User files have been completely revamped. Global options can now be easily saved and loaded using the 'Stack DB Options Panel'.

See Stack DB Options Panel

User files are text files where global options are specified and then loaded and applied within Map Manager. This is useful when you have mutiple users within one Map Manager installation.

User files are loaded using the main menu ‘mm3 -> Load User’ or in the Hard Drive Paths panel.

Important. When you load a user file, anything specified in the file will override existing options.

Rules

Make sure there is NO space surround the ‘=’ sign.

  • GOOD: root:line2:options:gDefaultSegmentRadius=0.35
  • BAD: root:line2:options:gDefaultSegmentRadius = 0.35

Make sure your text editor is using simple double quotes

  • GOOD: root:stackdb2:options:gFijiPath=”C:\Users\cudmore.linden-image2\Desktop\Fiji.app\fiji-win64.exe”
  • BAD: root:stackdb2:options:gFijiPath=“C:\Users\cudmore.linden-image2\Desktop\Fiji.app\fiji-win64.exe”

Some useful options

Specify default user folder to load/save maps:

root:MapManager3:gMapDriveDir="vasculature:Users:cudmore:Documents:MapManager3:"

The default radius of new segments (um)

root:line2:options:gDefaultSegmentRadius=0.3

The maximum distance along a segment when automatically connecting objects in a map (um)

Objects will only be connected if their position on the segment line is less than this. root:ObjMap:options:gMaxPDistConnDist=3

The number of segment points to search when auto-connecting a spine

root:StackDB2:options:gLinePointsToSearch=6

Here is an example user file…

# mac
root:stackdb2:options:gFijiPath="/Applications/Fiji.app/Contents/MacOS/Imagej-macosx"
# windows
# root:stackdb2:options:gFijiPath="C:\Users\cudmore.linden-image2\Desktop\Fiji.app\fiji-win64.exe"

# default point size for stack db objects
root:stackdb2:options:gPointSize=3

# default size for user selections
root:StackDB2:options:gPointSelSize=5

# default stack window width
root:bStack:gStackWindowWidth1=1000

# default segment radius
root:line2:options:gDefaultSegmentRadius=0.35

# set the number of image planes an object is visible
# controls mask as you scroll up/down with mouse wheel
root:bStack:gMaskWindow=2

# turn on real-time intnesity analysis
root:stackdb2:options:gAnalyzeIntOnNewSpines = 0
root:stackdb2:options:gShowSpineIntensity = 0

root:line2:options:gFIlterSWC_BoxWidth = 5
root:line2:options:gFIlterRadius_BoxWidth = 5

root:bNV:gUserName="cudmore"

# stack browser
root:bStack:gRootHDD=""

#
root:bStack:gRootHDD="fourt:jhu:data:"
#
root:bStack:gAnalysisPath="Vasculature:Users:cudmore:jhu:vascularAnalysis:"

# set defaults in ‘Process Image’
# ch1 defaults
root:bProcess:gAutoContrast=1
root:bProcess:gMinContrast=0
root:bProcess:gMaxContrast=200
root:bProcess:gColorTable="Green"

# ch2 default
root:bProcess:gAutoContrastCh2=1
root:bProcess:gMinContrastCh2=0
root:bProcess:gMaxContrastCh2=200
root:bProcess:gColorTable2="Grays"

#
root:bStack:gDefaultChannel=1

root:ObjMap:options:gDefaultPlusMinusRun=1
root:ObjMap:options:gDefaultRunWindowWidth=400
root:ObjMap:options:gDefaultZoomWidth=20
root:ObjMap:options:gDefaultZoomHeight=20

# only allow auto spine connections < this number
root:ObjMap:options:gMaxPDistConnDist=3

# default segment radius (um)
root:line2:options:gDefaultSegmentRadius=0.3

# line points to search when connecting spine/bouton
root:StackDB2:options:gLinePointsToSearch=6

# single stack window parameters
root:bStack:gStackWindowWidth1=800
root:bStack:gStackWindowWidth2=767.5

root:bStack:stackScaleBar=5

#“”