value determined from the parameter file or to zero (previously, the value was always set to zero). A checkbox has been added to the 'Options Specific To Omicron SCALA' section of the 'SPM Options' dialog box.
 ¥ I-V spectra from WA Technology, DME Rasterscope or RHK Technology SPMs are now handled in a consistent way Ñ they are smoothed, shifted or differentiated according to the options set in the 'STS Options' dialog box. Double-click or option-click in an I-V spectrum window to change the options.
 ¥ Support has been added for JEOL JSM image files.

Bug fixes:
 ¥ Molecular Imaging SPM images with file headers larger than 4 kbytes were read incorrectly.
 ¥ RHK Technology I-V spectra were displayed with an incorrect zero offset.
 ¥ Exporting DME Rasterscope I-V spectra produced voltage values with an incorrect zero offset.
 ¥ Displays of I-V spectra or line scans were not clipped correctly if the vertical axis limits were set manually.

Other changes:
 ¥ TIFF files with tags 266 or 274 are assumed, in the absence of any other evidence, to be JEOL SPM images.
 ¥ Minor cosmetic changes have been made to the progress bar and memory bar indicators. The memory bar indicator window can now be collapsed to show only the numeric values of memory used and total memory allocated to the application.
 ¥ The Paste Control window has been changed into a modeless dialog box. The popup menu, checkboxes and buttons are disabled unless a paste operation is in progress, giving the user better visual feedback when pasting.
 ¥ The 'Windows to Stack' item no longer requires that all open image windows are the same size Ñ those that are a different size to that of the front window are ignored. The front image window becomes the first image in the stack and the other images are added in the order in which they appear in the Windows menu.
 ¥ The code dealing with Open and Save dialog boxes has been modified to use Navigation Services to comply with the Carbon model of Mac OS X. The Import and Export dialog boxes now have 'Options' buttons that allow the relevant options to be set without cancelling the dialog box.
 ¥ The code dealing with printing and with cutting and pasting between applications has been modified to comply with the Carbon model of Mac OS X.
 ¥ Many of the code changes made in recent versions of Image SXM rely on features of the Mac OS introduced in Mac OS 8.5, and so this version will not run under Mac OS 8.0 or 8.1. If you are using any version of Mac OS 8, updating to Mac OS 9 is recommended.
 ¥ The installer now contains two applications: a 'P' version for any PowerMac and a Carbonised 'C' version. The installer checks the Mac OS running on the host Mac and installs either the P (Mac OS 8) or C (Mac OS 9) version. The C version requires that CarbonLib v1.2 or later is in the Extensions folder Ñ the latest version of CarbonLib can be downloaded from Apple's web site.

Changes to macros:
 ¥ None.
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v1.68-4    ( 30 Jun 02 )

Added features:
 ¥ None.

Bug fixes:
 ¥ A bug introduced when Carbonising the QuickDraw code gave rise to corruption of the contents of windows that do not fit entirely within the screen display.

Other changes:
 ¥ None.

Changes to macros:
 ¥ None.
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v1.68-3    ( 16 Jun 02 )

Added features:
 ¥ None.

Bug fixes:
 ¥ Changes to the code dealing with fonts (in 168-2) produced an immediate quit when running under Mac OS 8.6. There seems to be a bug in the OS that only affects Carbonised code on this particular OS version Ñ no problems have been reported when running under Mac OS 9. The problem has been circumvented by recoding the relevant procedures. If you are using any version of Mac OS 8, upgrading to Mac OS 9 is recommended.

Other changes:
 ¥ None.

Changes to macros:
 ¥ None.
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v1.68-2    ( 1 Jun 02 )

Added features:
 ¥ None.

Bug fixes:
 ¥ None.

