
Image SXM history        v1.78-1.91        ( Dec 2005 - Dec 2010 )
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v1.91-1    ( 22 Dec 10 )

Added features:
 ¥ A new 'Remove Low Frequencies' item has been added to the FFT submenu. The lowest-frequency discrete components of the FFT are used to determine the low-frequency cutoff. In addition, the highest frequencies are removed to reduce noise.
 ¥ A new 'Find Matching Shapes' item has been added to the Analyze/Specialist Analysis submenu. The user clicks on each of the reference objects in an image and a map is created which colour-codes all the objects that have been matched to one of the reference objects. Pressing the option key allows the user to specify how many reference objects are to be selected. As for the other items in this submenu, effective use of this routine requires some background information.
 ¥ A new 'Find XY Displacements' item has been added to the Analyze/Specialist Analysis submenu. The displacements of molecules relative to a smoothly varying curvilinear grid are displayed as a colour-coded map. As for the other items in this submenu, effective use of this routine requires some background information.
 ¥ A new 'Find Edges (5x5)' filter has been added to the Process menu (using the Option key) and to the Rank Filters dialog box.

Bug fixes:
 ¥ When grabbing images from a firewire camera there was a delay of a few seconds (Snow Leopard only).
 ¥ When opening Gatan DigitalMicrograph v3 images, the greyscale is now inverted.

Other changes:
 ¥ Colour look-up tables (LUTs) now explicitly set the RGB colours of 0 (white) and 255 (black).
 ¥ New algorithm in 'Parasite Counting Analysis' for greyscale images.
 ¥ 'Lymphocyte Flow Analysis' can now track up to 9999 cells and can handle left-to-right and right-to-left flow. 
 ¥ 3-point compensation now works correctly for SPM images with 32-bit image data.
 ¥ When grabbing images from a firewire camera cmd-G will grab a single frame (equivalent to clicking on the 'Grab Frame' button in the 'Capture Control' dialog - the dialog does not need to be open).
 ¥ A new 'Bounding Box' option has been added to the 'Measurement Options' dialog box (for use with 'Measure' and 'Analyze Particles'). The xy position (top left corner) and size (w x h) of the bounding rectangle of the object(s) are displayed in the Info and Results windows.
 ¥ Updated support for Molecular Imaging PicoScan v5.3 AFM image files.
 ¥ The number of XY coordinates that can be exported has been increased from 32K to 1M.

Changes to macros:
 ¥ The macro command 'Filter' has additional options 'HybridMedian' and 'FindEdges5x5' (see above).

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v1.90-1    ( 14 Apr 10 )

Added features:
 ¥ The XY coordinates of all objects found in 'Analyze Particles' can be exported.
 ¥ The data in the size/area/height distribution histograms displayed by 'Analyze Results' can be exported.
 ¥ The size/area/height distribution histograms have options for manually setting the bin sizes and ranges. Option-click or double-click on a histogram to change the settings.
 ¥ 'Convolve...' changes to 'Convolve With Gaussian' if an odd-sized square ROI is selected (sigma = size/3).
 ¥ 'Set Scale...' changes to 'Remove XY Scale' if the option key is pressed.
 ¥ 'Calibrate...' changes to 'Remove Z Calibration' if the option key is pressed.

Bug fixes:
 ¥ Maximum image sizes are now limited to 16 x 16 Kpix due to limitations of some Carbon code.
 ¥ Scaling with bilinear interpolation for images of width or height > 8 Kpix would give artefacts.
 ¥ Saving an image in a specified file format would apply that as the default format when importing images.
 ¥ Image compensation for JEOL SPM images was not applied correctly.
 ¥ Plot profiles from rectangular ROIs in images with uncalibrated z axes could appear to have calibrated scales.
 ¥ Calculation of a perimeter could give an underestimate by 0.5 pixels depending on the location of the first of the xy coordinates that define the perimeter.

