Listed here are all the changes that have been made to Image SXM from August 2000
to the present. For a list of earlier changes, see the
History 1993-2000 file.
Minor changes to 'Bacterial MicroCompartments' analysis to handle spatially uncalibrated images.
Changes to macros:
None.
205-4 (30 Sep 22)
Added features:
None.
Bug fixes:
None.
Other changes:
Minor changes to astrophotography image processing routines.
Changes to macros:
None.
205-3 (25 Apr 21)
Added features:
None.
Bug fixes:
None.
Other changes:
None.
Changes to macros:
Selecting a slice of a stack using 'SelectSlice' now updates the window title if each image in the stack has a different title.
205-2 (25 Nov 20)
Added features:
None.
Bug fixes:
None.
Other changes:
Rotate raw SNOM images 90° clockwise to agree with image orientation from optical microscope, rather than image orientation displayed when images are opened in MATLAB.
Minor changes to astrophotography image processing routines.
VVG Stain Analysis algorithm for elastin and collagen modified for smaller images.
Changes to macros:
None.
205-1 (21 May 20)
Added features:
A new 'VVG Stain Analysis' item has been added to the MIASMA menu.
Bug fixes:
None.
Other changes:
Minor changes to routines for opening and processing SNOM images.
Changes to macros:
None.
204-1 (4 Aug 19)
Added features:
None.
Bug fixes:
None.
Other changes:
Minor changes to astrophotography image processing routines.
Changes to macros:
None.
203-1 (20 Dec 18)
Added features:
Support has been added for Agilent PicoView SPM images.
Bug fixes:
Updated support for Nanoscope v9.2.
Bug fix in PrinCIPia routines for processing prestack.
Other changes:
None.
Changes to macros:
None.
202-1 (22 Apr 18)
Added features:
Added 'Random Grayscale' checkbox to 'LUT Options' dialog box.
Bug fixes:
When using the 'UpdateLUT' macro command the option key prevents LUT entry 0 being reset to white and LUT entry 255 being reset to black.
Other changes:
None.
Changes to macros:
Added 'ApplyRandomLUT' macro command to apply random greyscale values to all 0-255 LUT entries. If its argument N is non-zero then this value will be used to determine the random numbers used in the LUT. If N = 0 then Image SXM will continue generating its own random seeds.
201-2 (8 Oct 17)
Added features:
None.
Bug fixes:
Bug fix for opening files from Finder under macOS 10.13 High Sierra.
Other changes:
None.
Changes to macros:
None.
201-1 (10 Sep 17)
Added features:
Added routines to process stellar spectra produced by the Star Analyser 100 diffraction grating.
Bug fixes:
None.
Other changes:
When browsing images the maximum image size has been increased from 256 to 512 pixels.
Minor changes to the 'Fibre Texture Analysis' routines.
Changes to macros:
None.
200-2 (11 Jul 17)
Added features:
Support has been added for Hysitron TriboScan images.
Bug fixes:
The display of the prompting message in the 'GetString' macro function was inadvertently disabled.
Other changes:
None.
Changes to macros:
See above.
200-1 (26 Apr 17)
Added features:
A new 'Fibre Texture Analysis' item has been added to the MIASMA menu.
Bug fixes:
In the Intel (X) version when loading Omicron SCALA STS data only some of the data was byte-swapped and so the STS did not display correctly.
When opening an RGB image creating an 8-bit indexed image would leave the RGB image stack displaying the wrong slice.
Other changes:
In NanoScope v9 SPM image file headers the image data is declared as 16-bit even though it is actually 32-bit. Image SXM now loads all NanoScope images
pre-v9 as 16-bit and post-v9 as 32-bit.
As some 8-bit bitmaps are saved by third-party applications as 24-bit bitmaps, Image SXM checks for this when opening bitmaps and generates a warning dialog accordingly.
Modified the 'Image Correlation' routine with the addition of pixel correlation maps.
Changes to macros:
None.
199-2 (4 Dec 16)
Added features:
Typing or clicking in a text window now shows the line and column position of the cursor in the Info window.
Bug fixes:
In the Intel (X) version 'Update Stack Slice Titles' would result in opening stacks with undefined XY scales.
