April 30th, 2012Added 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.
April 21st, 2011· New 'Remove Low Frequencies'.
· New 'Find Matching Shapes'.
· New 'Find XY Displacements'.
· New 'Find Edges (5x5)' filter.
· Cmd-G will grab a frame from a firewire camera.
· New 'Bounding Box' added to 'Measurement Options'.
· Updated support for Molecular Imaging PicoScan v5.3.
December 26th, 2010Added 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.
· Orientation Imaging is now named 'PrinCIPia'.
· 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).
September 2nd, 2010Added 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).
May 21st, 2010· Updated support for Nanonis SPM images. New algorithm in 'Parasite Counting Analysis'. New algorithm in 'Lymphocyte Flow Analysis'. Convolutions now process to the edges. Video grabbing now works for images > 800x600. Scaling images of width > 8000 pixels could give artefacts. Image compensation for JEOL SPM images was not applied correctly. Calculation of a perimeter could give an underestimate by 0.5 pixels.
August 29th, 2009Added 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'
Changes to macros:
· The macro command 'PruneSkeleton' has been added (see above).
March 4th, 2009· Fixed NanoScope v5.12 SPM image z calibration issue.
· Fixed line-by-line compensation bug.
· Compensation can now be applied to images that are not SPM images.
· Added background subtraction to 'Particulate Matter Analysis' to compensate for vignetting.
October 6th, 2008· 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.
· 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.
· 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.
April 22nd, 2008· Limited support has been added for Omicron Matrix STM images.
· Omicron (pre-SCALA) STM images listed with SPM/Parameters/List Params...
· Options when browing Omicron SCALA images to display only channel 0 and/or only forward scan.
· Fixed bug that stopped macro command 'DepthOfFocus' working.
January 18th, 2008· Support for Nanonis SPM images.
· Support for Asylum Research MFP-3D AFM images.
· Maximum image size 32000 x 32000 pixels.
· Maximum number of measurements 99999.
· Browsing displays thumbnails in a stack.
· Macro command 'DepthOfFocus' now has arguments.
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