Other changes:
 ¥ Added support for non-topographic Park Scientific HDF images.
 ¥ Added support for PDS (Planetary Data System) images.
 ¥ Pressing the option key changes File/Open to 'Open As Text...' and displays the contents of image files as text.
 ¥ The coordinates for which Omicron SCALA single point spectroscopy (SPS) data exist can now be displayed by selecting 'Show SPS Coords' from the SPM/Spectroscopy submenu.
 ¥ Objects to be straightened using 'Straighten Curvilinear Object' can now be selected by simply clicking on the start and end points of the object rather than selecting a line along the object Ð the locus of the centreline of the object is determined automatically. The radius of curvature of the object should be no less than 5 pixels at any point (scale the image if necessary). Manual selection of the object using the freehand or segmented line tool can still be used if the automatic determination of the locus is not satisfactory.
 ¥ The code dealing with fonts, windows, QuickDraw and various utilities has been modified to comply with the Carbon model of Mac OS X.
 ¥ The version of Carbon is now displayed in the 'About This Mac' and 'User Feedback' windows. If the Mac OS under which Image SXM is running does not support Carbon applications, then the version shows as 'n/a'.

Changes to macros:
 ¥ None.
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v1.68-1    ( 23 Feb 02 )

Added features:
 ¥ A new 'Make Mosaic' item has been added to the Stacks menu. Where two, three or four images overlap, the pixel values of the mosaic are calculated to give no visible seams. Press the option key to set the mosaic orientation and other options.
 ¥ A new 'Straighten Curvilinear Object' item has been added to the Analyze/Specialist Analysis submenu. The user draws a line (straight, freehand or segmented) between the ends of a curvilinear object, such as a chromosome, and a window will be opened displaying the object as it would appear if it was straightened out.
 ¥ Support has been added for Omicron SCALA single point spectroscopy (SPS) data. The coordinates for which SPS data exist can be displayed by pressing 'C' or selecting 'Restore ROI' from the Options menu. The buffer used to load the SPS data is 256 Kb in size, which is sufficient to handle, for example, 50 spectra comprising 150 data points each. The maximum number of spectra is 256. The maximum number of data points per spectrum is 512.
 ¥ Support has been added for DME IV curves.

Bug fixes:
 ¥ Browsing Omicron SCALA images now does not open the parameter files.
 ¥ Pressing the space bar and dragging the mouse in a 3d Plot would not change the view angles if 'Suppress Diamond Symbols' was not checked in the Preferences dialog box.
 ¥ Changing the view of a 3d Plot such that the surface was clipped by the window would cause a crash.
 ¥ SPM calibration files stored in the Preferences folder, used to correct for miscalibration of the xy piezo crystals, were not read correctly due to recent changes to the code dealing with file handling.

Other changes:
 ¥ Opening image files is now more tolerant of files that have incorrect file types set. Note that to open an image by double-clicking on it in the Finder, the file type and creator must be set to 'iSXM' and 'Imag'. These can be set using SPM/Files/Change File Types or can be set automatically by your FTP application or by File Exchange (see Help pages 18, 36 and 37).
 ¥ A more explicit error message is now displayed if an image file format is not recognised.
 ¥ The maximum number of data points in an STS or SPS spectrum has been increased to 512.
 ¥ Updated support for Omicron SCALA v4.0.
 ¥ The code dealing with dialog boxes has been modified to comply with the Carbon model of Mac OS X.
 ¥ Compiling Image SXM using CodeWarrior 7 has resulted in an increase in execution speed of some routines by 10-30%. All data is now stored using the structure alignment of PowerPC processors, which is more efficient for PowerPC applications. For backwards compatibility with Macs that have 68K processors, the data in the preferences file and the headers of PICT and TIFF files still adopt the 68K structure alignment. 
 ¥ The default memory allocation has been increased from 12 to 16 Mb and the minimum allocation from 6 to 8 Mb.
 ¥ The installer now installs only the PowerMac 'P' version Ñ if you want the 68K 'F' version, please email me.

Changes to macros:
 ¥ None.
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