Other changes:
None.
Changes to macros:
Added 'arctan2' macro command. It has two parameters (x, y) to provide the arctan of y/x with the angle in the appropriate quadrant.
199-1 (26 Aug 16)
Added features:
A new edge-preserving smooth (Epsilon) algorithm has been added, but is not yet a menu item. See also 'Changes to macros'.
Added support for JEOL JSM 7001F SEM images. On loading the XY scale is calibrated using the scale bar imprinted in the bottom right of the image.
A new 'Bacterial Membrane Analysis' item has been added to the MIASMA menu.
Bug fixes:
Bug fix and tidy up to LEED I-V routines when manually extracting spot intensities.
Other changes:
None.
Changes to macros:
Added 'Epsilon' macro command (see above). Its argument N sets the size of the NxN ROI where 3 <= N <= 63.
Added macro commands for 'Distance Map', 'Ultimate Points' and 'Watershed' commands in Process/Binary submenu.
Added macro commands to access user arrays User7, User8 and User9.
198-2 (1 Feb 16)
Added features:
A new 'Rotating Mask' item has been added to the Process menu. The size of the mask is 11x11 unless a modifier key is pressed: option = 7x7, shift = 15x15.
Bug fixes:
Saving a stack whose titles change as the slices are selected (because the 'Update Stack Slice Titles' option is selected in Preferences)
no longer gives an unhelpful 'File I/O error'.
Opening TIFF image stacks saved by third-party software now loads all stack slices.
Other changes:
In 'Bacterial MicroCompartments' analysis the longitudinal and transverse compartment distribution data are now folded to make the distributions symmetric.
Opening TIFF image stacks with odd-pixel-width images now loads all stack slices.
Changes to macros:
Added 'CleanSkeleton' macro command to remove any skeletonised objects that have forks or junctions.
Added 'Blank' option to 'AnalyzeParticles' macro command to blank out particles that do not match criteria.
Added 'DuplicatePlot' macro command (as 'Duplicate' will only duplicate image windows).
198-1 (29 Jul 15)
Added features:
A new 'Skeleton To ROI' item has been added to the Process/Binary submenu. This creates a free line ROI from the pixels in a skeletonised image.
The skeleton should not have forks, junctions or loops. If the skeleton comprises separate objects then the command can be applied sequentially
to each object. Each ROI is saved and can be restored using Options/Restore ROI. See also 'Changes to macros'.
Bug fixes:
In 'Bacterial MicroCompartments' analysis folder and file names are now truncated to avoid output filenames longer than 30 characters.
Other changes:
'Prune Skeleton' is now a separate menu item in the Process/Binary submenu. The macro command is unchanged.
JPK images with 32-bit data values are now supported.
'Windows to Stack' and 'Stack to Windows' for up to 1000 images is now more memory efficient.
Modified 'Microneedle Analysis' to handle breached epidermal layers.
Changes to macros:
The macro command 'SkeletonToROI' has been added (see above).
Added 'RotatingMask' macro command. Its argument N sets the size of the NxN mask where 3 <= N <= 15.
197-2 (27 Jan 15)
Added features:
A new 'Microneedle Analysis' item has been added to the MIASMA menu.
Bug fixes:
Fixed a bug to ensure that values calculated for a rectangular ROI agree with values for a whole image of the same region.
Fixed a bug affecting density slicing in magnified histogram windows when the image had an inverted z calibration.
Other changes:
Increased 'Image Correlation' plot size to 512x512.
Microcirculation Analysis now works with QuickTime movies rather than AVI files.
Changes to macros:
None.
197-1 (24 Aug 14)
Added features:
None.
Bug fixes:
None.
Other changes:
Constraining rectangles and lines to power-of-2 sizes to allow FFT operations now works by pressing the tab key (no shift key required)
when the selection is being created or resized. Pressing tab before a mouse click suppresses the creation of a new selection.
Changes to 'Bacterial MicroCompartments' analysis:
Miscalculating bacteria lengths has been reduced.
Output of invalid values has been suppressed.
Added output of mean bacteria lengths and widths for all images in folder.
