Map Manager is a program to annotate 3D image time-series. It provides a rich user-interface to create, curate, and visualize 3D annotations. Map Manager is written in Igor Pro and conveniently saves all annotations as plain text.
Here, we provide a Matlab toolbox to load, visualize, and extend Map Manager annotations created with the Igor Pro version.
We also have a Python package PyMapManager, please see the Python API.
- Download the latest release
- Extract the .zip file
- See examples in /examples/mmExamples.m
- See the documentation
- mmMap - A Map Manager map
- mmStack - A Map Manager stack
- mmPlot - Utility class to plot mmMap and mmStack objects.
mapPath = 'exampleMaps/rr30a';
myMap = mmMap(mapPath);% Set up a plot struct to tell mmMap what to plot
ps = mmMap.defaultPlotStruct();
ps.stat = 'ubssSum'; % background subtracted spine sum
ps.channel = 2;
% Plot
mmPlot.plotStat(myMap, ps);
xps = mmMap.defaultPlotStruct();
xps.stat = 'ubsdSum'; % background subtracted dendrite sum
xps.channel = 2;
xps.session = 2;
yps = xps;
yps.session = 5;
mmPlot.plotStat2(myMap, xps, yps);
mmMap - A class to load, extract, and analyze annotations in a Map Manager map.
To construct a mmMap object:
myMap = mmMap(mapPath)
To get a default plot struct
ps = mmMap.defaultPlotStruct()
mmMap Properties:
mapName - Name of the map, same as enclosing folder name
mapPath - Path to map folder used in constructor
numChannels - Number of color channels in each stack
numSessions - Number of sessions in the map
numMapSegments - Number of segments in the map
mapNV - Text table of map, rows are labelled with names, columns are sessions
stacks - Array of mmStack
Extract Annotations:
GetMapValues(ps) - Get values of annotations from a map
GetMapDynamics(ps) - Get the dynamics (add, subtract, etc.) of each annotation.
Utility:
find(stat, findstr) - find annotations with notes, errors, and warnings
GetValue_NV(name, session) - Get value from a session in a map
getValidStats() - Return a cell array of valid stat names
isValidStat(stat) - Check if a stat is valid
Add new annotations:
addUserStat(newStatName,newStatValues) - Add a new stat to a map
save() - Save user stats. Please see help for important information.
Plotting:
plot0 - Plot a canonical map manager map of spine position versus session.
plotStat - Plot values of a stat versus sessions or days.
plotStat2 - Plot a stat (or two different stat) for two different session.
plotMaxProject - Plot the maximal intensity projection of a stack overlaid with tracing and annotations.
mmStack - A class to load, extract, and analyze annotations in a Map Manager stack.
To construct a mmStack:
myStack = mmStack(tiffPath)
mmStack Properties:
stackName (str) :
tiffPath (str) :
inMap (boolean) : True if stack is inserted into a mmMap, false otherwise.
stackdb (table of str) : table of annotations, one row per annotation
int1 (table of float) : table of intensity values for each annotations
int2 (table of float) :
int3 (table of float) :
userstat (table of float) : table of user created annotation values
linedb (table of float) : table of all segment tracings in the stack
Annotations:
getStackValues - Get annotation from stack
addUserStat -
Tracing:
getTracing - Get one or all segment tracings
Images:
loadStack - Load the image stack
unloadStack - Unload the image stack
Utility
find - find annotations by their note stat
save - save user annotations added with addUserStat
mmPlot - A class to plot mmMap annotations, tracings, and images
Static methods
mmPlot.mapPlot0 - Cannonical map manager map plot of pDist versus session
mmPlot.plotStat - Plot a map stat versus session or days
mmPlot.plotStat2 - Plot two stats, y versus x
mmPlot.mapPlotCondition - Plot a stat versus sessions only for sessions in a list