sliceOmatic 4.3 - Previous versions
Critical updates New features an updates Minor changes


  • Read sliceO-5 TAG files.


  • Fix a problem with Region Growing slider values.


  • Fix a problem for images that do not have pixel dimmentions (ex: JPEG) that would freeze the surface/volume computation.


  • Add a new system variable: "$REGIONAL_FLOAT" that you can set to "," to change the float values from xx.yy to xx,yy for european Excel. In the command line, type "$REGIONAL_FLOAT = ,". You can also create a script file with the same command.
  • Better control of the threshold values for Threshold and Region Growing modes.
  • Fix a problem with Spline masks and rectangular images: The mask was clipped on the right portion of the image.
  • Fix a problem with the surface/volume result file creation


  • Add a "Calibration" file to help compute densities from CT HF values. You need to provide a table of associated Houndsfield / density values, read that table with the "read: calibration file name" table, and the "Calibrated" values will be available in the surface/volume results. The table is in ASCII with 2 values per line: the HF and associated density. The HF must be sorted by increasing values. Any holes in the values will be filled by sliceO with linear interpolation.
  • Fix a problem with DICOM colormap images.
  • Fix a bug where the size of the text in the inteface was not changed immediately when the interface size was changed.
  • Fix a problem with volume computation if the slice thickness is larger than the distance between slices. In that case, we assume Delta_ab = ABS(Za-Zb) and Vab = Delta_ab * (1/3 ABS(Surf_a-Surf_b) + MIN(Surf_a,Surf_b)
  • Add a "Measure Roughness" tool in the 3D tools. This tool can be used to measure the "roughness" of a 3D polygon surface.


  • Fix a problem with the medi-browser that prevent it from displaying a dir where one of the image whas invalid.
  • Fix a a bug with the command "measure: * write file" that cause it to crash.
  • Add a propagate tool to the measurement mode.
  • Fix a 3D refresh problem on Windows-7.
  • Fix a license problem that prevent the program from seing the update license.


  • Fix a refresh problem in Windows Vista and 7.


  • Fix a memory problem intorduces in rev-8.
  • New license scheme (now valid after 2012).


  • Fix a crash with the script when some of the arguments are negative numbers.


  • Add the "Histogram" data to the DB surface result file. This will give the number of pixels for each TAG for each GLI value. This is usefull to compute densities from the Houndsfield values.


  • Re-work the measurement tools interface:
    • add top/but/up/down option per tool to help manipulate the tools.
    • just one "save" button, but you can select to save as "txt" for numerical values, or "scp" for a script that will enable to re-create the tool.
    • Clicking on a control of a tool will select it.
    • When manipulating multiples tools with overlapping controls, the control of the currently selected tool will be grabbed first. If it is not under the cursor, then the control of the top-most tool will be selected.
  • Re-work on the tag masks interface:
    • Add "quadrant" tool. This tool has 3 controls, the first 2 define a line, the 3rd define another line perpendicular to the first one. These 2 lines split the screen in 4 quadrants. The quadrant containing the top left corner of the image is 1, it will be tagged with the tool selected color, the 3 other quadrant will be tagged with the select color + 1 to 3.
  • Made sure that if the program incorrectly detect that the TAG file may not be the correct one for the GLI file, you can re-save the tag file to correct the warning.
  • Make some minor changes to support the Wacom tablettes. To take advantage of the tablette, start the "Wacom Tablette Properties" program,
    • in "Grip Pen" "Eraser" settings, set the eraser to "Right Click"
    • in "Functions", the Touch strip should be set to Auto Scoll/Zoom and the expressKeys can be remapped to any keys you like. The buttom button can be set to "Modifier Ctrl" to help manipulate images. The key mapping you chose here is associated with a key that can also be remapped to any functions inside sliceOmatic.

2008 and Before
Please contact TomoVision for versions dating before 2009.


  • Fix an error in the volume computation if there is an overlap of the slices. The volume was overestimated!

    The old (and incorect) eq. was (when Delta, the gap is < 0):
    Vab = (1/2 Ta + 1/2 Delta_ab) * Surf_a
        + (1/2 Tb + 1/2 Delta_ab) * Surf_b
        - Delta_ab * (1/3 ABS(Surf_a-Surf_b) + MIN(Surf_a,Surf_b)
    The correct equation is:
    Vab = (1/2 Ta + Delta_ab) * Surf_a
        + (1/2 Tb + Delta_ab) * Surf_b
        - Delta_ab * (1/3 ABS(Surf_a-Surf_b) + MIN(Surf_a,Surf_b)


  • Sync with DICOMatic DLL's version 1.8 rev-6d
  • Add a missing refresh when changing the threshold colors for color images in thresholding.
  • Add a slider's lock for region growing and thresholding operations. The "Scroll Lock" key can be used, when the cursor is over the slider, to lock a slider. The script coammnds "Segment: slider" and "region: ... slider" can also be used to lock the sliders.