Added image map of compartment density.
Added overlay map of compartment locations.
Changes to macros:
None.
196-3 (23 Mar 14)
Added features:
None.
Bug fixes:
Fixed a bug in the calculation of bounding boxes.
Other changes:
Suppressed the loading of hyperspectral data when browsing FTIR images.
The smallest image that can be opened is now 8 x 8 pixels.
Reduced the values of some global constants to reduce the size of static arrays.
Cancelling a dialog to save an image on quitting Image SXM cancels the Quit, not just the Save.
Changes to macros:
Added access to the array of modal density values (rMode) calculated using 'Measure' or 'Analyze Particles'.
196-2 (14 Feb 14)
Added features:
A new 'Merge RGB Stacks' item has been added to the Stacks menu. From separate stacks of red and green (or red, green and blue)
images it creates a colour stack with the System LUT.
Support has been added for Varian hyperspectral FTIR images.
Bug fixes:
Fixed a bug affecting selection and dragging of COI windows in PrinCIPia.
Fixed a bug that caused the 'Preferences' menu item to appear twice in the 'Image SXM' menu.
Other changes:
None.
Changes to macros:
Changed some window operations so that they look at the 'front' window rather than the 'active' window. This means that,
if the user clicks on and uses another application while a macro is running, the macros will continue to run as expected.
196-1 (28 Jan 14)
Added features:
Unchecking 'Update Stack Slice Titles' from the Options > Preferences dialog box now suppresses slice title updates
in stacks created from windows (as well as stacks loaded from files, as before).
Bug fixes:
Applying '3-Point Compensation' to a 32-bit or 64-bit image now works correctly.
Fixed a bug affecting window updates after a copy-paste-close operation.
Fixed an incompatibility between the GNU Pascal compiler and CodeWarrior that resulted in some TIFF tags not being read correctly by other applications.
Fixed a bug affecting saved 24-bit colour images. The bug did not affect 24-bit RGB image stacks.
Bugs fixed in PrinCIPia routines:
Working on a CIPstack load from an earlier session could give inconsistent results.
'Flatten Grain Map' gave incorrect colours if the window size was scaled below 100%.
Other changes:
Changes to PrinCIPia routines:
The standard CLUT has been rotated so that North = green/yellow, East = red, South = blue/magenta, West = cyan.
Moving a COI window moves its associated Pole Figure and CLUT windows such that they stay to the right of their parent COI.
Closing a COI window closes its associated Pole Figure and CLUT windows.
Changes to macros:
None.
195-2 (30 Aug 13)
Added features:
When stacks are loaded and the slices have individual names, then either (i) these names can be used to update the stack window
title when the slices are selected, or (ii) the stack can retain its fixed title when the slices are selected. This option has a checkbox
in the Options > Preferences dialog box.
The Histogram window can now be optionally displayed at a magnification factor of x2. This option has a checkbox in the
Options > Preferences dialog box.
Bug fixes:
Fixed a bug that could affect switching between windows, leaving the current (active) window undefined.
Resolved an ambiguity between different types of AFM images having a common '.afm' file suffix.
Fixed a bug that prevented a Zoom window (created with z-click or shift-Z-click) from updating correctly. The Zoom window is a small
window showing a magnified view of the region of the image around the cursor (default 2x magnification, 4x if the shift key is also pressed).
Other changes:
Changes to LEED I-V routines: (i) minor changes to tracking algorithm; (ii) fixed bug affecting small values of allowed tracking error;
(iii) sorted LEED spot output into order of distance from centre of LEED pattern; (iv) minor changes to format of output files.
Constraining ROIs to be a power-of-2 sized square now uses the shift and tab keys.
When clicking in a stack window, cmd-space (magnifier tool) takes priority over cmd (scroll through stack).
'Size Distribution' now works for radii up to 1000.
When doing a Rodbard fit to density calibration data, if negative fit parameters are produced that result in an invalid fit then those
parameters are reset to zero. This was unnecessary with versions of Image SXM written in Motorola code, but can cause problems
with Intel versions. If you use Rodbard fits to calibration data then I suggest you check the results and email me if you see any
inconsistencies between different versions of Image SXM.
