# Menus
"Edit" "View" "Process" "Filter" "Model" "Measure" "Conversions" "Utilities"
"E"    "V"    "P"        "i"     "M"        "s"    "C"           "U"
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# Menu Format: executable  name_in_menu menu_# license_category mnemonic accelerator accelerator_text
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# If "executable" is a full path name, use it as is
#
# Edit Menu
EditImageHeader  "Header"        0  "PRIISM"  "H"  "Ctrl<Key>h"  "Ctrl+H" "Edit image header metadata"
CopyRegion       "Copy Region"   0  "PRIISM"  "R" " "  " "  "Create a new image from a region-of-interest" 
ImgFusion        "Image Fusion"  0  "PRIISM"  "I" " "  " "  "Combine two images"
CutMask          "Cut Mask"      0  "PRIISM"  "M" " "  " "  "Create an image as a binary or data mask"
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# View Menu
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BlendColors  "Blend Colors"       1  "PRIISM"  "B" " "  " "  "Derive an image by blending channel colors"
/dev/null    "separator"          1  "PRIISM"  ""  
Movie        "Movie"              1  "PRIISM"  "M" " "  " "  "View image windows as animations"
Slider       "Slider"             1  "PRIISM"  "S" " "  " "  "Adjust Z or Time of several images at once"
GlobalScale  "Scale All Windows"  1  "PRIISM"  "c" " "  " "  "Adjust intensity scaling for all open windows"
/dev/null    "separator"          1  "PRIISM"  ""
RunProj      "Quick Projection"   1  "PRIISM"  "Q" " "  " "  "Derive an image by combining Z sections"
TrailsMovie  "Trails Movie"       1  "PRIISM"  "r" " "  " "  "Follow features over time"
vol_view     "Volume Viewer"      1  "PRIISM"  "V" " "  " "  "Create 3D projection image sequences using volume rendering"
/dev/null    "separator"          1  "PRIISM"  ""
Rotate3D     "Rotate3D"           1  "PRIISM"  "3" " "  " "  "Create a new image by arbitrary rotation of data volume"
Resample2D   "Resample2D"         1  "PRIISM"  "2" " "  " "  "Rotate, resample, scale, shift image frames in 2D"
FlipRotate   "Flip and Rotate"    1  "PRIISM"  "F" " "  " "  "Simple 2D flip and rotate"
stitch_ui    "Stitch"             1  "PRIISM"  "t" " "  " "  "Stitch panel-collection images"
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# Process Menu
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Correct                 "Correct"               2  "QPM"  "C" " "  " "  "Correct an image for time-varying illumination"
Calibrate               "Flat Field Correction (Resolve3D)" 2  "QPM"  "R" " "  " "  "Apply flat-field correction (Resolve3D images)"
UltraFFCorrect          "Flat Field Correction (Ultra)"     2  "QPM"  "U" " "  " "  "Apply flat-field correction (Ultra images)"
Deconvolve              "Deconvolve"            2  "QPM"  "e" " "  " "  "Apply Constrained Iterative Deconvolution to images"
Neighbor                "Nearest Neighbor"      2  "QPM"  "N" " "  " "  "Reduce blur by Nearest Neighbor method"
TimeEqualize            "Equalize Time Points"  2  "QPM"  "q" " "  " "  "Adjust time points to compensate for fading"
imgalign_ui             "Align Image"           2  "QPM"  "A" " "  " "  "Align image frames by correlation"
/dev/null               "separator"             2  "QPM"  ""
ProcessChainCreator     "Task Builder"          2  "QPM"  "T" " "  " "  "Set up chains of processing tasks"
/dev/null               "separator"             2  "OMX"  ""
OMXSIReconstruct        "OMX SI Reconstruction"               2  "OMX" "R" " "  " "  "Structured Illumination image Reconstruction"
OMXCreateOtfUI          "OMX PSF to OTF"                      2  "OMX" "S" " "  " "  "Create an Optical Transfer Function for SI Reconstruction"
OMXWarpAlignParameters  "Create OMX Image Alignment"          2  "OMX" "X" " "  " "  "Set up parameters for OMX Image Alignment"
OMXWarpAlignImageUI     "OMX Align Image"                     2  "OMX" "M" " "  " "  "Align OMX Image channels"
OMXGenerateWFImageUI    "Generate Widefield from SI Image"    2  "OMX" "G" " "  " "  "Create a Widefield image from a Structured Illumination image"
# Create a sub-menu
/dev/null                 "->Legacy"                            2  "OMX"  ""
OMXAlignParameters      "OMX Alignment Parameters"              2  "OMX" "P" " "  " "  "Set up parameters for Shift/Rotate alignment method"
OMXAlignParameters2     "OMX Image Registration Calibration"    2  "OMX" "I" " "  " "  "Calibrate for detailed Image Channel Registration"
OMXAlignImageUI         "OMX Image Registration"                2  "OMX" "X" " "  " "  "Align channels using Image Channel Registration parameters"
/dev/null                  "<-"                                 2  "OMX"  ""  
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#
# Filter Menu
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Convolution  "Convolution"        3  "PRIISM"  "C"  " "  " "  "Apply Convolution filters to an image"
EdgeEnh      "Edge Enhance"       3  "PRIISM"  "E"  " "  " "  "Create an edge-enhanced image"
Filter2D     "Filter2D"           3  "PRIISM"  "F"  " "  " "  "Apply statistical (mean, median, variance) filters"
ImgArith     "Image Arithmetic"   3  "PRIISM"  "A"  " "  " "  "Do arithmetic operations on images"
lce          "Enhance Contrast"   3  "PRIISM"  "n"  " "  " "  "Apply local contrast enhancement to an image"