Other changes:
 ¥ New algorithm in 'Parasite Counting Analysis' to reduce false negatives and false positives.
 ¥ New algorithm in 'Lymphocyte Flow Analysis' based on Hough transform to improve cell tracking.
 ¥ Updated support for Nanonis SPM images.
 ¥ Convolutions now process all pixels in an image including those at the edges.
 ¥ Paste Control dialog transfer mode popup menu now updates when the transfer mode is changed by a macro.
 ¥ Video grabbing now works for images larger than 800 x 600.
 ¥ Increased the maximum size of a 'marching ants' region from 32 Kpix to 256 Mpix.
 ¥ Increased Info window height to take advantage of larger screen sizes.
 ¥ Pressing 'C' when creating a rectangular/oval selection constrains it to be a centred square/circle.
 ¥ After loading a TIFF stack the window is reset to the first slice.
 ¥ After saving an RGB TIFF image the window is reset to the original colour slice.
 ¥ Autocorrelations and FFTs now behave the same way if a ROI is selected - if the ROI is a power-of-2-sized square then it will be used, otherwise the largest power-of-2-sized square will be selected.
 ¥ Added option in 'Analyze Particles' to stop when the particle count reaches the maximum number of measurements (set in the Measurement Options dialog box). If not selected, when the count reaches the maximum a beep will sound but the particle analysis will continue. See also 'Changes to macros'.

Changes to macros:
 ¥ The macro command 'AnalyzeParticles' has an additional option 'StopAtMax' (see above).

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v1.89-1    ( 23 Aug 09 )

Added features:
 ¥ A new 'Microcirculation Analysis' item has been added to the Analyze/Specialist Analysis/Cell Analysis submenu. This calculates the speed of red blood cells imaged in videos of sublingual blood vessel networks. As for the other items in this submenu, effective use of this routine requires some background information.
 ¥ A new 'Cornea Cell Analysis' item has been added to the Analyze/Specialist Analysis/Cell Analysis submenu. This calculates the size distribution of corneal cells and the mean, modal and median values.

Bug fixes:
 ¥ Omicron Matrix SPM images would sometimes display with a LUT using less than 256 shades of grey.

Other changes:
 ¥ The 'Skeletonize' command in the Process/Binary submenu now changes to 'Prune Skeleton' if the option key is pressed. This will prune all branches off a skeleton. See also 'Changes to macros'.
 ¥ 'Show Histogram' changes to 'Show Smoothed Histogram' if the shift key is pressed. Note that the histogram is smoothed, not the image.
 ¥ The 'Cell Analysis' submenu in the Analyze/Specialist Analysis submenu has been renamed 'MIASMA'. 
 ¥ For more information on the MIASMA routines, see http://www.liv.ac.uk/~sdb/MIASMA.

Changes to macros:
 ¥ The macro command 'PruneSkeleton' has been added (see above).

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v1.88-1    ( 14 Feb 09 )

Added features:
 ¥ None.

Bug fixes:
 ¥ Fixed a bug which prevented line-by-line compensation working within a user-specified region of interest (ROI).
 ¥ In NanoScope v5.12 SPM image file headers the parameter 'Sens. Zscan' has been relabelled 'Sens. Zsens'. I have modified the z calibration routines to accommodate this change.

Other changes:
 ¥ XY tilt or line-by-line compensation can now be applied to images that are not SPM images.
 ¥ The keyboard shortcut cmd-option-7 now zooms an image window to 75%.
 ¥ The 'Straighten Curvilinear Object' command in the Analyze/Specialist Analysis submenu changes if the option key is pressed to 'Straighten Outline'. Any internal structure within the object is ignored.
 ¥ Added background subtraction to 'Particulate Matter Analysis' to compensate for vignetting.

Changes to macros:
 ¥ None.

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v1.87-1    ( 4 Oct 08 )

Added features:
 ¥ Support has been added for Nanosurf SPM images with both easyScan (.ezd) and Nanosurf Image Document (.nid) file formats.
 ¥ Updated support for RHK Technology XPM Pro SPM images.

Bug fixes:
 ¥ Recoded some menu handling routines to avoid a crash on PowerMacs running Leopard. Intel macs running Leopard and PowerMacs running Puma/Jaguar/Panther/Tiger were unaffected.
 ¥ Fixed a bug which affected zooming of windows whose width or height was an odd value.
 ¥ Asylum Research SPM images with large footers (> 32 Kb) would not have the correct z calibration.