Added support for raw NEF images from Nikon D7100 DSLR cameras.
Changes to macros:
Macro command 'UpdatesOff' now has a more global effect on all screen updates, not just those involving ROIs.
195-1 (6 May 13)
Added features:
A new 'Pincushion/Barrel Distortion' item has been added to the Process menu. Click on the 4 vertices of a pincushion or barrel shape
that, after correction, will appear square. Then click on the 4 mid-points of the sides of the shape. If the image is a slice in a stack,
then all the slices of the stack will be corrected. Press the option key and select 'Set Pin/Barrel Options' to change the number of
vertices and sides from 4 to 3 (ie, squares to triangles).
A new 'Distort To Fit' item has been added to the SPM/Calibration submenu. This distorts one image such that the positions of four
fiducial points match those in a second image. Click on four features in the image to be distorted, then on points corresponding to
the same four features in the second image. If the first image is a slice in a stack, then all the slices of the stack will be distorted using
the same mapping.
Bug fixes:
Fixed a bug affecting the loading of TIFF images from SXM manufacturers JEOL, JPK, LEO and Zeiss.
Fixed a bug that affected scrolling in save dialogs.
Other changes:
Modified LEED I-V routines to load TIFF or BMP images rather than QuickTime movies.
In Microfibril Analysis, the user can now vary image brightness/contrast during analysis. Also, the algorithm used to find microfibril
beads (enhancing contrast, applying an unsharp mask, applying a histogram-dependent threshold) has been refined.
When appending a window title with a suffix to indicate the compensation that has been applied (T = Tilt, Q = Quadratic, L = Line-by-Line, etc)
the compensation suffix is now inserted before any filename suffix.
When duplicating an image the suffix 'copy' or 'copy x' is now inserted before any filename suffix. This is now consistent with way that
Finder names duplicated files.
Changes to macros:
Macro commands 'UpdatesOff' and 'UpdatesOn' have been added to allow user control of window updates. This can result in macro
execution speed increases of one or two orders of magnitude if windows are updated very often.
194-2 (2 Feb 13)
Added features:
None.
Bug fixes:
Fixed a bug that affected the visibility of text when using the text tool in images.
Fixed a bug affecting Image SXM macro commands (but not NIH Image macro commands).
Other changes:
None.
Changes to macros:
See above.
194-1 (20 Jan 13)
Added features:
None.
Bug fixes:
None.
Other changes:
RHK Technology XPMPro SM4 images now display image types (in the Get Info window) that are more descriptive of the image data.
Files with specific suffixes can be now opened by dragging on to the Image SXM icon, regardless of their file type. The file suffixes are:
Two arrays of measurement results (Xi and Yi) have been added to complement the built-in arrays (rX and rY) that hold the XY coordinates
of the centres of objects. The new arrays hold the XY coordinates of a point that is guaranteed to be inside the object. (Note that the
coordinates held in rX, rY may fall outside the boundary of an object if it has an irregular outline.)
193-5 (12 Dec 12)
Added features:
None.
Bug fixes:
Fixed a bug when saving 24-bit images (not 24-bit RGB stacks) on Intel Macs.
Fixed a bug affecting some NanoSurf SPM images.
Autosaving the Session Log when it exceeds 32 Kb now works correctly.
The Histogram window now updates with the correct LUT when switching windows.
Fixed an undo bug affecting some paste operations.
Other changes:
Added single-key shortcuts to select the paste transfer mode (C=Copy, A=And, O=Or, X=Xor, R=Replace, B=Blend) when the
Paste Control dialog window is open.
Added an option to the Paste Control dialog box to allow 'Copy' to be set as the default paste transfer mode for every paste operation.
Changes to macros:
Fixed a bug that, when the 'SetOption' macro command was followed by any of the 'DoCopy'/'DoReplace'/etc commands for changing
the paste transfer mode, resulted in the termination of any pending paste operation.
193-4 (14 Aug 12)
Added features:
None.
Bug fixes:
Fixed a low-level bug affecting 32-bit numbers on Intel Macs.
Other changes:
3d plots on Intel Macs have been speeded up by a factor of 10.