Threshold    "Threshold"          3  "PRIISM"  "T"  " "  " "  "Threshold intensities (upper and/or lower) to create a new image"
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# Model Menu
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EditPolygon  "Edit Polygon"        4  "PRIISM"   "P"  " "  " "  "Create arbitrary polygons to delineate features in 2D"
2DObjFinder  "2D Polygon Finder"   4  "PRIISM"   "2"  " "  " "  "Find 2D polygons based on intensity thresholds"
vol_build    "3D Object Builder"   4  "PRIISM"   "O"  " "  " "  "Associate 2D polygons across Z to build 3D objects"
3DModel      "3D Model"            4  "MODEL3D"  "M"  " "  " "  "Create and visualize models of features in 3D"
strait       "Straight"            4  "MODEL3D"  "S"  " "  " "  "Specialized extraction of linear features"
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# Measure Menu
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Distance        "Distance"                  5  "PRIISM"  "D"  " "  " "  "Interactively measure distances between features"
Point           "Point Values"              5  "PRIISM"  "P"  " "  " "  "Under-cursor readout of intensities and coordinates"
Profile         "Line Profile"              5  "PRIISM"  "L"  " "  " "  "Generate an intensity profile of one or more images"
Pick            "Pick Points"               5  "PRIISM"  "i"  " "  " "  "Record locations of points"
/dev/null       "separator"                 5  "PRIISM"  ""
ChromaticCorrection  "Chromatic Correction" 5  "PRIISM"  "C"  " "  " "  "Visualize and adjust for Z chromatic aberration"
Colocalization  "Colocalization"            5  "PRIISM"  "o"  " "  " "  "View colocalization measurements"
Colocalization2  "Colocalization (ROI)"     5  "PRIISM"  "R"  " "  " "  "View colocalization measurements with ROI polygons"
/dev/null                "separator"        5  "PRIISM"  ""
FRETCalculator  "FRET Analysis"             5  "PRIISM"  "F"  " "  " "  "Calculate Frster Resonance Energy Transfer"
/dev/null       "separator"                 5  "PRIISM"  ""
PKA_ui         "PK Analysis"                5  "PRIISM"  "K"  " "  " "  "Analyze PhotoKinetic behavior in images (FRAP, etc.)"
/dev/null      "separator"                  5  "PRIISM"  ""
DSSIAnalysisUI  "Localization Image Analysis"              5  "DSSI"  "A"  " "  " "  "Analyze results of Localization Imaging"
DSSIView        "Localization Results Viewer"              5  "DSSI"  "V"  " "  " "  "View the results of Localization Imaging"
DSSIReconstructionUI  "Localization Image Reconstruction"  5  "DSSI"  "e"  " "  " "  "Generate Super-resolution images"
DSSIPSFToolUI   "PSF Width"                                5  "DSSI"  "W"  " "  " "  "Measure the nominal Point Spread Function width"
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# Conversions Menu
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CalculateOTF    "Calculate OTF"             6  "QPM"     "C"  " "  " "  "Generate a theoretical OTF for an objective"
psf2otf_ui  "Convert PSF To OTF"            6  "QPM"     "O"  " "  " "  "Create an OTF from a collected PSF measurement"
/dev/null       "separator"                 6  "PRIISM"  ""
ConvertTiff2DV  "Import from TIFF"          6  "PRIISM"  "T"  " "  " "  "Create a DV image from TIFF images"
ConvertDV2Text  "Export to Text"            6  "PRIISM"  "E"  " "  " "  "Export a DV image as a table of ASCII numbers"
AUPlateScan2INCarta  "Export Ultra to IN Carta" 6  "PRIISM"  "U"  " "  " "  "Export an Ultra plate scan to IN Carta format"
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# Utilities Menu
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ConfigUserParams      "User Parameters"                  7  "PRIISM"     "P"  " "  " "  "User-level configuration parameters"
ConfigSysParams_w     "System Parameters"                7  "PRIISM"     "y"  " "  " "  "System-level configuration parameters (need root password)"
OMXSettingsMigration  "Migrate OMX Settings"             7  "OMX"        "O"  " "  " "  "Export/Import OMX-specific settings"
/dev/null             "separator"                        7  "PRIISM"  ""
DVQman                "softWoRx Queue Manager"           7  "PRIISM"     "Q"  " "  " "  "Manage the list of queued jobs"
/dev/null             "separator"                        7  "PRIISM"  ""
ShowTopUsers_w        "View Top CPU Users"               7  "PRIISM"     "U"  " "  " "  "System tool to show process information"
DVSnapshot            "Image Snapshot"                   7  "PRIISM"     "p"  " "  " "  "Tool to capture the screen or window as JPG"
R3DConfig_w           "Revise Microscope Configuration"  7  "RESOLVE3D"  "e"  " "  " "  "View/edit the Microscope configuration information"
LensInfo              "Lens Information"                 7  "PRIISM"     "I"  " "  " "  "Show information about an objective lens"
LensDatabase          "Revise Lens Database"             7  "PRIISM"     "n"  " "  " "  "View/edit the Lens Database"
ConvolutionKernels    "Revise Convolution Kernels"       7  "PRIISM"     "K"  " "  " "  "View/edit the available convolution kernels"
PlateBrowser          "Review Plate Scan"                7  "PRIISM"     "v"  " "  " "  "Tool to view results of a microtiter plate scan"
getDVLogs_w           "Get System Logs"                  7  "RESOLVE3D"  "g"  " "  " "  "Gather various log/config files for diagnostic purposes"