  • Add the possibility to change the tag associated with the thresholds in Threshold mode. You can us the optional "tag" argument in the command "segment: threshold id val [tag]" for ex: "segment: threshold 2 128 12" will set the second threshold to the value 128 and associate it with the tag #12. You can also change the associated tag of each of the 4 sliders by pressing the "Up" or "Down" arrow key while the cursor is over the slider.
  • Add blow-up pop-up windows for the Surface/Volume tool. if you click on the associated "wind" button or if you double click either on the graph or the value list, a new window with just that information will pop-up.
  • Add support for little-endian Varian images.
  • Fixed a problem that prevent "tag to snake" from working.
  • Fixed a problem where some Analyze files that had unexpected header size where not recognized.


  • Add "Transparency" to the "Display 2D Slices" tool in 3D modes. As soon as the transparency is turn on, pixel of the "fill" color will be invisible. The visibility of the rest of the image is controlled by the transparency slider. The slider select the transparency threshold. The transparency value of the slices is affected by the current color scheme:
    • For "Grey", the transparency is function of the GLI pixel value.
    • For "Mixed", the transparency of any untagged pixel is function of the GLI pixel value, The transparency of the tagged pixel is function of the tag number. (tag-1 will disapear before tag-2...).
    • For "Over" and TAG, The transparency of the tagged pixel is function of the tag number. (tag-1 will disapear before tag-2...).
  • You can now use the "Ctrl" key along with the "Insert,Home,Page_Up..." keys to display multiples slices with the "Display 2D Slices" tool in 3D modes.
  • Fixed a problem with re-sliced GLI files that occured when the slice thickness and spacings did not match.
  • Fix a bug with the interpolation for RGB images.


  • Add the "Lorensen" model to the 3D Polygon Shell mode. In this mode, the polygons are created using Lorenson's geometry instead of the usual "TomoVision" that we used before. This enable small 1 pixel wide detailed to be created. However, this model will create a lot more polygons, and the sub-sampling will be disabled.

    c.f. "Marching Cube: A High Resolution 3D Surface Construction Algorithm", William E.Lorensen, Harvey E. Cline, Siggraph 1987, P.163-169
  • Add missing Shell and Contour modes commands.
  • Add missing "Surface" commands.


  • Fix a bug with some DICOM images with multiple spaces in the pading of VR=DS value strings.

  • Recompile with DICOMatic 1.8 rev-4b DLL
  • Add a message if you drop a tag file instead of the GLI on sliceO
  • Work on the interface when the tag files are at the wrong place
  • Add black border on the lines of the Geometrical Mask mode
  • Add "Pilot Lines". The flag to display the pilot lines is associated with the key words "KEY_ACCEL_IMAGE_PILOT_ON", "KEY_ACCEL_IMAGE_PILOT_ON" and "KEY_ACCEL_IMAGE_PILOT_TOGGLE" by default, "KEY_ACCEL_IMAGE_PILOT_TOGGLE" is mapped to the key "/". You can also use the system variable: "$DISPLAY_2D_PILOT" and "$DISPLAY_2D_PILOT_ALL" to access this flag.
  • Add a new 3D tool: "Display 2D Slices" to show the 2D images in the 3D window. The "insert", "Delete", "Home" "End" "Page Up" and "Page Donw" keys can be used to change the displayed studies, groups and images.
  • Fix a problem with negative values in command lines. The support of the mathematical operations (+-/*) in the command line caused the negative values (ex: "-100") to be seen as 2 arguments ("-" and "100"), causing syntax errors in some commands.
  • Fix a bug with tag (0028,0030) "Pixel Spacing". The x and y values where inversed.

  • Decrease the influance of the "z" dir gradient to help the morpho segmentation for 3D volumes.
  • Match format changes of DICOmatic 1.8 rev-4.
  • Change the HASP license libraries
  • A few syntax changes in the script parser
  • Improved Raw_Header program

  • Some work on TIFF, Siemens SPI & Vision, FUJI DICOM, Kretz and JPEG formats.


  • Work on the slice Origin command in Admin and on the $IMAGE_CUR_ORG variable.


  • Fix another stack overflow in Morpho.


  • Use the new conversion libraries (DICOMatic 1.8).
  • Add the possibility of deleting measurement ROI key points.
  • Add th possibility of re-reading measurement script and applying them to the current image is the original image is not present.
  • Add a new measurement tool in the 3D modes to save geometries informations such as lenght, surface and volumes.


  • Fix a bug that prevent startup script path from being more than 80 char.
  • Fix a bug in the "preferences" menu that cause some of the "set" command from being skipped.


  • Fix a bug that cause a crash: when closing all slices, the "Image Info" tool was not properly refreshed.
  • Add a window to offer to "save modified tags" before closing slices with Admin "close" button.
  • Remove patient ID from the overlay in mode "Anonymous".