Changes to macros:
None.
193-3 (1 Jul 12)
Added features:
None.
Bug fixes:
Fixed a bug in creating 24-bit colour images from RGB stacks (introduced in GPC).
Fixed a bug in labelling particles in 'Analyze Particles' (introduced in GPC).
Other changes:
None.
Changes to macros:
None.
193-2 (14 May 12)
Added features:
None.
Bug fixes:
Fixed a bug in Microcirculation Analysis introduced by the port from CW to GPC.
Other changes:
None.
Changes to macros:
None.
193-1 (28 Apr 12)
Added features:
Support has been added for Leica SP5 confocal microscope LIF images.
Support has been added for RHK Technology XPMPro SM4 (v5) images.
Support has been added for Veeco Innova SPM images.
Support has been added for Zeiss AxioVision images.
A new 'Microfibril Analysis' item has been added to the MIASMA menu.
Bug fixes:
Pasting text could sometimes be disabled.
Other changes:
Extensive rewrite using Xcode and GNU Pascal Compiler to create Intel-native version.
Changes to macros:
None.
192-2 (15 Sep 11)
Added features:
None.
Bug fixes:
Nanonis SPM images with large file headers would not open correctly.
Other changes:
None.
Changes to macros:
None.
192-1 (18 Apr 11)
Added features:
None.
Bug fixes:
Opening an SPM image after applying an FFT could result in the SPM image displaying reciprocal xy scales.
Other changes:
Development of PrinCIPia routines. See PrinCIPia web page for details.
Changes to macros:
None.
191-1 (23 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).
190-1 (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 half a pixel 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).
189-1 (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.
None.
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'.
Changes to macros:
The macro command 'PruneSkeleton' has been added (see above).
188-1 (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.
187-1 (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 two–image 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.
186-1 (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/Cell Analysis submenu. 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 browsing 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.
185-1 (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.
184-1 (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.
183-1 (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.
182-1 (28 Jan 07)
Added features:
Support has been added for FITS image files with 32-bit real data.
Support has been added for compressed 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.
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).
The 'Differential' command can now also be used to differentiate Histogram plots.
Changes to macros:
None.
181-1 (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 (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.
Changes to macros:
The macro command 'FFT' now also works on line profiles.
180-1 (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.
179-2 (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.
179-1 (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.
178-1 (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.
177-1 (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.
176-1 (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.
175-2 (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.
175-1 (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.
174-2 (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 173-1 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).
174-1 (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 173-1 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.
173-1 (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.
172-1 (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.
171-1 (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.
170-1 (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.
169-3 (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 – 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 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.
169-2 (14 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.
169-1 (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 and the anisotropy of the particle distribution are displayed in the Info window and in the Session Log.
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. 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.
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.
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 – 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 – 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 – the latest version of CarbonLib can be downloaded from Apple's web site.
Changes to macros:
None.
168-4 (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 did not fit entirely
within the screen display.
Other changes:
None.
Changes to macros:
None.
168-3 (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 – 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.
168-2 (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 – 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.
168-1 (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 – if you want the 68K 'F' version, please email me.
Changes to macros:
None.
167-3 (28 Oct 01)
Added features:
A new 'Facet Calculator' item has been added to the SPM/Calculation submenu. This allows the facets that form vicinal surfaces to be calculated
from the Miller indices of the surface, or from the miscut angle and azimuth, or vice versa.
Bug fixes:
Scanning tunnelling spectroscopy (STS) data associated with Omicron SCALA images will now display correctly if the start point is greater than the
end point (ie, if the data are stored in the STS file 'backwards').
The STS Plot window will now update when the mouse is placed in the grow box (ie, the bottom-right-hand corner) of an image window.
For Omicron SCALA images, the SPM/Parameters/Display Parameters dialog box incorrectly displayed the scan rate as 'Scan Time'.
Changes made to the file handling code in 167-1 caused SPM/Files/Change File Types to work only with individual files – it now handles all files in a folder correctly.
The xy coordinates of the STS data displayed in the Info window had the x and y coordinates interchanged.