Other changes:
 ¥ Added options for Omicron SCALA images so that opening a forward (backward) scan image will automatically open the corresponding backward (forward) scan image if the file exists in the same folder. If both images are opened they are displayed as a twoÐimage stack. These options are set in the 'SPM Options' dialog under 'Show Options Specific To: Omicron SCALA'.
 ¥ Added option to 'SXM Options' to use a default colour look-up table (LUT) for every image. To set the default LUT, select the LUT from Options/Color Tables and then save the preferences file from File/Record Preferences or SXM Preferences. If this option is not selected then the image will be displayed with the LUT saved in the file or, if there isn't one, with the current LUT (note that in the latter case this can give odd results with PICT images).
 ¥ Added option to 'SXM Options' to use a default preset spatial calibration for every image. The default scale is selected from a popup menu, which displays the same presets as the Analyze/Preset Scale submenu. If selected, the preset scale will override any spatial calibration defined for the image, so use only if you are sure that you want a fixed spatial scale.
 ¥ Colour LUTs can now be selected by pressing the caps lock key and tabbing (or shift-tabbing) between LUTs.
 ¥ Changes to 'Parasite Counting Analysis' to improve the calculation of the multiplicity of touching parasites and the handling of structured background in images of parasites with no cells.
 ¥ Reinstated browsing of selected images (dropped when browsing was modified to use stacks in v1.85). Option-click to deselect an image. Press the option key and select 'Browse Selected Images' from the File or SEM or SPM/Files menus to redisplay a browse window without the deselected images.
 ¥ After browsing a folder, and optionally deselecting some images by option-clicking, the images can be opened by pressing shift and selecting 'Open Browsed Images' from the File or SEM or SPM/Files menus. If all the images are the same size, they will be opened as a stack. Otherwise they will open in separate windows, as if the user had double-clicked on each thumbnail.
 ¥ When nudging a rectangular region of interest (ROI) using the cursor keys, or stretching it using option-cursor keys, the coordinates of the corners and the width and height are displayed in the Info window.

Changes to macros:
 ¥ None.

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v1.86-1    ( 20 Apr 08 )

Added features:
 ¥ Limited support has been added for Omicron Matrix STM images. Only images with equal x and y dimensions as specified in the Matrix acquisition software can be loaded (though if the image acquisition was aborted before the y scan was complete then the non-square image will still load OK). The image will not have the xy or z scales calibrated as I do not know where the relevant information is stored in the Matrix file structure.
 ¥ A new 'Parasite Counting Analysis' item has been added to the Analyze/Specialist Analysis/Cell Analysis submenu. This calculates the number of parasites in images with or without cells. As for the other items in this submenu, effective use of these routines requires some background information. Email me for details.

Bug fixes:
 ¥ Omicron (pre-SCALA) STM images would not be listed with SPM/Parameters/List Params For Files.
 ¥ See also 'Changes to macros'.

Other changes:
 ¥ When browing Omicron SCALA images options have been added to display only z topographic (channel 0) images and/or only forward scan images. These options are set in the 'SPM Options' dialog under 'Show Options Specific To: Omicron SCALA'.
 ¥ Suppressed warning messages if Asylum Research AFM images have very long parameter lines (> 255 chars).
 ¥ Minor changes to 'Particulate Matter Analysis'.

Changes to macros:
 ¥ Fixed bug that stopped macro command 'DepthOfFocus' working.

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v1.85-1    ( 7 Jan 08 )

Added features:
 ¥ Support has been added for Nanonis SPM images.
 ¥ Support has been added for Asylum Research MFP-3D AFM images.

Bug fixes:
 ¥ RHK Technology XPM Pro SPM image files that have been corrupted by email transfer can now be opened if the images are topographic.

Other changes:
 ¥ Maximum image size has been increased to 32000 x 32000 pixels.
 ¥ Maximum number of measurements has been increased from 8000 to 99999.
 ¥ Default buffer size is now 4 Mb.
 ¥ Browsing large numbers of images now displays the thumbnails as slices in a stack to reduce window clutter.
 ¥ When opening or importing images as a stack the image filenames are now stored, so that if the stack is later converted into separate windows then the original window titles are restored.
 ¥ Selecting the slices of a stack now updates the Histogram window if it is open, but does not bring the Histogram window to the front.
 ¥ Minor changes to 'Particulate Matter Analysis'.