  • Fix a bug in the variance. The value was wrong for large surfaces (>40000 pix).
  • Add a rounding fudge factor for region growing paint mode


  • Use the latest DLL from the conversion library (rev-10)
  • Fix a bug that limit the region growing script to 3 tag values
  • Fix a bug with spaces in file names in preferences
  • Add the patient name in the Exel output
  • Now output surfaces for all groups in surface/volume in mode all
  • Fix a bug that prevented single work commands to be used


  • Fix a problem with saving TAG for files that have multiples images in the same file. (such as Bruker...)
  • Add a scroll bar to the overwrite warning message for long file names.


  • Fix a bug with pixel interpolation that mix 2 adjecent slices
  • Better support of float pixel types
  • Add a "*" to untrusted values in the text overlays
  • Add a colormap in the overlay. The visibility of this colormap is is controled by the 0x10 bit of the $DISPLAY_2D_OVERLAY_FLAG. Also the keyborad shortcuts "OVERLAY-COLORMAP-ON", "OFF" and "TOGGLE" have been added. The "OVERLAY-COLORMAP-TOGGLE" has been mapped to the "c" key in sliceO_key.scp.
  • Use new DICOM DLL (1.8 rev-a)


  • Add missing "mode" word in Geometric mask script files
  • Add "Surface" geometric mask. This new mask is a circle of fixed radius. The radius can be changed by a right click on the "surface" button.
  • Fix a bug that prevent DICOM images with "sequence tags" near the start of the image to be recognized.
  • Now check the number of valid geometries for the "write: geom ..." command to prevent a crash when no geometry exist.
  • Increase the stack size for Morpho computation to prevent a stack overflow.
  • Add a version number with the -v argument for GetFilename.exe


  • Fix a bug in the saving of GLI images. If not all images where selected, the results in the Data-base programs would be wrong!


  • Fix a bug in the edition of re-sliced images


  • Add a chksum and UID to the TAG files to ensure that different GLI with the same name do not overrite each other's TAG.
  • Add warning and confirmation if the above problem occur.
  • Fix a minor bug in re-slice & add axes
  • Add a warning message if attempt to measure an image with no pixel dimentions values (ex: Secondary Capture)
  • Add missing sliceOconfig in install batch


  • Fix a bug that prevent STL files from being read.
  • Enable the LAA flag for 4Gb address space on 64 bit windows


  • Fix a few bugs in 32 bit images that prevent Morpho from working.
  • Add more space to display 32 bit GLI values
  • Add save & read option for the measurement tool
  • Add horiz. scrool bar to the measurement tools window


  • Fix a few bugs with groups of images that change over time instead of over "depth".


  • Work on Admin Mode: The goal is to help create a 3D set from multiples series.
    • Slices are now grouped differently: by series and acquisition if these values are present.
    • Add 2 new buttons "Offset Selection" and "Reset Selection" to add a "d" offset to multiple slices at once
    • "Sort Group" now pop a warning window if it can not creat a 3D volume.
  • Change the default tag file name treatment. Now tag file name that have non-UNIX characters in their name are treated "as is" (like in sliceO 4.2). The file name can be "cleaned-up" by setting the TAG_UNIX_name flag with the command "set: TAG_UNIX_name 1". If sliceO can not read tag images created with previous versions of 4.3, set this flag to 1.
  • Add a "Units" tools to change the units of the distances surfaces and volumes in the program.
  • Add a "Color Map" tool to change the default B&W colors used to display the GLI images.


  • Add p=num and g=num in the file: read script command to preserve the image grouping when saving and reading slices with script files.
  • Some changes to the script parser to help when reading files with spaces in the names


  • Fix a refresh bug in Mode threshold (only the displayed images where refreshed correctly)
  • Add some info for groups in Admin
  • Implemented the automatic memory manager. It will automatcally clear seldom used memory to keep the amount of memory used by the program under the "high water" mark. The following variables can be used to control the memory manager: (c.f. manual)
    $MEMORY_HIGH_WATER R/W in Mbytes
    $MEMORY_LOW_WATER R/W in Mbytes
    $MEMORY_SYSTEM R/W in Mbytes
    $MEMORY_RAM R in Mbytes
    $MEMORY_TOTAL R in Mbytes
  • Fix a bug with te Snake from TAG function
  • Add the possibility to save/read Snakes with script files
  • Fix a graphic bug with the Measurement Mode icons
  • Implemented new variables and script commands to control the Volume rendering (Volume and MIP Modes)


  • Fix a bug that prevent thread from starting if the memory was to full
  • Remove first tab in surface db files
  • Prevent any refresh while files are reading to prevent crash
  • Fix a bug in the volume computation of the surface/volume tool


  • Add a number of new variables, and a few minor bug fixes


  • First non-beta release
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