Other changes:
Files of type '????' are now treated as SXM image files (though it is still advisable to change the file types to 'iSXM' to ensure that images can be
opened by double-clicking files in the Finder).
Changes made to the code to comply with the Carbon model of Mac OS X have resulted in the 68K code failing to run correctly in the 'M' version.
For the time being, the 68K 'F' version will be distributed separately.
Updated support for Digital Instruments NanoScope III v5.12.
Changes to macros:
None.
167-2 (15 Jul 01)
Added features:
None.
Bug fixes:
Fixed a memory leak that affected Leica TCS images.
Other changes:
Selecting all of an image does not now reset the magnification to unity.
The Session Log now displays the current window title only if it is different from the previous line.
Changes to macros:
None.
167-1 (30 Jun 01)
Added features:
A new 'Quasicrystal Symmetry' item has been added to the Specialist Analysis submenu (see below). This procedure finds and displays sites of local 5-fold or 10-fold symmetry.
Support has been added for Leica TCS images.
Bug fixes:
'Radial Distrib From Click' calculated the radial distribution about the centre of the image, ignoring the location of the mouse click.
Other changes:
A 'Browse' menu item has been added to the File menu by user request. This is identical to the 'Browse Images' items in the SEM and SPM/Files menus.
Help pages can now be navigated by clicking on items in the contents page, and returning to the contents page by clicking in the top left corner of any page.
All of the Help and History files have been moved into a new 'Documentation' folder. Also, a new 'Overview' file for new users and the documentation
provided with NIH Image have been included as pdf files.
Browsing now handles alias files correctly.
The maximum number of files in a folder that can be browsed has been increased to 2500.
Menu items at the bottom of the Analyze menu have been moved into a new 'Specialist Analysis' submenu.
Any routine that can be aborted with 'cmd-period' can also be aborted by pressing the escape key.
All of the code dealing with file handling has been modified to comply with the Carbon model of Mac OS X.
Changes to macros:
The maximum number of files in a folder that can be handled by the 'Open...File' macro commands has been increased to 2500.
Macro commands 'SaveROIarray' and 'RestoreROIarray' have been added to mirror their menu counterparts.
The maximum number of symbols in the Symbols Table has been increased to 600.
166-2 (14 Apr 01)
Added features:
None.
Bug fixes:
Radial Distributions applied to FFTs would produce plots with the zero of the x axis set incorrectly.
Azimuthal Distributions applied to FFTs would produce plots with the x axis labelled incorrectly.
Azimuthal Distributions would produce plots in which the 0° value did not equal the 360° value.
Duplicating the power spectrum of an FFT now produces an image with the correct xy calibration.
Loading TIFF images with invalid tags would give unpredictable results.
Other changes:
When creating an image caption (to appear under an image when printed or saved as an EPS or PDF file) the default caption is now the
Finder comment string. Use 'SXM Preferences... / Comment' to set the format of the Finder comment. See also 'Get Finder Comment'
and 'Set Finder Comment...' under 164-1.
The new menu item 'SPM/Parameters/Add Caption To Image' allows an image caption to be added to an image directly. If the caption
needs editing before being added to the image, use 'Create Image Caption' first.
Changes to macros:
None.
166-1 (10 Mar 01)
Added features:
Support has been added for Klocke Atomikro SPM and SNOM images.
Bug fixes:
Attempts to browse folders containing no files would give misleading error messages.
Image SXM will now run OK under any Mac OS from 7.0 to 9.1.
Other changes:
If the option key is pressed then the menu item 'Register...' in the Stacks menu changes to 'Register XY Only' and allows slices in a stack to be
brought into registry with the current slice without rotation. Only one mouse click per slice is required to identify a reference point that is
common to all slices.
The 'cmd-cursor arrow' shortcuts now allow modifier keys to be used when loading the next or previous file: pressing the option key will close
the current window before opening the next; pressing the shift key will skip through five files rather than load the next.
When the LUT tool is selected, option-clicking on a pixel in an image allows the colour of the LUT entry for that pixel to be changed using the
colour picker dialog.
When an FFT window is selected, the Info window now displays the base 10 log of the square root of the magnitude of the power spectrum for each pixel.