Changes to macros:
 ¥ The macro command 'DepthOfFocus' now takes four arguments corresponding to the items in the dialog box: nearLimit, farLimit, weightedAverage, reduceNoise.

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v1.84-1    ( 28 Jun 07 )

Added features:
 ¥ Support has been added for RHK Technology XPM Pro SPM images.
 ¥ Support has been added for NEF images from the Nikon D200 digital SLR camera. Both compressed and uncompressed file formats are supported.
 ¥ A new 'Mineral Phase Analysis' item has been added to the Analyze/Specialist Analysis submenu. This calculates the relative areas of two phases (with different grey values) in SEM images of mineral grains.
 ¥ A new 'Particulate Matter Analysis' item has been added to the Analyze/Specialist Analysis submenu. This calculates the relative areas of particulate matter in cells.

Bug fixes:
 ¥ None.

Other changes:
 ¥ SPECS STM 150 Aarhus files can now be split into a set of SXM files, with one image per file, using a new 'Split Multi-Image File' item in the SPM/Files submenu. The file header information is preserved so that the resultant files will also open with the manufacturer's data acquisition software.
 ¥ When opening Gatan DigitalMicrograph v3 images, the xy scale is now set using the 'Scale' parameter in the file header (the 'Magnification' parameter is ignored).
 ¥ When reslicing a stack a rectangular region of interest can be selected (rather than a line) and the reconstructed image will be calculated from the average intensity variation in the direction parallel to the longest side of the rectangle. The averaging is performed in the direction parallel to the shortest side of the rectangle (as for profile plots).

Changes to macros:
 ¥ None.

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v1.83-1    ( 17 Mar 07 )

Added features:
 ¥ Support has been added for SPECS STM 150 Aarhus images.

Bug fixes:
 ¥ None.

Other changes:
 ¥ Support for NT-MDT SPM images has been extended to handle up to 256 images per file.
 ¥ Conversion of RGB stacks (comprising 3 colour slices, each an 8-bit image) into a single 8-bit indexed image is now complemented by an alternative conversion into a single 24-bit colour image. Note that this 24-bit image is intended for display only - editing, analysis and processing operations are limited.
 ¥ Minor changes to the display of user data plots.

Changes to macros:
 ¥ None.

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v1.82-1    ( 28 Jan 07 )

Added features:
 ¥ Support has been added for FITS image files with 32-bit real data.
 ¥ Support has been added for PEF images from the Pentax K10-D digital SLR camera.

Bug fixes:
 ¥ Calling the FFT routine when a non-rectangular region of interest was selected would cause a quit - a bug left over from NIH Image!

Other changes:
 ¥ The 'Open' and 'Import' dialog boxes now have buttons to open/import all files in a folder as a stack (rather than opening each image into a separate window). When opening hundreds or thousands of large images, this should be significantly faster. Each image opened/imported must be the same size as the first.
 ¥ The 'Differential' command can now also be used to differentiate Histogram plots.
 ¥ For Nikon NEF and Pentax PEF images the algorithms used to convert the Bayer grid (RGGB) into RGB colours have been rewritten to improve the loading speeds by factors of between 2 and 5, depending on how the raw pixel values are scaled (linear or power law).

Changes to macros:
 ¥ None.

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v1.81-1    ( 2 Oct 06 )

Added features:
 ¥ Support has been added for Nanonics Imaging Quartz STM and SNOM images.
 ¥ Support has been added for Hamamatsu Image Sequence files with 8, 12 or 16-bit data. The time stamp of each image can be displayed from 'List All Time Stamps' in the SPM/Parameters submenu.

Bug fixes:
 ¥ Loading PICT images with colour LUTs could result in blank windows under Mac OS X (this was not a problem under OS 9).

