This was started on March 7, 2017 and is NOT FINISHED
This is an overview. Please see the main Plot Panel, Stack Plot, and Map Plot.
Map Manager plots values for each 3D annotation. Plots can be made from a stack, a map, and a pool of maps. These plots are very powerful because they are linked to the raw data. If a plot point looks suspicious, one can always return to the raw image data. Finally, these plots are powerful as they are publication ready.
Plotting from a single stack
For a single stack, open the Point List window. Use the ‘Plot’ button to make Y vs X plots for values from the stack. Each point plotted is for a single 3D object (e.g. a spine). Right click on column row in the table and select ‘Set X Stat’ or ‘Set Y Stat’ to use the values in the column for plotting.
Plotting from a map
Use the ‘Plot’ tab in the main time-series window. There are default plots provided here including ‘Spine Length’ as well as intensity measures such as:
- Spine Sum: sSum
- Spine Background Sum: sbSum
- Background Subtracted Spine Sum: bssSum
- Dendrite Sum: dSum
- Dendrite Background Sum: dbSum
- Background Subtracted Dendrite Sum: bsdSum
Advanced plotting with the Plot Panel
The general idea is to select a Y value from the list, a corresponding X value and make a plot. All plots will show the values for individual 3D annotations (one annotation per point in the plot). There are two types of plots
- Spine Plot Map - To plot a Y value versus an X map value such as days or hours. Add example
- Session Plot (Map) - To plot values from 2 different sessions/timepoints. Use this to see how objects change from one time-point to the next. Add example
Plotting a map pool
A map pool will make one plot holding data from a number of maps. There are two types of map pools, just like there are two types of plots.
- Time-series pool - Map Pool (Time-Series)
- Session pool - Map Pool(Sessions)
The interface to creating a map pool from a number of open maps is in the Plot Panel.
Plot Window Interface
Once a plot is made from a stack or a map, Map Manager provides a unified interface.
- To get back to the raw stack. Select a point, right-click and choose a menu option.
- Plot Stack
- Plot Spine
- Plot Run +/- 1
- Plot Run +/- All
- Plot Run +/- n
- For spines, show only spines on a single dendrite or all dendrites. Do this by setting ‘Map Segment ID’ and/or the ‘All Segments’ checkbox.
- Generate tables of numbers and statistics. Use the ‘Stats’ button. These can easily be copied and pasted into other analysis software.
- Click and drag to visually select subsets of objects. There are three different selections, turn each one on with the 1/2/3 radio buttons. Once created, the ‘Stats’ button will include the statistics for these manual selections in the output table.
Group plots allow you to plot the mean for a spine across a number of sessions.
- Specify session conditions for a map in main time-series window.
- Specify a list of conditions to plot in main plot panel ‘Session Conditions’. This is a semicolon separated list and accepts ‘’ as a wildcard. For example ‘a;b;c’
- Plot the group plot with the ‘Group Plot’ button in the main plot panel