It is now possible to browse in folders containing image files masquerading as text files.
Support for TopoMetrix SPMLab v5 has been updated to account for changes made to the image file format.
Many changes have been made to the code of Image SXM to comply with the Carbon model of Mac OS X.
Changes to macros:
None.
165-2 (23 Jan 01)
Added features:
None.
Bug fixes:
After using 'ReCalibrate XY...' to calibrate the piezo scanners of an SPM, a file containing the calibration data was not saved to disk.
DME SPM images are acquired from bottom-to-top and so are now flipped vertically before being displayed.
Other changes:
In the 'SPM Options' dialog box, a custom image data type has been added to the bottom of the pop-up menus to give the user more control over which
images are displayed when opening multi-image files.
When browsing files in a folder is complete, the 'cmd-cursor arrow' shortcuts will allow browsing to continue in another folder: 'cmd-right' or 'cmd-down'
will browse files in the next folder (at the same level as the original folder) and 'cmd-left' or 'cmd-up' will browse files in the previous folder.
Changes to macros:
None.
165-1 (10 Dec 00)
Added features:
Pop-up menus have been added to the 'SPM Options' dialog box to give the user control over which images are displayed when opening multi-image files.
The images can be specified by the image data type (amplitude, current, height, etc) or their location in the file (first, second, etc), depending on the SPM
file format. Also, the user can specify which images are displayed when browsing and which are loaded when executing 'Batch Conversion' (these can be
set independently). If no image is loaded from a multi-image file, the resultant alert box can be suppressed.
The 'XResolution', 'YResolution' and 'ResolutionUnit' tags are now set in TIFF image file headers. This allows other applications (Mac, PC and Unix) to display
the correct xy calibration when opening TIFF images saved by Image SXM. The TIFF file format specification is limited to an xy scale in units of cm. It does
not allow for smaller units or for z calibration. If the xy scale of an image is > 200 pixels per nm, then the resolution set in the header is reduced by a factor
of a million to keep the 'pixels per cm' value within the range of a long integer.
Support has been added for Quesant Instruments SPM images.
Support has been added for Philips SEM images.
Bug fixes:
Custom colour tables (CTs) would not be set correctly after displaying a (greyscale) dialog box. This was a problem only for CTs that had been modified by
the user with the eyedropper tool, not for those selected from the Color Tables submenus.
Two image file formats that use the same four-byte 'signature' at the start of the file could be confused with each other – Noran Vantage and Screen Machine.
Opening old 'Session Log' text files would cause a problem if a live 'Session Log' window was in use.
Other changes:
The 3d Plot routine has been speeded up by a factor of about 25 and the dialog box has been reorganised. The view, light and z scale parameters can now be
changed using the cursor keys and the option, control and shift keys, respectively. The view angle of a 3d plot can also be changed by holding down the space
bar and dragging the mouse around in the plot window. A 3d plot of a 256 x 256 pixel image can be recalculated and displayed in about 50 ms on a G4.
Non-square images from Digital Instruments NanoScope SPMs have the image size in pixels stored incorrectly in the 'image list' of the file header. Image SXM
now reads the image size from the 'scan list' and ignores the values in the 'image list'.
Selections from the SPM/Dimensions submenu now affect all open images or only the current image, depending on whether or not the option key is pressed.
Previously, this was dependent on the setting of a checkbox in the 'SPM Options' dialog box.
The stack type (RGB, HSV, movie, volume) of a stack saved by NIH Image is now read from the file header.
An unnecessary warning dialog box has been suppressed when opening RHK Technology SPM images.
Changes have been made to the zoom and scroll routines (using the magnifying glass and hand tools) to allow more flexibility when working with images that
have been scaled to fit the size of the monitor.
Changes to macros:
None.
164-1 (4 Aug 00)
Added features:
Two new items have been added to the SPM/files submenu, 'Get Finder Comment' and 'Set Finder Comment...'. The first gets the Finder comment of the image
file and uses this to set the comment of the image, and the second sets the Finder comment of the image file or all files in the same folder as the image file.
The 'image file' is taken to be either (i) the file to which the image was saved or, if the image has not yet been saved, (ii) the file from which the image was loaded.