Other changes:
 ¥ The 'Open' dialog box now has a button to open all files in a folder.
 ¥ The drag corner of rectangular regions of interest (ROIs) and the handles of line ROIs have been enlarged.
 ¥ The macro command 'FFT' now also works on line profiles.

Changes to macros:
 ¥ None.

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v1.80-1    ( 26 Jul 06 )

Added features:
 ¥ Support has been added for NanoMagnetics Instruments SPMSIF images.
 ¥ A new 'Nanotube Non-Linearity' item has been added to the Analyze/Specialist Analysis submenu. This calculates a coefficient that quantifies the non-linearity, or entanglement, of features such as carbon nanotubes  (0 = a randomly entangled network, 1 = a linear array of features). 

Bug fixes:
 ¥ Fixed a bug that would update background windows showing a region of interest (ROI) using the lookup table (LUT) of the frontmost window.

Other changes:
 ¥ The LUT, Tools, Map and Info windows have been changed to floating windows which always stay in front of image and text windows. As before, they can be moved anywhere on the screen and their positions saved with 'Save Prefs File' or 'Record Preferences'. If you prefer non-floating windows, uncheck the option in Preferences. Under Mac OS 9 floating windows are supported but they have been set to be non-floating.
 ¥ The 'Auto Register' command will now also work with a user selected power-of-two-sized square region of interest (ROI) to use for the cross-correlations. By placing a relatively small ROI over a (fixed) feature the alignment of slices in a stack may be improved compared to the default ROI selection (a square centred in the image).

Changes to macros:
 ¥ The macro command 'NonLinearity' has been added to mirror its menu counterpart (see above).
 ¥ The size of the macro interpreter's symbol table has been increased to allow macros with large numbers of variables. If you still see a 'symbol table overflow' error message, try reducing the number of variables that you use in your macros.

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v1.79-2    ( 17 Mar 06 )

Added features:
 ¥ None.

Bug fixes:
 ¥ Exporting data from profile plots, FFTs of profiles, autocorrelation plots, spectra, force curves and user data plots did not set the correct precision.

Other changes:
 ¥ None.

Changes to macros:
 ¥ None.

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v1.79-1    ( 7 Mar 06 )

Added features:
 ¥ Support has been added for PEF images from Pentax digital SLR cameras such as the *ist D.

Bug fixes:
 ¥ Omicron SPM images that have been converted from Matrix to SCALA file formats are now handled correctly.
 ¥ 'Apply XY Calibration' would not work for SPM images other than those from Burleigh, Digital Instruments, Omicron, Park Scientific, TopoMetrix or WA Technology. It now also works for DME, JEOL, JPK, Klocke, Molecular Imaging, Nanotec, NT-MDT, Oxford Instruments, Quesant, RHK, Seiko and Unisoku SPM images.

Other changes:
 ¥ Support for NT-MDT SPM images has been updated to include images from the Windows-based Nova data acquisition software. Previously only images from the older DOS-based software would load.
 ¥ 'Display Calib Bar' now has an option to suppress the display of the dimension of the bar.
 ¥ The 'Import' dialog box now has a button to import all files in a folder.
 ¥ 'Analyze Results' now displays three distribution histograms for particle size (diameter), area and height.

Changes to macros:
 ¥ None.

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v1.78-1    ( 17 Dec 05 )

Added features:
 ¥ None.

Bug fixes:
 ¥ Executing convolution filters from text windows (rather than from text files) would not work under OS X if the Image SXM application was not installed in the user's account.
 ¥ See also 'Changes to macros'.

Other changes:
 ¥ The 'Export' routines have been rewritten to get around the 32 Kb limit of the TextEdit toolbox in the Mac OS when exporting plot data to text files. Data from profile plots, FFTs of profiles, autocorrelation plots, spectra, force curves and user data plots can now be exported with up to 16384 data points.

Changes to macros:
 ¥ The 'SetOptions' macro command did not set the measurement options correctly if 'minor' (ellipse minor axis) was one of the selected options. 
 ¥ The 'ChangeValues' macro command, and probably some other LUT-related commands, did not work correctly when applied to non-rectangular regions of interest. 
 ¥ The macro command 'CalcLineShift' has been added to return the relative shift between the profiles of two lines of an image.

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