The Map Manager Options panel provides global options to control the behavior of Map Manager. Options can be saved using the Save Options button. Values shown in red will effect analysis and those in black effect program behavior..

The options panel is opened from the main menu ‘MapManager - Options’.


  • Stack Browser On Open. Open the stack browser when Map Manager is opened.
  • Time Series On Open. Open the time-series panel when Map Manager is opened.
  • Hide Code. Hide code windows when Map Manager is opened.

Stack Display

Options that control the display of stack windows. Changes will be applied the next time a stack window is opened. Already opened stack windows can be updated on-the-fly by pressing keyboard ‘r’ (in the stack window).

  • Points. Toggle stack db objects.

  • Spine Line. Toggle the line connecting the spine head to the segment radius.

  • Point mask. Turn point masking on/off. If off, annotations will be shown in all image planes. If on, annotations will only be shown near the image plane corresponding to each annotations Z position. See Mask Points.

  • Segment Color For All Points. Display all points using the segment color specified in the stack window.

  • User Type.

  • Line and Radii. Toggle the segment tracing and radius lines

  • Line Mask. Similar to Point mask, toggle masking the line to only display around the image plane it is in.

  • Channel Order.

  • Tag Font Size. In a stack window, the tags are the stack db point number. In a map, the tags are the run number of the point.

  • Scale Bar. Displayed in the bottom right of all stack windows. Cycle through stack window candy options with keyboard shift+c.

  • Left/Right Arrows Will Scroll Through Line (Otherwise Pan).

  • Mask Points. If Point Mask is on, this controls the number of image planes an annotation is visible above and below its Z position..

  • Flash Ticks. A number that controls the speed that a point is flashed when selected. Smaller numbers are faster. Point flashing is used to make it easier to see where there is a point selection. See ‘flashSel’ to control the size and shape of the point that is flashed.

  • Window With 1/2. Default stack window size. Each stack window has two sizes that can be cycled using keyboard ‘]’.

  • Default Zoom. Default zoom (in um) to zoom points in a stack and run plot. This is used when an annotation is right-clicked and ‘plot point’ or ‘plot run’ is selected.

  • Default Stack Candy. Default window candy for each stack. There are 5 options.
    • All.
    • None.
    • Scale.
    • Scale + Label.
    • Scale + Label + Axis.
  • Kill Stack (from memory) on window close.

  • Click and Drag.

  • Keyboard edits ‘User Type’.

Stack DB

  • Warn On New Objects.
  • Warn On Delete Objects.
  • New Objects On Mouse Click (no shift).
  • Allow New Objects When Viewing Sliding Z-Projection.
  • Search line points when connecting spine/bouton.
  • New Object (Shift+Click). The default object to make on shift+click.
  • Default plot object.

Object Map

  • Connect points within this distance (um). When auto connecting points in a map and generating a Guess in Find points.

  • Connect spines within this distance (um). When auto connecting spines in a map and generating a Guess in Find points. This is the distance from the segment pivot points along a dendritic segment (um). You can see this distance (pDist) in the Point Info panel of a stack.

  • Run Window Width (pixels). The size of each window in a spine run.
  • Show timepoint in stack window.
  • Always show stack DB indices (tags). xxx
  • Fixed posiiton for each run window. xxx
  • Lock segment selection in run plot. xxx
  • Shift + left/right to go to prev/next timepoint. xxx
  • Auto plot object map on load. xxx
  • Check map before save. xxx
  • Allow Jumping Objects.

Intensity Analysis

See the intensity analysis page for a thouough decription.

  • Intensity Analysis. Turn intensity analysis on/off. When on, spine selections will show intensity ROIs in the stack window.
  • Debug.
  • Debug On Error.
  • Width (um).
  • +/- Slices.
  • Extend Head (um).
  • Extend Tail (um).
  • +/- Segment (um).
  • Background Candidates
    • Both Sides.
    • Rows and Row Mult.
    • Columns and Column Mult.

Importing Segments From FIJI

  • Default Segment Radius (um).

  • Box Filter Line (points).

  • Box Filter Radius (points).

  • Convert To 8-bit. Will convert to 8-bit (in Fiji). This makes line fit much faster.

  • Close Fiji When Done. Always leave this on. This has been depreciated and will be remove.

Object Properties

Use this table to set how annotations and lines are displayed. Right-click on ‘marker’ or ‘color’ to set. Double-click on ‘size’ to set. Note, ‘size’ is in arbitrary Igor centric units, generally between 1 and 10.

Idx Name Meaning
Annotation Display   Set the size, color and marker of annotations
0 spineROI Spine marker in stack and map plot
1 boutonROI  
2 controlPnt  
3 pivotPnt  
4 otherROI  
5 lineROI  
6 rectROI  
7 ovalROI  
Annotation Selection    
8 pntSel Point selection, when an annotation is selected
9 runSel Run selection, when a run is selected
10 maskSel Mask selection, when a mask is selected
11 flashSel On selection, annotations are flashed
12 globalPivot  
13 lineSel Not sure any more, go figure out the brain
14 line Segment tracing line
15 radius Segment tracing radius
16 plotLine Line connecting corresponding annotations in map plots
Spine Intensity    
17 sROI Spine intensity ROI
18 dROI Dendrite/segment intensity ROI
19 sbROI Spine background ROI
20 dbROI Dendrite/segment background ROI
Annotation dynamics    
21 Bad Bad annotations
22 Add Added
23 Subtract Subtracted
24 Persistent Persistent
25 Transient Transient
User 1/2/3    
26 User 1_1 Not used
27 User 1_2 Not used
28 User 1_3 Not used
29 User 1_4 Not used
30 User 1_5 Not used
User Type    
31 User Type 0 User type 0
32 User Type 1 User type 1
33 User Type 2 User type 2
34 User Type 3 User type 3
35 User Type 4 User type 4
36 User Type 5 User type 5
37 User Type 6 User type 6
38 User Type 7 User type 7
39 User Type 8 User type 8
40 User Type 9 User type 9

Load Stacks From Special Folder

Each of the check boxes will redirect the loading of image stacks to different folders. In particular, the channels8 option will load 8-bit versions which is useful to speed annotations of larger 16-bit images. See Fiji plugin bConvertTo8Bit_v5_.py to convert entire directories of tiff stacks to 8-bit.

  • folder_channels
  • folder_channels_channels8
  • folder_channels8
  • folder_userRaw
  • folder_out:folder_out_aligned
  • Raw Prairie

Stack Browser Options

Additional option are available in the Stack Browser Options panel.

Open the Stack Browser Options panel using the ‘Options’ button in the stack browser.

Sorry for the inconvenience, we are moving all option to the main map manager options and downgrading the stack browser options.