A dialog box allows the user to select image parameters that can be concatenated with the image comment to form the Finder comment. If the option key is
pressed or if the command is called from a macro (see below) then the dialog box is suppressed. The dialog box can also be accessed from the 'Comment' button
in the 'SXM Preferences' dialog box.
Two checkboxes have been added to the 'SXM Options' dialog box that allow the Finder comment to be read from or saved to image files automatically on loading or
saving. Setting both of these options simultaneously is not recommended, as the concatenation can lead to the comment growing in length each time it is loaded/saved.
A new 'Invert Selection' item has been added to the Edit menu. This procedure changes the selection from all pixels inside the current region of interest (ROI) to all
pixels outside the ROI.
A new 'Autocorrelation' item has been added to the FFT submenu. For images, this is equivalent to the macro command of the same name supplied with NIH Image.
If a line selection has been made on an image, or if the current window is a Profile Plot or an FFT of a Profile Plot, then the autocorrelation of the Profile Plot will be
calculated and displayed.
Two new items have been added to the Analyze menu, 'Radial Distribution' and 'Azimuthal Distribution'. The first produces a profile plot which is the average of 360
line profiles obtained from line selections arranged radially from the centre of the image. The second produces a profile plot in which each data point is the average
of the data points for a line selection arranged radially from the centre of the image.
Support has been added for Omicron SPA-LEED images and spot profiles.
Bug fixes:
'Browse Selected Images' could display the wrong selection of images if multiple Browse windows were open.
Loading macros would cause an unexpected quit on 68K Macs.
Exporting the data from plots created using the macro command 'PlotUserData' resulted in empty text files.
Convoluting with kernels larger than 31x31 would cause a crash. The maximum is now set to 63x63.
Other changes:
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 application created, but the probability of introducing a bug in the process is not insignificant.
All previous versions of Image SXM have had version numbers that indicated the release of NIH Image into which all the SXM-related routines were grafted or
spliced. There will be no further development of NIH Image and so it will remain frozen at v1.62. Image SXM is compiled from 95,000 lines of source code (almost
double that of NIH Image) and so justifies a new version number. From here on, version numbers will increment from 164-1, with major new features incrementing
the version number and minor bug fixes incrementing the release number (the digit after the dash).
Many floating point operations now execute significantly faster. As an example, on a G4/400 an FFT of a 512x512 image now takes < 0.7s compared to 1.4s previously.
The speed comparison chart on the last page of the online Help pages has been updated.
The maximum number of data points in STS spectra has been increased to 250.
The 'Page Up', 'Page Down', 'Home' and 'End' keys now work in text windows.
Routines that calculate the size of hard disks now recognise disks in Mac OS Extended (HFS+) format.
Changes to macros:
Macro commands have been added to handle Finder comments: a 'GetFinderComment' function and a 'SetFinderComment' command. These two macros mirror
their menu counterparts as described above, and in addition the GetFinderComment function returns the comment as a string.
Macro commands 'PlotRadialDistrib' and 'PlotAzimDistrib' have been added to mirror their menu counterparts as described above.
Four macro commands have been added to improve user access to the data corresponding to a plot (such as a force curve, scope data, line scan, I-V spectrum,
spot profile, etc) in the current window: 'GetUserData', 'GetPlotScales', 'GetXYfromPix' and 'GetPixFromXY'. See the 'Image SXM Macros' help pages for more details.
Four macro functions have been added to enable the user to batch process files in a folder: 'GetFolderInfo', 'OpenFirstFile', 'OpenNextFile' and 'OpenPrevFile'.
See the 'Image SXM Macros' help pages for more details.
The 'SetPalette' macro command can now set any of the colour tables (CTs) in the Options/Colour Tables menu. To set the Digital Instruments CTs use the parameters
'CT0', ..., 'CT25' and to set the remaining CTs use 'Red', 'Green', 'Blue', 'RedGreen', 'GreenBlue', 'BlueRed', 'RedGreenBlue', 'RedMagBlue', 'RedYellGreen', 'Gold',
'GoldRed', 'Pastel' or 'Mandelbrot', respectively.
